Editorial Ten Simple Rules for Getting Published Philip E. Bourne

journal in which you plan to publish. Rule 6: The ingredients of good Outstanding editors demand and get science are obvious—novelty of he student council (http://www. outstanding reviews. Put your energy iscbsc.org/) of the International research topic, comprehensive into improving the quality of the Society for Computational coverage of the relevant literature, T manuscript before submission. Ideally, Biology asked me to present my good data, good analysis including the reviews will improve your paper. thoughts on getting published in the strong statistical support, and a But they will not get to imparting field of computational biology at the thought-provoking discussion. The that advice if there are fundamental Intelligent Systems in Molecular ingredients of good science flaws. Biology conference held in Detroit in reporting are obvious—good late June of 2005. Close to 200 bright Rule 4: If you do not write well in the organization, the appropriate use of young souls (and a few not so young) English language, take lessons early; tables and figures, the right length, crammed into a small room for what it will be invaluable later. writing to the intended audience— proved to be a wonderful interchange This is not just about grammar, but do not ignore the obvious. among a group of whom approximately more importantly comprehension. The Be objective about these ingredients one-half had yet to publish their first best papers are those in which complex when you review the first draft, and do paper. The advice I gave that day I have ideas are expressed in a way that those not rely on your mentor. Get a candid modified and present as ten rules for who are less than immersed in the field opinion by having the paper read by getting published. can understand. Have you noticed that colleagues without a vested interest in Rule 1: Read many papers, and learn the most renowned scientists often give the work, including those not directly involved in the topic area. from both the good and the bad the most logical and simply stated yet work of others. stimulating lectures? This extends to Rule 7: Start writing the paper the It is never too early to become a their written work as well. Note that day you have the idea of what critic. Journal clubs, where you critique writing clearly is valuable, even if your questions to pursue. ultimate career does not hinge on a paper as a group, are excellent for Some would argue that this places producing good scientific papers in having this kind of dialogue. Reading at too much emphasis on publishing, but English language journals. Submitted least two papers a day in detail (not just it could also be argued that it helps in your area of research) and thinking papers that are not clearly written in define scope and facilitates hypothesis- about their quality will also help. Being good English, unless the science is truly driven science. The temptation of well read has another potential major outstanding, are often rejected or at novice authors is to try to include benefit—it facilitates a more objective best slow to publish since they require everything they know in a paper. Your view of one’s own work. It is too easy extensive copyediting. thesis is/was your kitchen sink. Your after many late nights spent in front of Rule 5: Learn to live with rejection. papers should be concise, and impart as a computer screen and/or laboratory much information as possible in the A failure to be objective can make bench to convince yourself that your least number of words. Be familiar with rejection harder to take, and you will work is the best invention since sliced the guide to authors and follow it, the be rejected. Scientific careers are full of bread. More than likely it is not, and editors and reviewers do. Maintain a rejection, even for the best scientists. your mentor is prone to falling into the good bibliographic database as you go, The correct response to a paper being same trap, hence rule 2. and read the papers in it. rejected or requiring major revision is Rule 2: The more objective you can to listen to the reviewers and respond be about your work, the better that in an objective, not subjective, manner. work will ultimately become. Reviews reflect how your paper is being Alas, some scientists will never be judged—learn to live with it. If objective about their own work, and reviewers are unanimous about the Citation: Bourne PE (2005) Ten simple rules for will never make the best scientists— poor quality of the paper, move on—in getting published. PLoS Comput Biol 1(5): e57. learn objectivity early, the editors and virtually all cases, they are right. If they Copyright: Ó 2005 Philip E. Bourne. This is an open- reviewers have. request a major revision, do it and access article distributed under the terms of the address every point they raise both in Creative Commons Attribution License, which permits unrestricted use, distribution, and Rule 3: Good editors and reviewers your cover letter and through obvious reproduction in any medium, provided the original will be objective about your work. revisions to the text. Multiple rounds of author and source are properly credited. The quality of the editorial board is revision are painful for all those DOI: 10.1371/journal.pcbi.0010057 an early indicator of the review concerned and slow the publishing Philip E. Bourne is Editor-in-Chief of PLoS process. Look at the masthead of the process. Computational Biology. E-mail: [email protected]

PLoS Computational Biology | www.ploscompbiol.org0341 October 2005 | Volume 1 | Issue 5 | e57 Rule 8: Become a reviewer early in which is an important ingredient in like Google Scholar and the ISI Web of your career. deciding where to send your paper. Science are being used by tenure committees and employers to define Reviewing other papers will help you Rule 9: Decide early on where to try write better papers. To start, work with metrics for the quality of your work. It to publish your paper. your mentors; have them give you used to be that just the journal name This will define the form and level of papers they are reviewing and do the was used as a metric. In the digital detail and assumed novelty of the work first cut at the review (most mentors world, everyone knows if a paper has you are doing. Many journals have a will be happy to do this). Then, go little impact. Try to publish in journals presubmission enquiry system through the final review that gets sent that have high impact factors; chances available—use it. Even before the paper in by your mentor, and where allowed, are your paper will have high impact, is written, get a sense of the novelty of as is true of this journal, look at the too, if accepted. the work, and whether a specific When you are long gone, your reviews others have written. This will journal will be interested. provide an important perspective on scientific legacy is, in large part, the the quality of your reviews and, Rule 10: Quality is everything. literature you left behind and the hopefully, allow you to see your own It is better to publish one paper in a impact it represents. I hope these ten work in a more objective way. You will quality journal than multiple papers in simple rules can help you leave behind also come to understand the review lesser journals. Increasingly, it is harder something future generations of process and the quality of reviews, to hide the impact of your papers; tools scientists will admire. &

PLoS Computational Biology | www.ploscompbiol.org0342 October 2005 | Volume 1 | Issue 5 | e57 Editorial Ten Simple Rules for Getting Grants Philip E. Bourne*, Leo M. Chalupa

his piece follows an earlier and that you are the best person to do an inappropriately formulated Editorial, ‘‘Ten Simple Rules it. Different granting programs require application may aggravate the T for Getting Published’’ [1], differing amounts of preliminary data. reviewers, and will have a negative which has generated significant For certain programs, it can be said impact even if the science is sound. interest, is well read, and continues to that the work must be essentially done Length and format are the most generate a variety of positive before the grant is awarded, and that frequent offenders. comments. That Editorial was aimed at the funds are then used for the next students in the early stages of a life of phase of the research program. There is Rule 5: Obey the Three Cs—Concise, scientific paper writing. This interest some truth in this. So where Clear, and Complete has prompted us to try to help appropriate, do provide some The grant does not have to fill the scientists in making the next academic tantalizing preliminary result, making allotted page count. Your goal should career step—becoming a young sure to tell the reviewers what these be to provide a complete reckoning of principal investigator. Leo Chalupa has results imply with respect to the what is to be done, as briefly as joined us in putting together ten simple specific aims of your proposal. In possible. Do not rely on supplements rules for getting grants, based on our formulating the motivation for your (which may not be allowed) or on Web many collective years of writing both proposal, make sure to cite all relevant sites (review may be actively successful and unsuccessful grants. work—there is nothing worse than not discouraged since it has the potential While our grant writing efforts have appropriately citing the work of a to compromise anonymity). Specify the been aimed mainly at United States reviewer! Finally, convince the reviewer scope up-front and make sure it is government funding agencies, we that you have the technical and realistic with respect to the funds believe the rules presented here are scientific background to perform the requested. A common temptation for generic, transcending funding work as proposed. inexperienced grant writers is to institutions and national boundaries. propose to do too much. Such At the present time, US funding is Rule 3: Find the Appropriate Funding applications are usually judged as frequently below 10% for a given grant Mechanism, Read the Associated overly ambitious and consequently program. Today, more than ever, we Request for Applications Very poorly rated. need all the help we can get in writing Carefully, and Respond Specifically to Rule 6: Remember, Reviewers Are successful grant proposals. We hope the Request you find these rules useful in reaching People, Too Most funding organizations have your research career goals. Typically, reviewers will have a large specific staff to assist in finding funding number of grants to review in a short opportunities, and most funding Rule 1: Be Novel, but Not Too Novel period. They will easily lose agencies have components of their Web Good science begins with new and concentration and miss key points of sites designed to help investigators find fresh ideas. The grant writing process your proposal if these are buried in an the appropriate programs. Remember, should be a pleasure (no, we are not overly lengthy or difficult-to-read programs want to give away money— kidding), for it allows you to articulate document. Also, more than likely, not the jobs of the program’s staff depend those ideas to peers who have to read all the reviewers will be experts in your your grants but not necessarily your on it. The program staff can help you papers. Look at grant writing as an identify the best opportunities. If your opportunity to have an impact. Feel grant does not fit a particular program, save your time and energy, and apply Citation: Bourne PE, Chalupa LM (2006) Ten simple passionate about what you are rules for getting grants. PLoS Comput Biol 2(2): e12. writing—if you are not passionate elsewhere, where there is a better programmatic fit. Copyright: Ó 2006 Bourne and Chalupa. This is an about the work, it is probably not a open-access article distributed under the terms of good grant and is unlikely to get Rule 4: Follow the Guidelines for the Creative Commons Attribution License, which funded. ‘‘Me-too’’ science will not get permits unrestricted use, distribution, and Submission Very Carefully and reproduction in any medium, provided the original funded when funding levels are low. On author and source are credited. the other hand, science that is too Comply Many funding bodies will Philip E. Bourne is a professor in the Department of speculative will not be supported Pharmacology, University of California San Diego, La either, particularly when funds are immediately triage grants that do not Jolla, California, United States of America, and is tight—sad but true. comply with the guidelines—it saves Editor-in-Chief of PLoS Computational Biology. Leo M. Chalupa is a professor and chair in the Section of the program time and money. This Neurobiology, Physiology, and Behavior, University of Rule 2: Include the Appropriate extends to all the onerous supporting California Davis, Davis, California, United States of Background and Preliminary Data as material—budget justification, America. Required bibliographies, etc. Get them right and DOI: 10.1371/journal.pcbi.0020012 You need to convince reviewers that keep them updated for future * To whom correspondence should be addressed. E- the work you propose needs to be done applications. Even if it goes to review, mail: [email protected]

PLoS Computational Biology | www.ploscompbiol.org0059 February 2006 | Volume 2 | Issue 2 | e12 discipline. It is a skill to capture the understand each other can make a defensive; address each criticism head interest of experts and nonexperts difference. Many grant administrators on and respond with facts and not alike. Develop that skill. Unlike a paper, have some measure (limited to emotional arguments. When a grant provides more opportunity to complete) discretionary control over resubmission is necessary, make it very apply literary skills. Historical what they fund. The more they know clear to the reviewer that you perspectives, human interest, and and understand you and your work, the understand what was wrong the first humor can all be used judiciously in better your chances of success. Do not time. Indicate precisely how you have grants to good effect. Use formatting rely just on E-mail to get to know the fixed the problems. In the resubmitted tricks (without disobeying rule 4), for grant administrator. Do not be application, never argue with the example, underlining, bolding, etc., and intimidated. Talk to them on the validity of the prior review. If the grant restate your key points as appropriate. telephone and at meetings where was close to being funded the first time Each section can start with a summary possible—they want to help. around, remind the reviewers of that of the key points. Rule 9: Become a Grant Reviewer fact by including the previous score if appropriate, and make it crystal clear Rule 7: Timing and Internal Review Early in Your Career why this version is much improved. Are Important Being on review panels will help you There are no previously unrevealed Give yourself the appropriate lead write better grants. Understanding why secrets to grant writing presented here. time. We all have different approaches grants get triaged before complete Rather, it is a concise picture intended to deadlines. Ideally, you should review, how a panel reacts to a grant, complete a draft, leave sufficient time what the discretionary role of program to help our early career readers take to get feedback from colleagues, and officers is, and what the role of the next step. If you feel like you need then look at the grant again yourself oversight councils is provide valuable more detail, take a look at Kraicer’s with a fresh eye. Having a spectrum of lessons for writing successful grants of article [2]. Good luck on getting those “ scientific colleagues who are similar to your own and for giving others advice grants. the likely reviewer pool critique your about this process. grant is very valuable. Rule 10: Accept Rejection and Deal References Rule 8: Know Your Grant 1. Bourne PE (2005) Ten simple rules for getting with It Appropriately published. PLoS Comput Biol 1: DOI: 10.1371/ Administrator at the Institution Rejection is inevitable, even for very journal.pcbi.0010057 Funding Your Grant good grants when funding levels are 2. Kraicer J (1997) The art of grantmanship. Strasbourg: Human Frontier Science Program. At the end of the day, this person is low. Learn to live with rejection and to Available: http://www.hfsp.org/how/ your best advocate. How well you respond appropriately. Do not be ArtOfGrants.htm. Accessed 19 January 2006.

PLoS Computational Biology | www.ploscompbiol.org0060 February 2006 | Volume 2 | Issue 2 | e12 Editorial Ten Simple Rules for Reviewers Philip E. Bourne*, Alon Korngreen

ast summer, the Student feature to suggest their own rules and not be known to the authors, the Editor Council of the International comments on this important subject. knows who you are, and your reviews Society for Computational are maintained and possibly analyzed L Rule 1: Do Not Accept a Review Biology prompted an Editorial, ‘‘Ten by the publisher’s manuscript tracking Simple Rules for Getting Published’’ Assignment unless You Can system. Your profile as a reviewer is [1]. The interest in that piece (it has Accomplish the Task in the known by the journal—that profile of been downloaded 14,880 times thus far) Requested Timeframe—Learn to review quality as assessed by the Editor prompted ‘‘Ten Simple Rules for Say No and of timeliness of review should be Writing a Grant’’ [2]. With this third Late reviews are not fair to the something you are proud of. Many contribution, the ‘‘Ten Rules’’ series authors, nor are they fair to journal journals, including this one, provide would seem to be established, and more staff. Think about this next time you you with the reviews of your fellow rules for different audiences are in the have a paper under review and the reviewers after a paper is accepted or making. Ten Simple Rules for Reviewers is reviewers are unresponsive. You do not rejected. Read those reviews carefully based upon our years of experience as like delays when it is your paper, and learn from them in writing your next review. reviewers and as managers of the neither do the authors of the paper you review process. Suggestions also came are reviewing. Moreover, a significant Rule 4: As a Reviewer You Are Part of part of the cost of publishing is from PLoS staff and Editors and our the Authoring Process associated with chasing reviewers for research groups, the latter being new Your comments, when revisions are overdue reviews. No one benefits from and fresh to the process of reviewing. requested, should lead to a better this process. The rules for getting articles paper. In extreme cases, a novel finding published included advice on Rule 2: Avoid Conflict of Interest in a paper on the verge of rejection can becoming a reviewer early in your Reviews come in various forms— be saved by (often) multiple rounds of career. If you followed that advice, by anonymous, open, and double-blind, revision based on detailed reviewers’ working through your mentors who where reviewers are not revealed to the comments and become highly cited. will ask you to review, you will then authors and authors are not revealed to You are an unacknowledged partner in hopefully find these Ten Rules for reviewers. Whatever the process, act the success of the paper. It is always Reviewers helpful. There is no magic accordingly and with the highest moral beneficial to remember that you are formula for what constitutes a good or principles. The cloak of anonymity is there to help the authors in their work, even if this means rejecting their a bad paper—the majority of papers not intended to cover scientific manuscript. fall in between—so what do you look misconduct. Do not take on the review if there is the slightest possibility of for as a reviewer? We would suggest, conflict of interest. Conflicts arise above all else, you are looking for what when, for example, the paper is poor the journal you are reviewing for and will likely be rejected, yet there prides itself on. Scientific novelty— might be good ideas that you could there is just too much ‘‘me-too’’ in apply in your own research, or, scientific papers—is often the someone is working dangerously close Citation: Bourne PE, Korngreen A (2006) Ten simple rules for reviewers. PLoS Comput Biol 2(9): e110. DOI: prerequisite, but not always. There is to your own next paper. Most review 10.1371/journal.pcbi.0020110 certainly a place for papers that, for requests first provide the abstract and DOI: 10.1371/journal.pcbi.0020110 example, support existing hypotheses, then the paper only after you accept Copyright: Ó 2006 Philip E. Bourne. This is an open- or provide a new or modified the review assignment. In clear cases of access article distributed under the terms of the interpretation of an existing finding. conflict, do not request the paper. With Creative Commons Attribution License, which conflict, there is often a gray area; if permits unrestricted use, distribution, and After journal scope, it comes down to reproduction in any medium, provided the original a well-presented argument and you are in any doubt whatsoever, author and source are credited. everything else described in ‘‘Ten consult with the Editors who have asked you to review. Philip E. Bourne is a professor in the Department of Simple Rules for Getting Published’’ Pharmacology, University of California San Diego, La [1]. Once you know what to look for in Jolla, California, United States of America, and is Rule 3: Write Reviews You Would Be Editor-in-Chief of PLoS Computational Biology. Alon a paper, the following simple reviewer Satisfied with as an Author Korngreen is a Lecturer in the Mina and Everard guidelines we hope will be useful. Faculty of Life Sciences and the Leslie and Susan Terse, ill-informed reviews reflect Gonda Multidisciplinary Brain Research Center, Bar- Certainly (as with all PLoS badly on you. Support your criticisms Ilan University, Ramat-Gan, Israel. Computational Biology material) we or praise with concrete reasons that are * To whom correspondence should be addressed. E- invite readers to use the PLoS eLetters well laid out and logical. While you may mail: [email protected]

PLoS Computational Biology | www.ploscompbiol.org0973 September 2006 | Volume 2 | Issue 9 | e110 Rule 5: Be Sure to Enjoy and to Learn but effective way to help improve a paper. If English is not your strong from the Reviewing Process paper. A good review touches on both point, have someone else read the Peer review is an important major issues and minor details in the paper and the review, but without community service and you should manuscript. violating other rules, particularly Rule participate. Unfortunately, the more 2. Further, as passionate as you might Rule 7: Spend Your Precious Time on you review, in all likelihood the more be about the subject of the paper, do you will be asked to review. Often you Papers Worthy of a Good Review not push your own opinion or will be asked to review boring papers The publish-or-perish syndrome hypotheses. Finally, give the Editors a that are of no interest to you. While it leads to many poor papers that may not clear answer as to your is important to serve as a reviewer, be filtered out by the Editors prior to recommendation for publication. only accept papers in which you are sending it out for review. Do not spend Reviewers frequently do not give a keenly interested, because either they a lot of time on poor papers (this may rating even when requested. Provide a are close to your area of research or not be obvious when you take on the rating—fence-sitting prolongs the you feel you can learn something. You paper by reading only the abstract), but process unnecessarily. might say, should I not know the work be very clear as to why you have spent very well to be a reviewer? Often a limited time on the review. If there are Rule 10: Make Use of the ‘‘Comments perspective from someone in a slightly positive aspects of a poor paper, try to to Editors’’ different area can be very effective in find some way of encouraging the Most journals provide the improving a paper. Do not hesitate to author while still being clear on the opportunity to send comments to the indicate to the Editor the perspective reasons for rejection. Editors, which are not seen by the that you can bring to a paper (see Rule Rule 8: Maintain the Anonymity of authors. Use this opportunity to 10); s/he can then decide how to weigh provide your opinion or personal the Review Process if the Journal your review. Editors would of course perspective of the paper in a few clear like to see you review papers even if Requires It sentences. However, be sure those you are not particularly interested in Many of us have received reviews comments are clearly supported by them, but the reality is that good where it is fairly obvious who reviewed your review—do not leave the Editor reviewers must use their reviewing the work, sometimes because they guessing with comments like ‘‘this time wisely. suggest you cite their work. It is hard to really should not be published’’ if your maintain anonymity in small scientific Rule 6: Develop a Method of review does not strongly support that communities, and you should reread statement. It is also a place where Reviewing That Works for You your review to be sure it does not anonymity can be relaxed and reasons This may be different for different endanger the anonymity if anonymous for decisions made clearer. For people. A sound approach may be to reviews are the policy of the journal. If example, your decision may be based read the manuscript carefully from anonymity is the rule of the journal, do on other papers you have reviewed for beginning to end before considering not share the manuscript with the journal, which can be indicated in the review. This way you get a complete colleagues unless the Editor has given the Editor-only section. It is also a sense of the scope and novelty of the the green light. Anonymity as a journal good place to indicate your own work. Then read the journal’s Guide to policy is rather a religious rule—people shortcomings, biases, etc., with regard Authors, particularly if you have not are strongly for and against. Conform to the content of the paper (see Rule published in the journal yourself, or if strictly to the policy defined by the 5). This option is used too infrequently the paper is a particular class of article journal asking you to review. with which you are not overly familiar, and yet can make a great deal of a review for example. With this broad Rule 9: Write Clearly, Succinctly, and difference to an Editor trying to deal “ background, you can move to analyzing in a Neutral Tone, but Be Decisive with a split decision. the paper in detail, providing a A poorly written review is as bad as a summary statement of your findings as poorly written paper (see Rule 3). Try well as detailed comments. Use clear to be sure the Editors and the authors References reasoning to justify each criticism, and can understand the points you are 1. Bourne PE (2005) Ten simple rules for getting highlight the good points about the making. A point-by-point critique is published. PLoS Comput Biol 1 (5): DOI: 10. work as well as the weaker points. valuable since it is easy to read and to 1371/journal.pcbi.0010057 2. Bourne PE, Chalupa LM (2006) Ten simple Including citations missed by the respond to. For each point, indicate rules for getting grants. PLoS Comput Biol 2 author (not your own) is often a short how critical it is to your accepting the (2): DOI: 10.1371/journal.pcbi.0020012

PLoS Computational Biology | www.ploscompbiol.org0974 September 2006 | Volume 2 | Issue 9 | e110 Editorial Ten Simple Rules for Selecting a Postdoctoral Position Philip E. Bourne*, Iddo Friedberg

ou are a PhD candidate and and the surrounding environment followed by more publications. Does your thesis defense is already in satisfy your nonwork interests? the laboratory you are entering have a Y sight. You have decided you track record in producing high-quality would like to continue with a Rule 3: Select a Laboratory and a publications? Is your future mentor postdoctoral position rather than Project That Develop New Skills well-respected and recognized by the moving into industry as the next step in community? Talk to postdocs who have Maximizing your versatility increases your career (that decision should be the left the laboratory and find out. If the your marketability. Balance this against subject of another ‘‘Ten Simple Rules’’). mentor is young, does s/he have the the need to ultimately be recognized Further, you already have ideas for the promise of providing those outcomes? for a particular set of contributions. type of research you wish to pursue and Strive to have at least one quality Avoid strictly continuing the work you perhaps some ideas for specific publication per year. projects. Here are ten simple rules to did in graduate school. A postdoctoral help you make the best decisions on a position is an extension of your Rule 6: Negotiate First graduate training; maximize your gain research project and the laboratory in Authorship before You Start which to carry it out. in knowledge and experience. Think very carefully before extending your The average number of authors on a Rule 1: Select a Position that graduate work into a postdoc in the paper has continued to rise over the Excites You same laboratory where you are now— years: a sign that science continues to to some professionals this raises a red become more collaborative. This is If you find the position boring, you flag when they look at your resume. good for science, but how does it will not do your best work—believe us, Almost never does it maximize your impact your career prospects? Think of the salary will not be what motivates gain of knowledge and experience, but it this way. If you are not the first you, it will be the science. Discuss the that can be offset by rapid and author on a paper, your contribution is position fully with your proposed important publications. viewed as 1/n where n is the number of mentor, review the literature on the authors. Journals such as this one try to proposed project, and discuss it with Rule 4: Have a Backup Plan document each author’s contributions; others to get a balanced view. Try and this is a relatively new concept, and few evaluate what will be published during Do not be afraid to take risks, the process of your research. Being although keep in mind that pursuing a people pay any attention to it. Have an scooped during a postdoc can be a big risky project does not mean it should understanding with your mentor on setback. Just because the mentor is be unrealistic: carefully research and your likelihood of first authorship excited about the project does not plan your project. Even then, the most before you start a project. It is best to mean you that will be six months into it. researched, well-thought-out, and well- tackle this problem early during the planned project may fizzle; research is interview process and to achieve an Rule 2: Select a Laboratory That like that. Then what? Do you have a Suits Your Work and Lifestyle backup plan? Consider working on at least two projects. One to which you Citation: Bourne PE, Friedberg I (2006) Ten simple If at all possible, visit the laboratory devote most of your time and energy rules for selecting a postdoctoral position. PLoS before making a decision. Laboratories Comput Biol 2(11): e121. doi:10.1371/ and the second as a fallback. The journal.pcbi.0020121 vary widely in scope and size. Think second project should be more of the about how you like to work—as part of a ‘‘bread and butter’’ type, guaranteed to Copyright: Ó 2006 Bourne and Friedberg. This is an team, individually, with little open-access article distributed under the terms of generate good (if not exciting) results the Creative Commons Attribution License, which supervision, with significant no matter what happens. This permits unrestricted use, distribution, and supervision (remembering that this is contradicts Rule 1, but that is allowed reproduction in any medium, provided the original author and source are credited. part of your training where you are for a backup plan. For as we see in Rule supposed to be becoming 5, you need tangible outcomes. Philip E. Bourne is a professor in the Department of independent), etc. Talk to other Pharmacology, University of California San Diego, La Jolla, California, United States of America, and is graduate students and postdoctoral Rule 5: Choose a Project with Editor-in-Chief of PLoS Computational Biology. Iddo fellows in the laboratory and determine Friedberg is a research assistant in the Bioinformatics Tangible Outcomes That Match and Systems Biology program at the Burnham the work style of the laboratory. Also, Your Career Goals Institute for Medical Research, La Jolla, California, your best work is going to be done when United States of America. you are happiest with the rest of your For a future in academia, the most * To whom correspondence should be addressed. E- life. Does the location of the laboratory tangible outcomes are publications, mail: [email protected]

PLoS Computational Biology | www.ploscompbiol.org1327 November 2006 | Volume 2 | Issue 11 | e121 understanding; this prevents conflicts option of a three-year postdoc own financing gives you a level of and disappointments later on. Don’t be fellowship is desirable. independence and an important extra shy about speaking frankly on this line on your resume. This requires issue. This is particularly important Rule 8: Evaluate the Growth Path forward thinking, since most sources of when you are joining an ongoing study. funding come from a joint application Many independent researchers with the person who will mentor you as a continue the research they started Rule 7: The Time in a postdoc. Few graduate students think during their postdoc well into their Postdoctoral Fellowship Should about applying for postdoctoral first years as assistant professors, and Be Finite fellowships in a timely way. Even if you they may continue the same line of do not apply for funding early, it Mentors favor postdocs second only work in industry, too. When remains an attractive option, even after to students. Why? Postdocs are second researching the field you are about to your postdoc has started with a different only to students in providing a talented enter, consider how much has been funding source. Choosing one to two labor pool for the least possible cost. If done already, how much you can potential mentors and writing a grant at you are good, your mentor may want contribute in your postdoc, and least a year before you will graduate is you to postdoc for a long period. Three whether you could take it with you recommended. years in any postdoc is probably after your postdoc. This should be enough. Three years often corresponds discussed with your mentor as part of to the length of a grant that pays the Rule 10: Learn to Recognize an ongoing open dialog, since in the Opportunities postdoctoral fellowship, so the grant future you may be competing against may define the duration. Definitely find your mentor. A good mentor will New areas of science emerge and out about the source and duration of understand, as should you, that your become hot very quickly. Getting funding before accepting a position. Be horizon is independence—your own involved in an area early on has very wary about accepting one-year future lab, as a group leader, etc. advantages, since you will be more appointments. Be aware that the length easily recognized. Consider a of a postdoc will likely be governed by Rule 9: Strive to Get Your Own laboratory and mentor that have a the prevailing job market. When the Money track record in pioneering new areas or job market is good, assistant at least the promise to do so. “ professorships and suitable positions in The ease of getting a postdoc is industry will mean you can transition correlated with the amount of early to the next stage of your career. independent research monies available. Acknowledgments Since the job market even a year out is When grants are hard to get, so are The authors would like to thank Mickey unpredictable, having at least the postdocs. Entering a position with your Kosloff for helpful discussions.

PLoS Computational Biology | www.ploscompbiol.org1328 November 2006 | Volume 2 | Issue 11 | e121 Editorial Ten Simple Rules for a Successful Collaboration Quentin Vicens, Philip E. Bourne*

cientific research has always getting that grant or working with this you will get from the work. The history been a collaborative person would look good on your of science is littered with stories of S undertaking, and this is curriculum vitae. Attending meetings is unacknowledged contributions. particularly true today. For example, a perfect opportunity to interact with between 1981 and 2001, the average people who have shared interests [5]. Rule 3: Stick to Your Tasks number of coauthors on a paper for Take time to consider all aspects of the Scientific research is such that every the Proceedings of the National potential collaboration. Ask yourself, answered question begs a number of Academy of Sciences U S A rose from will this collaboration really make a new questions to be answered. Do not 3.9 to 8.4 [1]. Why the increase? Biology difference in my research? Does this digress into these new questions has always been considered the study of grant constitute a valid motivation to without first discussing them with your living systems; many of us now think of seek out that collaboration? Do I have collaborators. Do not change your it as the study of complex systems. the expertise required to tackle the initial plans without discussing the Understanding this complexity proposed tasks? What priority will this change with your collaborators. requires experts in many different teamwork have for me? Will I be able to Thinking they will be pleased with your domains. In short, these days success in deliver on time? If the answer is no for new approach or innovation is often being a biologist depends more on even one of these questions, the misplaced and can lead to conflict. one’s ability to collaborate than ever collaboration could be ill-fated. Rule 4: Be Open and Honest before. The Medical Research Centers Share data, protocols, materials, etc., in the United Kingdom figured this out and make papers accessible prior to long ago, and the new Janelia Farm Enter a collaboration publication. Remain available. A research campus of the Howard trusting relationship is important for Hughes Medical Institute in the United because of a shared the collaborative understanding of the States has got the idea, as it strongly passion for the science . . . problem being tackled and for the promotes intra- and inter-institutional subsequent joint thinking throughout collaborations [2]. the evolution of the collaboration. Given that collaboration is crucial, Rule 2: Decide at the Beginning Who how do you go about picking the right Will Work on What Tasks Rule 5: Feel Respect, Get Respect collaborators, and how can you best If you do not have respect for the Carefully establishing the purpose of make the collaboration work? Here are scientific work of your collaborators, the collaboration and delegating ten simple rules based on our you should definitely not be responsibilities is priceless. Often the experience that we hope will help. collaborating. Respect here especially collaboration will be defined by a grant. Additional suggestions can be found in means playing by Rules 2–4. If you do In that case, revisit the specific aims the references [3,4]. Above all, keep in not respect your collaborators, it will regularly and be sure the respective mind that these rules are for both you show. Likewise, if they don’t respect responsibilities are being met. and your collaborators. Always you. Look for the signs. The signs will Otherwise, consider writing a memo of remember to treat your collaborators depend on the personality of your as you would want to be treated understanding, or, if that is too formal, yourself—empathy is key. at least an e-mail about who is responsible for what. Given the Rule 1: Do Not Be Lured into Just Any delegation of tasks, discuss Citation: Vicens Q, Bourne PE (2007) Ten simple rules Collaboration expectations for authorship early in the for a successful collaboration. PLoS Comput Biol 3(3): e44. doi:10.1371/journal.pcbi.0030044 Learn to say no, even if it is to an work. Having said that, leave room for attractive grant that would involve evolution over the course of the Copyright: Ó 2007 Vicens and Bourne. This is an significant amounts of money and/or if collaboration. New ideas will arise. open-access article distributed under the terms of the Creative Commons Attribution License, which it is a collaboration with someone more Have a mutual understanding up-front permits unrestricted use, distribution, and established and well-known. It is easier such that these ideas can be embraced reproduction in any medium, provided the original to say no at the beginning—the longer as an extension of the original author and source are credited. an ill-fated collaboration drags on, the collaboration. Discuss adjustments to Quentin Vicens is a Howard Hughes Medical Institute Fellow at the University of Colorado, Boulder, harder it is to sever, and the worse it the timelines and the order of authors Colorado, United States of America. Philip E. Bourne will be in the end. Enter a collaboration on the final published paper, is the Editor-in-Chief of PLoS Computational Biology. because of a shared passion for the accordingly. In any case, be * To whom correspondence should be addressed. E- science, not just because you think comfortable with the anticipated credit mail: [email protected]

PLoS Computational Biology | www.ploscompbiol.org0335 March 2007 | Volume 3 | Issue 3 | e44 collaborators and range from being outside of their control and Well, it is like any good recipe: when aggressive to being passive–aggressive. unanticipated at the time the you find one that works, you cook it For example, getting your tasks done in collaboration started. After three again and again. Successful teamwork a timely manner should be your chances, if it feels like the collaboration will tend to keep flourishing—the first priority. There is nothing more cannot be saved, move on. At that point paper will stimulate deeper and/or frustrating for your collaborators than try to minimize the role of your broader studies that will in turn lead to to have to throttle their progress while collaborators in your work: think more papers. As you get to know your they are waiting for you to send them carefully about the most basic help you collaborators, you begin to understand your data. Showing respect would be to need from them and get it while you can work habits, strengths but also inform your collaborator when you (e.g., when having a phone call or a weaknesses, as well as respective areas cannot make a previously agreed-upon meeting in person). You may still need of knowledge. Accepting these things deadline, so that other arrangements to deal with the co-authorship, but and working together can make the can be made. hopefully for one paper only! work advance rapidly, but do not hurry: it takes time and effort from both sides Rule 6: Communicate, Communicate, Rule 8: Always Acknowledge and Cite to get to this point. and Communicate Your Collaborators Collaborations often come Consistent communication with your This applies as soon as you mention unexpectedly, just like this one. One of collaborators is the best way to make preliminary results. Be clear on who us (PEB) as Editor-in-Chief was sure the partnership is going in the undertook what aspect of the work approached not just with the idea for planned direction. Nothing new here, it being reported. Additionally, citing these Ten Rules, but with a draft set of is the same as for friendship and your collaborators can reveal your rules that needed only minor marriage. Communication is always dynamism and your skills at developing reworking. As you can see, we have better face-to-face if possible, for prosperous professional relationships. obeyed Rule 8. & example by traveling to meet your This skill will be valued by your peers collaborators, or by scheduling throughout your career. Acknowledgments discussion related to your collaborations during conferences that Rule 9: Seek Advice from We wish to thank Tom Cech for insightful the people involved will attend. Experienced Scientists discussions, and Chrysa Latrick, David Zappulla, Barbara Cohen, Emma Veitch, Synchronous communication by Even though you may not encounter Catherine Nancarrow, and Hemai telephone or video teleconferencing is severe difficulties that would result in Parthasarathy for helpful suggestions on the preferred over asynchronous the failure of the partnership, each manuscript. collaboration will come with a Author contributions. QV and PEB wrote collaboration by e-mail (data could be the paper. exchanged by e-mail prior to a call so particular set of challenges. To Funding. The authors received no specific that everyone can refer to the data overcome these obstacles, interact with funding for this article. while talking). colleagues not involved in the work, Competing interests. The authors have such as your former advisors or declared that no competing interests exist. Rule 7: Protect Yourself from a professors in your department who Collaboration That Turns Sour References have probably been through all kinds of 1. Borner K, Maru JT, Goldstone RL (2004) The The excitement of a new collaborations. They will offer simultaneous evolution of author and paper collaboration can often quickly insightful advice that will help you networks. Proc Natl Acad Sci U S A 101: 5266– 5273. dissipate as the first hurdles to any new move beyond the current crisis. 2. Rubin GM (2006) Janelia Farm: An experiment project appear. The direct consequence Remember, however, that a crisis can in scientific culture. Cell 125: 209–212. can be a progressive lack of interest and 3. Smalheiser NR, Perkins GA, Jones S (2005) occasionally lead to a breakthrough. Do Guidelines for negotiating scientific focus to get the job done. To avoid the not, therefore, give up on the collaboration. PLoS Biol 3: e217. subsequent frustrations and collaboration too easily. 4. Burroughs Wellcome Fund, Howard Hughes Medical Institute (2006) Making the right resentment that could even impact your move. A practical guide to scientific work in general, give three chances to Rule 10: If Your Collaboration management for postdocs and new faculty. your collaborators to get back on track. Satisfies You, Keep It Going Chevy Chase. Available: http://www.hhmi.org/ labmanagement. Accessed 21 February 2007. After all, your collaborators could just Ever wondered why a pair of authors 5. Aiken JW (2006) What’s the value of be having a difficult time for reasons has published so many papers together? conferences? Scientist 20: 54–56.

PLoS Computational Biology | www.ploscompbiol.org0336 March 2007 | Volume 3 | Issue 3 | e44 Editorial Ten Simple Rules for Making Good Oral Presentations Philip E. Bourne

ontinuing our ‘‘Ten Simple your presentation was either Rule 7: Practice and Time Your Rules’’ series [1–5], we consider incomprehensible or trite. A side Presentation C here what it takes to make a effect of too much material is that you This is particularly important for good oral presentation. While the rules talk too quickly, another ingredient of inexperienced presenters. Even more apply broadly across disciplines, they a lost message. important, when you give the are certainly important from the presentation, stick to what you perspective of this readership. Clear Rule 3: Only Talk When You Have practice. It is common to deviate, and and logical delivery of your ideas and Something to Say even worse to start presenting material scientific results is an important Do not be overzealous about what that you know less about than the component of a successful scientific you think you will have available to audience does. The more you practice, career. Presentations encourage present when the time comes. Research the less likely you will be to go off on broader dissemination of your work never goes as fast as you would like. tangents. Visual cues help here. The and highlight work that may not Remember the audience’s time is more presentations you give, the better receive attention in written form. precious and should not be abused by you are going to get. In a scientific presentation of uninteresting environment, take every opportunity to Rule 1: Talk to the Audience preliminary material. do journal club and become a teaching We do not mean face the audience, assistant if it allows you to present. An although gaining eye contact with as Rule 4: Make the Take-Home important talk should not be given for many people as possible when you Message Persistent the first time to an audience of peers. present is important since it adds a A good rule of thumb would seem to You should have delivered it to your level of intimacy and comfort to the be that if you ask a member of the research collaborators who will be presentation. We mean prepare audience a week later about your kinder and gentler but still point out presentations that address the target presentation, they should be able to obvious discrepancies. Laboratory audience. Be sure you know who your remember three points. If these are the group meetings are a fine forum for audience is—what are their key points you were trying to get this. backgrounds and knowledge level of across, you have done a good job. If Rule 8: Use Visuals Sparingly but the material you are presenting and they can remember any three points, what they are hoping to get out of the but not the key points, then your Effectively presentation? Off-topic presentations emphasis was wrong. It is obvious what Presenters have different styles of are usually boring and will not endear it means if they cannot recall three presenting. Some can captivate the audience with no visuals (rare); others you to the audience. Deliver what the points! audience wants to hear. require visual cues and in addition, Rule 5: Be Logical depending on the material, may not be Rule 2: Less is More Think of the presentation as a story. able to present a particular topic well A common mistake of There is a logical flow—a clear without the appropriate visuals such as inexperienced presenters is to try to beginning, middle, and an end. You set graphs and charts. Preparing good say too much. They feel the need to the stage (beginning), you tell the story visual materials will be the subject of a prove themselves by proving to the (middle), and you have a big finish (the further Ten Simple Rules. Rule 7 will audience that they know a lot. As a end) where the take-home message is result, the main message is often lost, clearly understood. and valuable question time is usually Rule 6: Treat the Floor as a Stage curtailed. Your knowledge of the Citation: Bourne PE (2007) Ten simple rules for subject is best expressed through a Presentations should be making good oral presentations. PLoS Comput Biol clear and concise presentation that is entertaining, but do not overdo it and 3(4): e77. doi:10.1371/journal.pcbi.0030077 provocative and leads to a dialog do know your limits. If you are not Copyright: Ó 2007 Philip E. Bourne. This is an open- during the question-and-answer humorous by nature, do not try and be access article distributed under the terms of the Creative Commons Attribution License, which session when the audience becomes humorous. If you are not good at permits unrestricted use, distribution, and active participants. At that point, your telling anecdotes, do not try and tell reproduction in any medium, provided the original knowledge of the material will likely anecdotes, and so on. A good author and source are credited. become clear. If you do not get any entertainer will captivate the audience Dr. Philip E. Bourne is a Professor in the Department of Pharmacology, University of California San Diego, questions, then you have not been and increase the likelihood of obeying La Jolla, California, United States of America. E-mail: following the other rules. Most likely, Rule 4. [email protected]

PLoS Computational Biology | www.ploscompbiol.org0593 April 2007 | Volume 3 | Issue 4 | e77 help you to define the right number of violation of the other rules. Work hard presentation will go well, and visuals for a particular presentation. A on breaking bad habits; it is afterward you feel it did not go well. useful rule of thumb for us is if you important. Other times you dread what the have more than one visual for each audience will think, and you come minute you are talking, you have too Rule 10: Provide Appropriate away pleased as punch. Such is life. As many and you will run over time. Acknowledgments always, we welcome your comments on Obviously some visuals are quick, People love to be acknowledged for these Ten Simple Rules by Reader others take time to get the message their contributions. Having many Response. & across; again Rule 7 will help. Avoid gratuitous acknowledgements degrades the people who actually contributed. If reading the visual unless you wish to Acknowledgments emphasize the point explicitly, the you defy Rule 7, then you will not be audience can read, too! The visual able to acknowledge people and The idea for this particular Ten Simple should support what you are saying organizations appropriately, as you will Rules was inspired by a conversation with run out of time. It is often appropriate Fiona Addison. either for emphasis or with data to Funding. The author received no specific prove the verbal point. Finally, do not to acknowledge people at the funding for this article. overload the visual. Make the points beginning or at the point of their Competing interests. The author has declared that no competing interests exist. few and clear. contribution so that their contributions are very clear. References Rule 9: Review Audio and/or Video of As a final word of caution, we have 1. Bourne PE (2005) Ten simple rules for getting Your Presentations found that even in following the Ten published. PLoS Comp Biol 1: e57. 2. Bourne PE, Chalupa LM (2006) Ten simple There is nothing more effective than Simple Rules (or perhaps thinking we rules for getting grants. PLoS Comp Biol 2: listening to, or listening to and are following them), the outcome of a e12. viewing, a presentation you have presentation is not always guaranteed. 3. Bourne PE, Korngreen A (2006) Ten simple rules for reviewers. PLoS Comp Biol 2: e110. made. Violations of the other rules will Audience–presenter dynamics are hard 4. Bourne PE, Friedberg I (2006) Ten simple rules become obvious. Seeing what is wrong to predict even though the metric of for selecting a postdoctoral fellowship. PLoS is easy, correcting it the next time depth and intensity of questions and Comp Biol 2: e121. 5. Vicens Q, Bourne PE (2007) Ten simple rules around is not. You will likely need to off-line followup provide excellent for a successful collaboration. PLoS Comp Biol break bad habits that lead to the indicators. Sometimes you are sure a 3: e44.

PLoS Computational Biology | www.ploscompbiol.org0594 April 2007 | Volume 3 | Issue 4 | e77 Editorial Ten Simple Rules for a Good Poster Presentation Thomas C. Erren*, Philip E. Bourne

osters are a key component of truth is that you have to sell your work. hypothesis to be tested, major results, communicating your science One approach is to pose your work as and conclusions, so does your poster. and an important element in a addressing a decisive question, which P Rule 6: Good Posters Have Unique successful scientific career. Posters, you then address as best you can. Once while delivering the same high-quality you have posed the question, which Features Not Pertinent to Papers science, offer a different medium from may well also be the motivation for the The amount of material presented in either oral presentations [1] or study, the focus of your poster should a paper far outweighs what is presented published papers [2], and should be be on addressing that question in a on a poster. A poster requires you to treated accordingly. Posters should be clear and concise way. distill the work, yet not lose the considered a snapshot of your work message or the logical flow. Posters intended to engage colleagues in a Rule 3: The Title Is Important need to be viewed from a distance, but can take advantage of your presence. dialog about the work, or, if you are not The title is a good way to sell your Posters can be used as a distribution present, to be a summary that will work. It may be the only thing the medium for copies of associated encourage the reader to want to learn conference attendee sees before they papers, supplementary information, more. Many a lifelong collaboration [3] reach your poster. The title should and other handouts. Posters allow you has begun in front of a poster board. make them want to come and visit. to be more speculative. Often only the Here are ten simple rules for The title might pose a decisive titles or at most the abstracts of posters maximizing the return on the time- question, define the scope of the study, consuming process of preparing and can be considered published; that is, or hint at a new finding. Above all, the presenting an effective poster. widely distributed. Mostly, they may title should be short and never be seen again. There is the comprehensible to a broad audience. Rule 1: Define the Purpose opportunity to say more than you The title is your equivalent of a The purpose will vary depending on would in the traditional literature, newspaper headline—short, sharp, and the status and nature of the work being which for all intents and purposes will compelling. presented, as well as the intent. Some be part of the immutable record. Take advantage of these unique features. posters are designed to be used again Rule 4: Poster Acceptance and again; for example, those making Rule 7: Layout and Format conference attendees aware of a shared Means Nothing resource. Others will likely be used Do not take the acceptance of a Are Critical once at a conference and then be poster as an endorsement of your work. Pop musician Keith Richards put the relegated to the wall in the laboratory. Conferences need attendees to be matter well in an interview with Der ‘‘ Before you start preparing the poster, financially viable. Many attendees who Spiegel [4]: If you are a painter, then ask yourself the following questions: are there on grants cannot justify the most important thing is the bare What do you want the person passing attending a conference unless they canvas. A good painter will never cover by your poster to do? Engage in a present. There are a small number of all the space but will always leave some discussion about the content? Learn speaking slots compared with enough to go off and want to try attendees. How to solve the dilemma? something for themselves? Want to Enter posters; this way everyone can Citation: Erren TC, Bourne PE (2007) Ten simple rules collaborate? All the above, or none of present. In other words, your poster for a good poster presentation. PLoS Comput Biol 3(5): e102. doi:10.1371/journal.pcbi.0030102 the above but something else? Style has not been endorsed, just accepted. your poster accordingly. To get endorsement from your peers, Copyright: Ó 2007 Erren and Bourne. This is an open-access article distributed under the terms of do good science and present it well on the Creative Commons Attribution License, which Rule 2: Sell Your Work in Ten Seconds the poster. permits unrestricted use, distribution, and Some conferences will present reproduction in any medium, provided the original author and source are credited. hundreds of posters; you will need to Rule 5: Many of the Rules for Writing fight for attention. The first a Good Paper Apply to Posters, Too Thomas C. Erren is with the Institute and Policlinic for Occupational and Social Medicine, School of impressions of your poster, and to a Identify your audience and provide Medicine and Dentistry, University of Cologne, lesser extent what you might say when the appropriate scope and depth of Lindenthal, Germany. Philip E. Bourne is a Professor in the Department of Pharmacology, University of standing in front of it, are crucial. It is content. If the conference includes California San Diego, La Jolla, California, United analogous to being in an elevator and nonspecialists, cater to them. Just as the States of America. having a few seconds to peak someone’s abstract of a paper needs to be a * To whom correspondence should be addressed. interest before they get off. The sad succinct summary of the motivation, E-mail: [email protected]

PLoS Computational Biology | www.ploscompbiol.org0777 May 2007 | Volume 3 | Issue 5 | e102 blank. My canvas is silence.’’ Your where the passerby’s eyes will wander. Leave the visitors space and time—they canvas as poster presenter is also white Only then will they go to the results, can ‘‘travel’’ through your poster at space. Guide the passerby’s eyes from followed by the methods. their own discretion and pace. If a one succinct frame to another in a visitor asks a question, talk simply and logical fashion from beginning to end. Rule 9: Posters Should Have openly about the work. This is likely Unlike the literature, which is linear by Your Personality your opportunity to get feedback on virtue of one page following another, A poster is a different medium from a the work before it goes to publication. the reader of a poster is free to wander paper, which is conventionally dry and Better to be tripped up in front of your over the pages as if they are tacked to impersonal. Think of your poster as an poster than by a reviewer of the the poster board in a random order. extension of your personality. Use it to manuscript. Guide the reader with arrows, draw the passerby to take a closer look Good posters and their presentations numbering, or whatever else makes or to want to talk to you. Scientific can improve your reputation, both sense in getting them to move from one collaboration often starts for reasons within and outside your working group logical step to another. Try to do this other than the shared scientific interest, and institution, and may also guiding in an unusual and eye-catching such as a personal interest. A photo of contribute to a certain scientific way. Look for appropriate layouts in you on the poster not only helps freedom. Poster prizes count when the posters of others and adopt some of someone find you at the conference peers look at your resume. their approaches. Finally, never use less when you are not at the poster, it can These ten rules will hopefully help than a size 24 point font, and make sure also be used to illustrate a hobby or an you in preparing better posters. For a interest that can open a conversation. the main points can be read at eye level. more humorous view on what not to do Rule 8: Content Is Important, but Rule 10: The Impact of a Poster in preparing a poster, see [6], and for Keep It Concise Happens Both During and After the further information, including the opportunity to practice your German, Everything on the poster should help Poster Session see [7]. & convey the message. The text must When the considerable effort of conform to the norms of sound making a poster is done, do not blow scientific reporting: clarity, precision it on presentation day by failing to Acknowledgments of expression, and economy of words. have the poster achieve maximum Thomas Erren’s contributions to this piece The latter is particularly important for impact. This requires the right are based on [7] and were stimulated by posters because of their inherent space presenter–audience interaction. Work exchanges with Michael Jacobsen. Thanks limitations. Use of first-rate pictorial to get a crowd by being engaging; one also to Steven E. Brenner for useful input. Funding. The authors received no specific material to illustrate a poster can engaged viewer will attract others. funding for this article. sometimes transform what would Don’t badger people, let them read. Be Competing interests. The authors have otherwise be a bewildering mass of ready with Rule 2. Work all the declared that no competing interests exist. complex data into a coherent and audience at once, do not leave visitors convincing story. One carefully waiting for your attention. Make eye References 1. Bourne PE (2007) Ten simple rules for making produced chart or graph often says contact with every visitor. good oral presentations. PLoS Comput Biol 3: more than hundreds of words. Use Make it easy for a conference e77. doi:10.1371/journal.pcbi.0030077 graphics for ‘‘clear portrayal of attendee to contact you afterward. 2. Bourne PE (2005) Ten simple rules for getting published. PLoS Comput Biol 1: e57. doi:10. complexity’’ [5], not to impress (and Have copies of relevant papers on hand 1371/journal.pcbi.0010057 possibly bewilder) viewers with as well as copies of the poster on 3. Vicens Q, Bourne PE (2007) Ten simple rules complex artistry. Allow a figure to be standard-sized paper. For work that is for a successful collaboration. PLoS Comput Biol 3: e44. doi:10.1371/journal.pcbi.0030044 viewed in both a superficial and a more mature, have the poster online 4. (1998) Interview with Keith Richards. Meine detailed way. For example, a large table and make the URL available as a Leinwand ist die Stille. Der Spiegel 45: 167– might have bold swaths of color handout. Have your e-mail and other 170. 5. Tufte ER (2001) The visual display of indicating relative contributions from demographics clearly displayed. Follow quantitative information. Cheshire different categories, and the smaller up with people who come to the poster (Connecticut): Graphics Press. p. 191. by having a signup sheet. 6. Wolcott TG (1997) Mortal sins in poster text in the table would provide gritty presentations or how to give the poster no one details for those who want them. The visitor is more likely to remembers. Newsletter Soc Integr Compar Likewise, a graph could provide a bold remember you than the content of your Biol Fall: 10–11. Available: http://www.sicb.org/ newsletters/fa97nl/sicb/poster.html. Accessed trend line (with its interpretation poster. Make yourself easy to 23 April 2007. clearly and concisely stated), and also remember. As the host of the work 7. Erren TC (2006). Schau mich an! Ein Leitfaden have many detailed points with error presented on the poster, be attentive, zur Erstellung und Pra¨ sentation von Postern in der Medizin und den Naturwissenschaften. bars. Have a clear and obvious set of open, and curious, and self-confident Mu¨ nchen/Wien/New York: W. Zuckschwerdt conclusions—after the abstract, this is but never arrogant and aggressive. Verlag.

PLoS Computational Biology | www.ploscompbiol.org0778 May 2007 | Volume 3 | Issue 5 | e102 Editorial Ten Simple Rules for Doing Your Best Research, According to Hamming Thomas C. Erren*, Paul Cullen, Michael Erren, Philip E. Bourne

his editorial can be considered Rule 1: Drop Modesty the best physics ever. By turning the the preface to the ‘‘Ten Simple problem around a bit, great scientists To quote Hamming: ‘‘Say to yourself: Rules’’ series [1–7]. The rules often transform an apparent defect T ‘Yes, I would like to do first-class work.’ presented here are somewhat into an asset. ‘‘It is a poor workman Our society frowns on people who set philosophical and behavioural rather who blames his tools—the good man out to do really good work. But you than concrete suggestions for how to gets on with the job, given what he’s should say to yourself: ‘Yes, I would like tackle a particular scientific got, and gets the best answer he can.’’ to do something significant.’’’ professional activity such as writing a Rule 6: Work Hard and Effectively paper or a grant. The thoughts Rule 2: Prepare Your Mind presented are not our own; rather, we Most great scientists have Many think that great science is the condense and annotate some excellent tremendous drive, and most of us result of good luck, but luck is nothing and timeless suggestions made by the would be surprised how much we but the marriage of opportunity and mathematician Richard Hamming two would know if we worked as hard as preparation. Hamming cites Pasteur’s decades ago on how to do ‘‘first-class some great scientists did for many adage that ‘‘luck favours the prepared research’’ [8]. As far as we know, the years. As Hamming says: ‘‘Knowledge mind.’’ transcript of the Bell Communications and productivity are like compound Research Colloquium Seminar Rule 3: Age Is Important interest. Given two people with exactly provided by Dr. Kaiser [8] was never the same ability, the one person who formally published, so that Dr. Einstein did things very early, and all manages day in and day out to get in Hamming’s thoughts are not as widely the ‘‘quantum mechanic fellows,’’ as one more hour of thinking will be known as they deserve to be. By well as most mathematicians and tremendously more productive over a distilling these thoughts into something astrophysicists, were, as Hamming lifetime.’’ But, Hamming notes, hard that can be thought of as ‘‘Ten Simple notes, ‘‘disgustingly young’’ when they work alone is not enough—it must be Rules,’’ we hope to bring these ideas to did their best work. On the other hand, applied sensibly. broader attention. in the fields of music, politics, and Hamming’s 1986 talk was literature, the protagonists often Rule 7: Believe and Doubt Your remarkable. In ‘‘You and Your produce what we consider their best Hypothesis at the Same Time work late in life. Research,’’ he addressed the question: Great scientists tolerate ambiguity. How can scientists do great research, Rule 4: Brains Are Not Enough, They believe the theory enough to go i.e., Nobel-Prize-type work? His You Also Need Courage insights were based on more than forty years of research as a pioneer of Great scientists have more than just Citation: Erren TC, Cullen P, Erren M, Bourne PE computer science and brainpower. To again cite Hamming: (2007) Ten simple rules for doing your best research, ‘‘Once you get your courage up and according to Hamming. PLoS Comput Biol 3(10): telecommunications who had the e213. doi:10.1371/journal.pcbi.0030213 privilege of interacting with such believe that you can do important things, then you can. If you think you Copyright: Ó 2007 Erren et al. This is an open-access luminaries as the physicists Richard article distributed under the terms of the Creative Feynman, Enrico Fermi, Edward can’t, almost surely you are not going Commons Attribution License, which permits Teller, Robert Oppenheimer, Hans to. Great scientists will go forward unrestricted use, distribution, and reproduction in any medium, provided the original author and source Bethe, and Walter Brattain, with under incredible circumstances; they are credited. Claude Shannon, ‘‘the father of think and continue to think.’’ Thomas C. Erren is with the Institute and Policlinic for information theory,’’ and with the Rule 5: Make the Best of Your Occupational and Social Medicine, School of statistician John Tukey. Hamming Medicine and Dentistry, University of Cologne, Ko¨ln, ‘‘became very interested in the Working Conditions Lindenthal, Germany. Paul Cullen is with the Medizinisches Versorgungszentrum fu¨r difference between those who do and To paraphrase Hamming, what most Laboratoriumsmedizin Dr. Lo¨er, Dr.Treder, Mu¨nster, those who might have done,’’ and he Germany. Michael Erren is with the Institute of people think are the best working Clinical Chemistry and Laboratory Medicine, offered a number of answers to the conditions clearly are not, because Westphalian Wilhelms-University of Mu¨nster, question ‘‘why . . . so few scientists people are often most productive when Mu¨nster, Germany. Philip E. Bourne is a Professor in the Department of Pharmacology, University of make significant contributions and so working conditions are bad. One of the California San Diego, La Jolla, California, United many are forgotten in the long run?’’ better times of the Cambridge Physical States of America. We have condensed Hamming’s talk Laboratories was when they worked *To whom correspondence should be addressed. into the ten rules listed below: practically in shacks—they did some of E-mail: [email protected]

PLoS Computational Biology | www.ploscompbiol.org1839 October 2007 | Volume 3 | Issue 10 | e213 ahead; they doubt it enough to notice immersed in and committed to a topic, with your colleagues is often worth the errors and faults so they can step day after day, your subconscious has much more than a trip to the library. forward and create the new nothing to do but work on your However, when choosing your replacement theory. As Hamming says: problem. Hamming says it best: ‘‘So the lunchmates (and, by implication, your ‘‘When you find apparent flaws, you’ve way to manage yourself is that when institution), be on your toes. As got to be sensitive and keep track of you have a real important problem you Hamming says: ‘‘When you talk to other those things, and keep an eye out for don’t let anything else get the center of people, you want to get rid of those how they can be explained or how the your attention—you keep your sound absorbers who are nice people theory can be changed to fit them. thoughts on the problem. Keep your but merely say ‘Oh yes,’ and to find Those are often the great scientific subconscious starved so it has to work those who will stimulate you right back.’’ contributions.’’ on your problem, so you can sleep peacefully and get the answer in the Acknowledgments Rule 8: Work on the Important morning, free.’’ Problems in Your Field Funding. The authors received no specific funding for this article. Rule 10: Leave Your Door Open It is surprising but true that the Competing interests. The authors have declared that no competing interests exist. average scientist spends almost all his Keeping the door to your office time working on problems that he closed makes you more productive in References believes not to be important and not to the short term. But ten years later, 1. Bourne PE (2005) Ten simple rules for getting be likely to lead to important results. somehow you may not quite know what published. PLoS Comp Biol 1: e57. doi:10.1371/ journal.pcbi.0010057 By contrast, those seeking to do great problems are worth working on, and all 2. Bourne PE, Chalupa LM (2006) Ten simple work must ask: ‘‘What are the the hard work you do will be ‘‘sort of rules for getting grants. PLoS Comp Biol 2: important problems of my field? What e12. doi:10.1371/journal.pcbi.0020012 tangential’’ in importance. He (or she) 3. Bourne PE, Korngreen A (2006) Ten simple important problems am I working on?’’ who leaves the door open gets all kinds rules for reviewers. PLoS Comp Biol 2: e110. Hamming again: ‘‘It’s that simple. If of interruptions, but he (or she) also doi:10.1371/journal.pcbi.0020110 you want to do great work, you clearly 4. Bourne PE, Friedberg I (2006) Ten simple rules occasionally gets clues as to what the for selecting a postdoctoral position. PLoS must work on important problems. . . . I world is and what might be important. Comp Biol 2: e121. doi:10.1371/journal.pcbi. finally adopted what I called ‘Great Again, Hamming deserves to be quoted 0020121 Thoughts Time.’ When I went to lunch 5. Vicens Q, Bourne PE (2007) Ten simple rules verbatim: ‘‘There is a pretty good for a successful collaboration. PLoS Comp Biol Friday noon, I would only discuss great correlation between those who work 3: e44. doi:10.1371/journal.pcbi.0030044 6. Bourne PE (2007) Ten simple rules for making thoughts after that. By great thoughts I with the doors open and those who mean ones like: ‘What will be the good oral presentations. PLoS Comp Biol 3: ultimately do important things, e77. doi:10.1371/journal.pcbi.0030077 impact of computers on science and although people who work with doors 7. Erren TC, Bourne PE (2007) Ten simple rules how can I change it?’’’ for a good poster presentation. PLoS Comp closed often work harder. Somehow Biol 3: e102. doi:10.1371/journal.pcbi.0030102 they seem to work on slightly the wrong 8. Hamming R (1986) You and your research. In: Rule 9: Be Committed to Your Kaiser JF Transcription of the Bell Problem thing—not much, but enough that they Communications Research Colloquium miss fame.’’ Seminar; 7 March 1986; Morristown, New In our view, Rule 10 may be the key to Jersey, United States. Available: http://www.cs. Scientists who are not fully virginia.edu/;robins/YouAndYourResearch. committed to their problem seldom getting the best research done because html. Accessed 24 September 2007. produce first-class work. To a large it will help you to obey Rules 1–9, and, 9. Erren TC (2007) Hamming’s ‘‘open doors’’ and group creativity as keys to scientific excellence: extent, creativity comes out of the most importantly, it will foster group The example of Cambridge. Med Hypotheses subconscious. If you are deeply creativity [9]. A discussion over lunch 2007 Sep 3: 17804173.

PLoS Computational Biology | www.ploscompbiol.org1840 October 2007 | Volume 3 | Issue 10 | e213 Editorial Ten Simple Rules for Graduate Students Jenny Gu, Philip E. Bourne*

hoosing to go to graduate Rule 2: Select the Right Mentor, mentor (Rule 2), eventually you will school is a major life decision. Project, and Laboratory have to be more independent than C Whether you have already Finding the right mentor can be hard when you started graduate school. The made that decision or are about to, since it is not always possible to know earlier you start on that path to now it is time to consider how best to the kind of mentoring that is going to independence the better. Independence be a successful graduate student. Here work best for you until you actually start will play a critical part in your career as are some thoughts from someone who doing research. Some of us like to work an innovative scientist. As much as holds these memories fresh in her mind independently, others like significant possible define your own research (JG) and from someone who has had a feedback and supervision. Talk to other project with a view to make a significant whole career to reflect back on the students in the laboratory and get their and unique scientific contribution. decisions made in graduate school, impressions of how the principle both good and bad (PEB). These investigator’s mentoring works for Rule 4: Remember, Life Is All about thoughts taken together, from former them. In a large laboratory, chances are Balance student and mentor, represent you will get less direct mentoring from Take the time to meet your own experiences spanning some 25 or more the principle investigator. In that case, needs. Graduate school is highly years. For ease, these experiences are other senior scientists in the laboratory demanding, both mentally and presented as ten simple rules, in become important. What mentoring are physically. Your health comes first, approximate order of priority as they likely to offer? Judge, as best you spend the time being healthy or else defined by a number of graduate can, if the overall environment will you might find yourself spending more students we have consulted here in the work for you. A key element is the time being sick. Hard work should be US; but we hope the rules are more standing of your mentor in his or her balanced with other activities that you globally applicable, even though length, scientific field. When you graduate, the enjoy and give you a break. These method of evaluation, and institutional laboratory you graduate from is going activities can often become important structure of graduate education varies to play a role in determining what in your future scientific career. widely. These rules are intended as a opportunities exist for your Collaborations sometimes start not companion to earlier editorials postdoctoral work, either in academia, because of a shared scientific interest covering other areas of professional industry, or other sectors. Your initially, but because you share the development [1–7]. proposed mentor should be very same hobby or other interest. enthusiastic about the project you Rule 1: Let Passion Be the Driving discuss. If he or she is not, you have the Rule 5: Think Ahead and Develop Force of Your Success wrong mentor and/or project. At the Your Professional Career Early As with so many other things in life, same time, beware that such There are two parts to this. The your heart and then your head should enthusiasm, however senior the mentor, first part relates to professional dictate what thesis project makes sense may be misplaced as far as your development. Being a successful to embark on. Doing your best work interests are concerned. Gauge the scientist is more involved than just requires that you are passionate about novelty of the research project and doing good science. You need to be able what you are doing. Graduate school is potential for high-quality publications to write good papers, submit an investment of up to a seven-year by doing your own background check compelling scholarship and grant commitment, a significant chunk of through reading previously published applications, make powerful your life. Use the time wisely. The research and talking to other scientists educational system provides a variety in related areas. Also consider if the of failsafe mechanisms depending on project can be reasonably completed in Citation: Gu J, Bourne PE (2007) Ten simple rules for the part of the world where you study. the allocated time for graduation. To graduate students. PLoS Comput Biol 3(11): e229. 10. Laboratory rotations and other forms propel your career, you want to come 1371/journal.pcbi.0030229 of apprenticeship should not be out of a higher degree as a recognized Copyright: Ó 2007 Gu and Bourne. This is an open- overlooked, for they are opportunities individual having made a significant access article distributed under the terms of the to test the waters and measure your Creative Commons Attribution License, which scientific contribution. Thus, it is permits unrestricted use, distribution, and passion in a given subject area. It is also absolutely critical that you do take the reproduction in any medium, provided the original a chance to test your aptitude for time to find the project and mentor that author and source are credited. research. Take advantage of it! is going to fulfill this goal. Jenny Gu is with the University of Texas, Medical Research is very different from simply Branch, Galveston, Texas, United States of America. Philip E. Bourne is with the University of California taking courses. If you do not feel Rule 3: Independent Thinking Is a San Diego, La Jolla, California, United States of excited about doing research and the Mark of a True Scientist America. project selected, do not do it; Regardless of your initial work habits * To whom correspondence should be addressed. E- reevaluate your career decisions. and how much you depend on your mail: [email protected]

PLoS Computational Biology | www.ploscompbiol.org2045 November 2007 | Volume 3 | Issue 11 | e229 presentations, and communicate and needed. A good mentor will understand institutions do not convene a thesis collaborate with other researchers. The that you come first. committee until near the end of your other Ten Simple Rules editorials are a work. For those institutions that start here [1–7], but you need to work on Rule 8: Share Your Scientific Success require a thesis committee to be developing these skills at the same time with the World convened early, talk with your mentor as you work on your thesis. The second Being recognized by your peers as and be involved in the selection part involves using these emergent skills someone who does good science is process. The committee is there to to figure out what to do with the higher important both within your institution, work for you as secondary mentors. postgraduate degree. Do not wait until nationally, and internationally. When Consider people whose own research you graduate to take the next step. Have opportunities arise to give seminars experience will be valuable to you or a position and a fellowship, if possible, and presentations to other groups, take who have a reputation for ongoing lined up ahead of time. them. Before starting with a mentor, mentoring in all areas of professional come to an agreement as to when and development. Make a point of talking what meetings you can attend locally Rule 6: Remain Focused on Your to members of the committee from and globally. Scientific meetings are a Hypothesis While Avoiding Being time to time and keep them abreast of fun and fruitful venue for exchange. Be Held Back what you are doing. On occasion, you sure to venture beyond the comfort Formulation of the hypothesis is the and your primary mentor may have zone of familiar faces, because it is first thing you’ll learn in Science 101, disagreements; committee members important to meet other colleagues in and yet somehow it seems to get can be invaluable here. & occasionally thrown out the window. your field. These people may become When you find yourself lost in the details your future collaborators, friends, of your research, take a step back and advocates, and employers. Acknowledgments remind yourself of the big picture. Rule 9: Build Confidence and a Thick Revaluate your hypothesis from time to Skin Thanks to Kristine Briedis, Jo-Lan Chung, time to see if it still makes sense, because As you pave the road to scientific Ruben Valas, and Song Yang, current and you may find yourself needing a new one. former students in the Bourne Laboratory, fame with Rule 8, expect your work to and members of the Bioinformatics and Always keep this in mind in discussions be criticized and scoffed at, for that is Chemistry/Biochemistry Programs at the with your mentor. As you have these part of the scientific process of University of California San Diego, for their insightful comments on these rules. As discussions, remember you are cheap challenging new ideas. The best way to labor, and, if you are a good student, a always, we invite you to comment, either build self-confidence for these formally through the journal, via blogs and source of success to your mentor. The otherwise defensive moments is to be list servers, and to the authors directly. temptation is that your mentor will want prepared and to present your work Funding. The authors received no specific to keep you around as long as possible. clearly with a confident display of your funding for this article. Define the scope of your project early Competing interests. The authors have expansive knowledgebase of the declared that no competing interests exist. with your mentor and agree that this is relevant related work. Do not be what you will attempt to complete in intimidated by big names who question order to receive the degree. A career your work; counter knowledge with awaits you beyond the laboratory of your knowledge. Another reason to have a References graduate student days. Do not prolong thick skin is that the path to success will 1. Bourne PE (2005) Ten simple rules for getting moving on to new challenges. not be without setbacks—setbacks such published. PLoS Comp Biol 1: e57. doi:10.1371/ as experiments that fail, and journal.pcbi.0010057 Rule 7: Address Problems Earlier 2. Bourne PE, Chalupa LM (2006) Ten simple experiments that succeed but do not rules for getting grants. PLoS Comp Biol 2: Rather Than Later yield a useful result causing you to have e12. doi:10.1371/journal.pcbi.0020012 If graduate school wasn’t quite what wasted significant time. Undergraduate 3. Bourne PE, Korngreen A (2006) Ten simple you thought it would be, be it rules for reviewers. PLoS Comp Biol 2: e110. training is usually much more doi:10.1371/journal.pcbi.0020110 scientifically or otherwise, find out structured and does not prepare you 4. Bourne PE, Friedberg I (2006) Ten simple rules what your options are to address the for such setbacks. Learn as much as you for selecting a postdoctoral fellowship. PLoS problem. Discuss these problems with Comp Biol 2: e121. doi:10.1371/journal.pcbi. can from these situations both about 0020121 your mentors. A good mentor is there the science and yourself and move on. 5. Vicens Q, Bourne PE (2007) Ten simple rules not just to guide you scientifically, but for a successful collaboration. PLoS Comp Biol Rule 10: Help Select and 3: e44. doi:10.1371/journal.pcbi.0030044 also in your personal development. 6. Bourne PE (2007) Ten simple rules for making Remember, they have been there Subsequently Engage Your Thesis good oral presentations. PLoS Comp Biol 3: themselves and have likely seen similar Committee e77. doi:10.1371/journal.pcbi.0030077 7. Erren TC, Bourne PE (2007) Ten simple rules issues with earlier students. Take time This rule depends somewhat on how for a good poster presentation. PLoS Comp off to reflect on your future if this is your institution is structured. Some Biol 3: e102. doi:10.1371/journal.pcbi.0030102

PLoS Computational Biology | www.ploscompbiol.org2046 November 2007 | Volume 3 | Issue 11 | e229 Editorial Ten Simple Rules for Aspiring Scientists in a Low-Income Country

Edgardo Moreno1*, Jose´-Marı´a Gutie´rrez2 1 Programa de Investigacio´n en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica, 2 Instituto Clodomiro Picado, Facultad de Microbiologı´a, Universidad de Costa Rica, San Jose´, Costa Rica

Being a scientist entails a common set of although investigating topics marginal to same problems constitute excellent sources characteristics. Admiring nature and having your own, are capable of understanding for research and offer comparative advan- concern for social issues; possessing a strong the relevance of your work. At the initial tages. Try to choose a topic that is not academic background, team work abilities, phases of your career, belonging to a directly pursued by many or strong inter- honesty, discipline, skepticism, communica- creative scientific environment in which national research teams. At the beginning of tion skills, competitiveness, ability to accept your knowledge and skills are appreciated your career, you cannot compete with them and give criticism, and productive relation- is of major importance. Be part of a team and your efforts may be frustrated. Identify ships are some of the most obvious traits before trying to lead one. the potential bottlenecks. Remember that in that scientists should have. To be a scientist LICs research time runs slower and that in a low-income country (LIC), however, Rule 2: Focus on Your Scientific good science is not so much related to the requires a complementary set of qualities Work subject as to the answers you extract from that are necessary to confront the draw- your investigations. Frequently, local mod- backs that work against the development of Your formal education has finished, but els become universal once a coherent story science. The failure of many young re- your scientific career is just beginning. is built around them. Become an expert searchers to mature as professional scientists Research should be your main professional and, simultaneously, broaden your knowl- upon their return to their country from activity. Consider that you may be the edge in collateral areas that may open new advanced training elsewhere, motivated us country’s only specialist in a particular topic, possibilities. to propose these ten rules. but keep in mind that science is global. You are a small fish in a big pond and part of an Rule 4: Improve Your Rule 1: Understand Your international community. Grow within this Communication Skills Country global context. Concentrate on your work, and do not pay attention to flattering English is the language of natural Most LIC scientists want to live in their comments. Above all, keep away from sciences, and you cannot avoid this fact. home country. Nevertheless, you must be activities that distract you from scientific Consequently, you should be proficient in realistic and prepared to face rudimentary endeavor, such as excessive administrative this language. The international scientific laboratories, power cuts, poor water sup- duties, and too many committees. Limit the community is lenient about strong accents. ply, deficient libraries, slow Internet, and number of meetings and attend only the However, the same community does not scarce or non-existent national funds for relevant ones. Even though you are well tolerate poor writing. Thus, writing skills supporting research, hiring personnel, and prepared, modestly declare yourself as are essential, since research begins with providing maintenance or equipment. You ‘‘ignorant’’ in topics that may distract you, written proposals [2] and does not end must understand that science is a minor and fight against excessive lecturing. How- until your results have been published [3]. component of the cultural environment of ever, participate in graduate programs and You, more than native English speakers, an LIC and that, for most people and seminars. This is the right environment for must practice your oral presentations [4]. many politicians, science is a curiosity the promotion of academic knowledge and performed in high-income countries [1]. skills. Within this adverse scenario, you should Rule 5: Collaborate Locally and establish broad and strong links with your Internationally community and country. This involves Rule 3: Be Wise When Selecting Your Research Topic Collaboration is essential for the ad- becoming interested in historical, social, vancement of science. Although this holds and political issues. LIC researchers have LICs face many problems that await true for any researcher in the world [5], it to enjoy the idiosyncrasies of their country, creative solutions. Bizarre as it sounds, you is crucial for LIC investigators. Identify and cultivate the desire to contribute to can turn this into an advantage since these local groups who share your scientific the scientific development of their home- land and to the well-being of its people. Do not endorse deep doubts about the Citation: Moreno E, Gutie´rrez J-M (2008) Ten Simple Rules for Aspiring Scientists in a Low-Income Country. PLoS Comput Biol 4(5): e1000024. doi:10.1371/journal.pcbi.1000024 possibilities of performing research. It can be done—but not alone. Try to join efforts Published May 30, 2008 with other investigators facing the same Copyright: ß 2008 Moreno, Gutie´rrez. This is an open-access article distributed under the terms of the problems. Learn how they sidetrack diffi- Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. culties, and incorporate yourself into a research team. If you are not able to find a Funding: No funding was received for the work presented. group that fits your specific interest, then Competing Interests: The authors have declared that no competing interests exist. procure a group of researchers who, * E-mail: [email protected]

PLoS Computational Biology | www.ploscompbiol.org 1 May 2008 | Volume 4 | Issue 5 | e1000024 interest, have equipment, or perform commitment. Inform yourself about local community in an LIC is in short supply activities or techniques that are useful for and international granting agencies, and and lacks redundancy. In order to con- your research. Keep in touch with your apply for money [2]. There are interna- front the drawbacks and deficiencies of the former tutor and colleagues and explore tional agencies and programs that provide system, you must acquire a wide scientific new collaborations abroad. Do not be shy grant and travel funds for LIC investigators knowledge, and become a well educated about requesting help, and offer some- (e.g., TWAS, IFS, EU, NIH, etc.). Although person in a broad sense. In addition to thing that attracts the attention of your funds are limited, they will help you to build helping the quality of your research, this counterparts. Attend international meet- your scientific career. Incorporate yourself will give you the credentials to participate ings and present your work. Research is, in into international consortia; they may find in political decisions related to science, to a way, a trade market of ideas, methods, your ideas and resources interesting. If you promote your ideas, and to spread scien- and goods. Travel and visit research do not have access to essential publications, tific knowledge in your country. Acquaint institutions. If some experiments cannot send requests to authors, editors, or col- yourself with local and international trends be carried out in your country, arrange to leagues abroad. Avoid publishing your related to scientific performance and keep perform them abroad, or convince people results in magazines or low-quality journals, track of the major breakthroughs in to do them for you. There are interna- and instead submit your work to interna- science. Give talks and write about science tional funds available for this purpose. tional journals. Do not overestimate or whenever you consider it pertinent, but underestimate your work, be realistic when without diverting your attention too much Rule 6: Commit Yourself to the choosing a suitable journal [3], and, above from your main scientific duties. Education of Young Scientists all, do not be overly frustrated when grants or papers are rejected; instead, use the Rule 10: Appreciate Being a LIC researchers should participate in experience as a source of learning. Even graduate training programs since this is though some reviewers may undervalue Scientist the best way to build a strong scientific research performed in LICs, most of them As most scientists from high income community. It is also a way to identify pay more attention to the results and ideas countries and from LICs know, we are good young students and potential part- than to nationalities [6]. prone to facing economic difficulties at the ners. Carefully choose the subjects for beginning of our careers. Generally, sala- your students, pondering the possibilities Rule 8: Develop Endurance ries for scientists are comparatively low. of your research center, and be realistic When Confronting Difficulties Nevertheless, in time scientists can achieve about what they can achieve and the tasks a satisfying income; furthermore, there are you are imposing on them. Upgrade your It is understandable that the limitations compensations, especially if you become a students’ education by sending them of performing research in LICs sometimes successful scientist. A sense of achievement abroad for seminars and for learning weaken your enthusiasm. Remain calm and contribution to your community, specific methodologies (http://iscbsc.org/ and try to identify the source of the prestige, travel, meeting interesting people, scs3/index.htm). There are international problem; avoid complaining excessively and consulting opportunities are some of fellowships for this purpose (http://www. in front of students, colleagues, or your twas.org/). Be strict but generous with partners abroad. A negative attitude is them, but nothing is more rewarding than your students and colleagues, and, when- contagious, lowers your prestige, and has the intellectual stimulation of science itself. ever possible, share your facilities and the tendency to attract unproductive This was your original motivation; nourish knowledge. Do not be self-centered. Pro- people. Share your problems with other it with more and better science. moting the success of others is also a way local scientists and confront them as a to promote your own success. team. You should cultivate your abilities to Acknowledgments find alternative solutions, as well as skills to The style for this article was inspired by the Rule 7: Write Research Grants improvise and to persuade people. ‘‘Ten Simple Rules…’’ papers published by and Publish in International Philip E. Bourne in PLoS Computational Biology. Journals Rule 9: Educate Yourself as a We acknowledge the comments and revision of Professional Scientist our colleagues and former students. Scientific amateurism is common in LICs. Science is not a hobby but a To be a specialist in an LIC is not professional activity that requires strong enough. Be aware that the scientific

References 1. Moreno E, Alveteg T (2002) Collaboration 3. Bourne PE (2005) Ten simple rules for getting 6. Yousefi-Nooraie R, Shakiba B, Mortaz-Hejri S between Sweden and the Public Universities of published. PLoS Comput Biol 1: e57. doi: (2006) Country development and manuscript Nicaragua. Swedish International Development 10.1371/journal.pcbi.0010057. selection bias: a review of published studies. Cooperation Agency (Sida, Evaluation 03/31). 4. Bourne PE (2007) Ten simple rules for making BMC Med Res Methodol 6: 37. Stockholm. http://www.oecd.org/dataoecd/43/ good oral presentations. PLoS Comput Biol 3: 21/35213123.pdf. e77. doi:10.1371/journal.pcbi.0030077. 2. Bourne PE, Chalupa LM (2006) Ten simple rules 5. Vicens Q, Bourne PE (2007) Ten simple rules for for getting grants. PLoS Comput Biol 2: e12. a successful collaboration. PLoS Comput Biol 3: doi:10.1371/journal.pcbi.0020012. e44. doi:10.1371/journal.pcbi.0030044.

PLoS Computational Biology | www.ploscompbiol.org 2 May 2008 | Volume 4 | Issue 5 | e1000024 Editorial Ten Simple Rules for Organizing a Scientific Meeting

Manuel Corpas1, Nils Gehlenborg1,2, Sarath Chandra Janga3, Philip E. Bourne4* 1 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom, 2 Graduate School of Life Sciences, University of Cambridge, Cambridge, United Kingdom, 3 Medical Research Council–Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom, 4 Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, California, United States of America

Scientific meetings come in various Rule 1: The Science Is the Most Rule 3: Study All Potential flavors—from one-day focused workshops Important Thing Financial Issues Affecting Your of 1–20 people to large-scale multiple-day Event meetings of 1,000 or more delegates, Good science, above all else, defines a including keynotes, sessions, posters, social good meeting; logistics are important, but Sponsors are usually your primary events, and so on. These ten rules are secondary. Get the right people there, source of funds, next to the delegates’ intended to provide insights into organiz- namely the best in the field and those who registration fees. To increase the chances ing meetings across the scale. will be the best, and the rest will take care of being sponsored by industry, write them Scientific meetings are at the heart of a of itself. When choosing a topic for your a clear proposal stating how the money scientist’s professional life since they conference, map it to the needs of your will be spent and what benefits they can provide an invaluable opportunity for target audience. Make sure that you have expect to get in return. You may also want learning, networking, and exploring new a sufficiently wide range of areas, without to reserve a few time slots for industry talks ideas. In addition, meetings should be being too general. The greater the number or demos as a way of attracting more enjoyable experiences that add exciting of topics covered, the more likely people sponsors, but be wary that the scientific breaks to the usual routine in the labora- are to come, but the less time you will have flavor of the meeting is not impacted by tory. Being involved in organizing these to focus on particular subject matter. blatant commercialism. Make sure you meetings later in your career is a commu- Emerging areas can attract greater inter- first approach the sponsors that match nity responsibility. Being involved in the est; try to include them in your program as your interest topics the closest. If they say organization early in your career is a much as possible; let your audience decide they are not interested this year, keep their valuable learning experience [1]. First, it the program through the papers they contact information, as they might be able provides visibility and gets your name and submit to the general call for papers. This to sponsor you in future events. Approach can be done with broad and compelling them early rather than later in any case. face known in the community. Second, it topic areas such as ‘‘Emerging Trends in The cost of your conference will be is useful for developing essential skills in …’’ or ‘‘New Developments in …’’. proportional to the capacity of the venue; organization, management, team work, therefore, a good estimation of the number and financial responsibility, all of which of attendees will provide you with a good are useful in your later career. Notwith- Rule 2: Allow for Plenty of estimate of your costs. You will need to standing, it takes a lot of time, and Planning Time include meals and coffee breaks together agreeing to help organize a meeting Planning time should range from nine with the actual cost of renting your venue. should be considered in the context of months to more than a year ahead of the Be aware that audiovisual costs can be your need to get your research done and conference, depending on the size of your additional as well as venue staff—look out so is also a lesson in time management. event. Allow plenty of time to select your for hidden costs. Aside from venue-related What follows are the experiences of meeting venue; to call for, review, and costs, additional expenditures might in- graduate students in organizing scientific accept scientific submissions; to arrange clude travel fellowships, publication costs meetings with some editorial oversight for affordable/discounted hotel rooms; to for proceedings in a journal, and awards from someone more senior (PEB) who book flights and other transportation for outstanding contributors. All these has organized a number of major meet- options to the conference. Having out- issues will determine how much you need ings over the years. standing keynote speakers at your event to charge your participants to attend. Map The International Society for Compu- will also require you contact them months all this out on a spreadsheet and do the tational Biology (ISCB) Student Council in advance—the bigger the name, the math. Allow for contingencies, such as [2] is an organization within the ISCB more time is required. currency fluctuations and world-changing that caters to computational biologists early in their career. The ISCB Student Council provides activities and events to its members that facilitate their scientific development. From our experience in Citation: Corpas M, Gehlenborg N, Janga SC, Bourne PE (2008) Ten Simple Rules for Organizing a Scientific organizing the Student Council Sympo- Meeting. PLoS Comput Biol 4(6): e1000080. doi:10.1371/journal.pcbi.1000080 sium [3,4], a meeting that so far has Published June 27, 2008 been held within the context of the Copyright: ß 2008 Corpas et al. This is an open-access article distributed under the terms of the Creative ISMB [5,6] and ECCB conferences, we Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, have gained knowledge that is typically provided the original author and source are credited. not part of an academic curriculum and Funding: The authors have received no specific funding for this article. which is embodied in the following ten Competing Interests: The authors have declared that no competing interests exist. rules. * E-mail: [email protected]

PLoS Computational Biology | www.ploscompbiol.org 1 June 2008 | Volume 4 | Issue 6 | e1000080 events that will impact attendance. For sions and review; 5) posters; 6) keynotes; 7) the venue managers. All attendees should large meetings, consider insurance against local organization; 8) program and speak- be reachable as far as possible during the such events. Starting with a template that ers; 9) awards. Your organizing committee conference. If an attendee has an emer- others have used for previous similar should be large enough to handle all the gency at home, his or her family should be conferences can be a big help. above but not too large, avoiding free- able to reach them through the conference loaders and communication issues. It is desk—mobile phones are not perfect after Rule 4: Choose the Right Date invaluable to have a local organizing all. and Location committee since they know local institu- tions, speakers, companies, and tourist Rule 9: Wrap Up the Conference Your conference needs to be as far away attractions. Local organizations may also Properly as possible from established conferences help you with administrative tasks; for and other related meetings. Alternatively, example, dealing with registration of At the end of the conference, you you may want to organize your event attendees and finding suitable accommo- should give credit to everyone who helped around a main conference, in the form of dations around the venue. to make the event a success. If you have a satellite meeting or Special Interest awards to present, this is the right time for Group (SIG). Teaming up with established Rule 7: Have the Members of the awards ceremony. Dedicate some time conferences may increase the chances of the Organizing Committees to thank your speakers and sponsors as attracting more people (especially if this is well as everyone involved in the organiza- Communicate Regularly your first time) and also save you a great tion of the conference. Also collect feed- deal of administrative work. If you decide It is good to have planning sessions by back about the event from the delegates to do it on your own, you should consider teleconference ahead of the meeting. As through questionnaires. This evaluation how easy it is to travel to your chosen far as possible, everyone should be familiar will help you to understand the strengths location, whether it has a strong local with all aspects of the meeting organiza- and weaknesses of your conference and community in your field, and whether it tion. This collective wisdom will make it give you the opportunity to improve has cultural or other tourist attractions. less likely that important issues are forgot- possible future events. Have a party or Inexpensive accommodation and airfares ten. The local organizers should convince some other event for all those organizing to your conference are always a plus. everyone that the venue will work. Use the conference. these sessions to assign responsibilities Rule 5: Create a Balanced ahead of the meeting. Tasks such as Rule 10: Make the Impact of Agenda manning the registration tables, carrying Your Conference Last microphones for attendees to ask ques- A conference is a place for people tions, introducing sessions and speakers, Published proceedings are the best way wanting to share and exchange ideas. checking presentations ahead of time, and to make the results of your conference last. Having many well-known speakers will having poster boards, materials to attach Negotiate with journals far in advance of raise the demand for your event (and the posters, etc., are easily overlooked. In the conference to publish the proceedings. cost) but that has to be balanced with short, good communication will lead to Make those proceedings as widely acces- enough time for presentation of submitted you covering all the little things so easily sible as possible. Upload photos and videos materials. A mix of senior scientists and forgotten. of the event to the conference Web site junior scientists always works for the better. Good communication continues and post the names of presenters who have Young researchers may be more enthusias- throughout the meeting. All organizers received awards or travel fellowships. It is tic and inspiring for students, while top should be able to contact each other also a good idea to link the results of your senior scientists will be able to present a throughout the meeting via mobile phone evaluation to the Web site. Send one last more complete perspective of the field. and e-mail. Distribute to all organizers the e-mail to all delegates, including a sum- Allow plenty of time for socializing, too; names and contact information of caterers, mary of the activities since the conference breaks, meals, and poster sessions are ideal building managers, administrative person- and thanking them for their participation. occasions to meet potential collaborators nel, technicians, and the main conference This is particularly important if you are and to foster networking among peers. organizer if you are having your event as considering holding the conference again part of another conference. Onsite chang- in future years, in which case include some Rule 6: Carefully Select Your es that incur additional costs, however, information on your plans for the next Key Helpers: the Organizing should require the approval of a single, key event. Committees organizer rather than all organizers oper- As always, we welcome your comments ating independently of one another. This and experiences that you think would A single person will not have all the will ensure there are no financial surprises enrich these ten rules so that they might skills necessary to organize a large meet- in the end. It is also important that you be useful to others. The comment feature ing, but the organizing committee collec- have a designated meeting point where now supported by this journal makes it tively needs to have the required expertise. someone from the organizing committee is easy to do this. You might want to separate the areas of going to be available at all times to help responsibilities between your aides de- with problems. Acknowledgments pending on their interests and availability. Some potential responsibilities you might We would like to acknowledge the International Rule 8: Prepare for Emergencies Society for Computational Biology (ISCB) for delegate are: 1) content and design of the their support in the organization of the Student Web site promoting the meeting; 2) Attendees need to be aware of all Council Symposiums, in particular BJ Morri- promotion materials and marketing; 3) emergency procedures in terms of evacu- son-McKay and Steven Leard. Thanks to finance and fundraising; 4) paper submis- ation, etc. This should be discussed with Michal Linial and Rita Casadio (our liaisons

PLoS Computational Biology | www.ploscompbiol.org 2 June 2008 | Volume 4 | Issue 6 | e1000080 at the ISCB Board of Directors), Burkhard Rost the Student Council. We are also grateful to all siasm and hard (unpaid) work. You all have (the ISCB President), and all the ISCB Board of the Student Council leadership and current and made the Student Council a great organization. Directors for being so supportive of the work of past Student Council members for their enthu-

References 1. Tomazou EM, Powell GT (2007) Look who’s 4. Gehlenborg N, Corpas M, Janga SC (2007) putational biology. PLoS Comput Biol 3: e96. talking, too: Graduates developing skills through Highlights from the Third International Society doi:10.1371/journal.pcbi.0030096. communication. Nat Rev Genet 8: 724–726. for Computational Biology (ISCB) Student Coun- 6. Third ISCB Student Council Symposium. Avail- doi:10.1038/nrg2177. cil Symposium at the Fifteenth Annual Interna- able: http://www.iscbsc.org/scs3 Accessed 22 2. The International Society for Computational tional Conference on Intelligent Systems for April 2008. Biology Student Council. Available: http:// Molecular Biology (ISMB). BMC Bioinformatics www.iscbsc.org. Accessed 22 April 2008. 8 (Supplement 8):I1. 3. Corpas M (2005) Scientists and societies. Nature 5. Lengauer T, McKay BJM, Rost B (2007) ISMB/ 436: 1204. doi:10.1038/nj7054–1204b. ECCB 2007: The premier conference on com-

PLoS Computational Biology | www.ploscompbiol.org 3 June 2008 | Volume 4 | Issue 6 | e1000080 Editorial Ten Simple Rules To Combine Teaching and Research

Quentin Vicens1, Philip E. Bourne2* 1 University of Colorado, Boulder, Colorado, United States of America, 2 Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, California, United States of America

The late Lindley J. Stiles famously made to engage students to brainstorm about the (2) Administer a Web site for your himself an advocate for teaching during risks of GMOs) and your research (e.g., course. Many universities and some his professorship at the University of finish experiments for this project and start textbooks now offer you the possibility Colorado: ‘‘If a better world is your aim, writing before Easter; this week do the of hosting a Web site with course- all must agree: The best should teach’’ control for my primer binding assay). Make related materials, including automat- (http://thebestshouldteach.org/). In fact, sure you achieve them. If you don’t—this is ically graded assessments. See, for dispensing high-quality teaching and pro- likely to happen at first—ask yourself how example, the CULearn suite used at fessional education is the primary goal of legitimate your reason is. Then review and the University of Colorado (http:// any university [1]. Thus, for most faculty adjust the goals accordingly. www.colorado.edu/its/culearn/), or positions in academia, teaching is a more general automatic grading tools significant requirement of the job. Yet, Rule 3: ‘‘Don’t Reinvent the presented at http://ctl.stanford.edu/ the higher education programs offered to Wheel’’ Tomprof/postings/227.html. Ph.D. students do not necessarily incorpo- (3) Gather a solid team of motivated rate any form of teaching exposure. We We borrowed the title for this rule from teaching or learning assistants, who offer 10 simple rules that should help you excellent suggestions on How To Prepare New will both serve as an intermediary to get prepared for the challenge of Courses While Keeping Your Sanity [2]. Most between you and your students and teaching while keeping some composure. likely, you will not be the first one ever to help you grade. In short, don’t be teach a particular topic. So get in touch afraid to ask for help! Rule 1: Strictly Budget Your with the colleagues in your department who Time for Teaching and for have taught the class you are going to Doing Research teach, or who teach similar topics. You can Rule 4: Don’t Try To Explain also use your network and contact former Everything This rule may seem straightforward, but colleagues or friends at other institutions. respecting it actually requires more disci- They will usually be happy to share their Class time should be spent guiding pline and skill than it first appears to. The course material, and along the way you students to create their own explanation key is to set aside time for both teaching and might also glean precious tips from their of the material and to develop cognitive research from the beginning, with a well- teaching experience (e.g., a list of do’s and abilities that will help them become critical marked separation (e.g., mornings will be don’ts on how to approach a notoriously thinkers. In other words, you don’t want to devoted to course preparation, afternoons to difficult topic). You will also learn a lot from present all aspects related to a certain topic experiments and manuscript writing). Firm- sitting in one of their classes and watching or to lay out all the explanations for them. ly stick to this agenda, particularly if this is how they handle their topic and their Thus, an effective way to teach is to get your first time teaching. Failure to do so students. Here are more examples of students to learn by transformative learn- would eventually affect the quality of your precious time-savers: ing: beyond memorizing and comprehend- teaching or the progress of your research (or ing basic concepts, they will learn to reflect both). Over time, you will become more (1) Choose a textbook that is accompa- on what they learn and how they learn it skilled at jumping from one commitment to nied by rich online resources such as (see, for example, http://en.wikipedia.org/ the other, and therefore allowing the annotated figures, pre-made Power- wiki/Transformative_learning and refer- boundaries to fluctuate somewhat. Avoid Point slides, animations, and videos. ences within). Such teaching practices underestimating the time necessary to fulfill Students will thank you for showing require that a significant part of the teaching-related obligations (e.g., office movies, for example, as they often are learning process happens outside the class- hours, test preparation, grading, etc.) by a better option to break down com- room, through reading assignments, home- consulting with your colleagues. plex mechanisms or sequences of work, writing essays, etc. So make sure you events into distinct steps. budget time to organize these, as specified Rule 2: Set Specific Teaching and Research Goals Citation: Vicens Q, Bourne PE (2009) Ten Simple Rules To Combine Teaching and Research. PLoS Comput Biol 5(4): e1000358. doi:10.1371/journal.pcbi.1000358 In order not to have one occupation Published April 24, 2009 overpower the other one—which would transgress Rule #1—it is a good idea to Copyright: ß 2009 Bourne, Vicens. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, decide on specific aims for each enterprise. provided the original author and source are credited. Compile a list of reasonable but specific Funding: The authors received no specific funding for this article. long-term goals (for the month or the semester) and short-term ones (for the week) Competing Interests: The authors have declared that no competing interests exist. for both your teaching (e.g., finish Chapter * E-mail: [email protected] 3 by Nov. 1; this week propose a discussion Philip E. Bourne is the Editor-in-Chief of PLoS Computational Biology.

PLoS Computational Biology | www.ploscompbiol.org 1 April 2009 | Volume 5 | Issue 4 | e1000358 in Rule #2. Remember that in the end this chapter in someone else’s book that you offer to organize a series of seminars, or to will be a win–win situation: you will save would eventually give as a reading assign- edit the newsletter of your department, is time by not having to fit everything into ment in your class. Conversely, there is legitimate if it cuts into your productivity. your class time, and students will learn how wisdom in crowds. Consider having stu- Similarly, keep your ability to career to find answers through their own thinking. dents review aspects of your research that fit advance in mind when considering taking the course and get feedback. You will be on another teaching assignment. Rule 5: ‘‘Be Shameless in surprised at what useful information can Bringing Your Research come from students critiquing a new Rule 9: Start Teaching Early in Interests into Your Teaching’’ manuscript or proposing new experiments. Your Career This is yet another great time-saver, and Rule 7: Compromise, This will be the best way to get exposed to this rule title is actually from Confessions Compromise, Compromise some of the difficulties mentioned in the about Stress and Time: Thoughts for Faculty other Rules sooner rather than later. You (available at http://www.colorado.edu/ A significant part of the compromise once can see this as an opportunity to learn how ftep/publications/confessions.html). Stu- you accept a joint research/teaching com- to add on various responsibilities in a dents want to know how what you teach mitment is to realize that your list of ‘‘things gradual rather than an immediate manner relates to the world around them. They that in principle you would like to do but (e.g., when ‘‘jumping’’ from a post-doc to a also like to know what is happening in won’t have time to do’’ will get longer. faculty position at a university). Many science right now, so this is where you can Maybe you would like to personally respond options are available to teach at the graduate feed in some of your research interests (for to all the students who e-mail you about any level (e.g., by becoming a teaching/learning some examples of how researchers around problem they may have, but, realistically, assistant), as well as at the post-graduate level the world have been bringing their such things can’t happen. Instead, a solution (e.g., by teaching part-time on campus or at research into the classroom, refer to the would be to send some general feedback in a local school while doing your post-doc). special section of the July 6, 2007, issue of answer to the common queries and to write You may need to be proactive about looking the magazine Science entitled The World of occasional brief personal responses. As you for such opportunities, but an increasing Undergraduate Education [3]. Students will get more skilled at combining research and number of universities and institutions are welcome such connections, especially in an teaching, you will be able to progressively developing programs that formally offer introductory course or in a course for non- bring back activities such as scanning the teaching experience to graduate students majors. Additionally, they will feel the most recent scientific literature and attend- and post-docs [4,5]. passion that makes you love being a ing seminars and lectures more often. But scientist. On your end, you might find remember to accept that no matter how Rule 10: Budget Time for that preparing course materials will be skilled you are at budgeting your time for Yourself, Too easier (because you are already a master of teaching and research, you will still face the that topic), and you might learn to be conflicting demands of both, and you will A lot of stress can build up from a more comfortable at presenting your have to keep compromising. In the end, constant shuttle between teaching de- research in layman’s terms. compromising will sometimes imply learn- mands and research occupations. In order ing to say no when pondering about taking to be able to evacuate some of that Rule 6: Get the Most in Career on a novel and exciting assignment that tension, it is a good idea to hide some Advancement from Bringing would unequivocally conflict with your time for yourself that you will spend with current research/teaching agenda. your family, or to do your hobby, to Your Research into Your exercise, to travel, etc. An unfulfilling Teaching Rule 8: Balance Administrative personal life is incompatible with success- As a sort of followup to Rule #5, ful teaching and research careers. Conse- Duties with Your Teaching and quently, don’t forget to spend some energy presenting your research in class could Research Workload bring you a solid return on your investment. learning how to balance both areas. For example, teaching gives you exposure; Your responsibility as a teacher and as a Finally, keep in mind that your experi- talking about your research may help you researcher is to be as productive as you ence can make for a valuable contribution recruit motivated students in your lab, can be in these two areas, at the same to the scientific community, for example, which will help you advance your research, time. This is what your colleagues and the in the form of a report on your efforts in possibly by taking it in original directions. In faculty board will expect from you when science education, or by posting comments parallel, you could also use your research to evaluating you for tenure, for example. to this Editorial! design a novel course and possibly evaluate Doing service within your community (for student learning in a fashion that would example by sitting on committee meetings, Acknowledgments make for a publication in a science or by being part of a local scientific club) We thank Joe Ma, Clayton Lewis, and Jamie education journal. Another option would counts as well, but not as much. In Williamson for careful reading of the manu- be to write or edit a book, or to contribute a consequence, turning down yet another script.

References 1. Editorial (2007) Those who can teach, should. Teaching and Learning at http://ctl.stanford.edu/ research and disciplinary teaching. ACS Chem Nat Chem Biol 3: 737. Tomprof/postings/800.html]. Biol 2: 518–520. 2. Brent R, Felder RM (2007) Random thoughts: How 3. Mervis J (2007) Special section—The world of 5. Tahmassebi DC, Williamson JR (2007) Balancing to prepare new courses while keeping your sanity. undergraduate education. Science 317(5834): teaching and research in obtaining a faculty Chem Engr Education 41: 121–122. [Reprinted in 63–81. position at a predominantly undergraduate insti- a posting by Rick Reis on the Tomorrow’s Professor 4. Coppola BP, Banaszak Holl MM, Karbstein K tution. ACS Chem Biol 2: 521–524. mailing list at the Stanford University Center for (2007) Closing the gap between interdisciplinary

PLoS Computational Biology | www.ploscompbiol.org 2 April 2009 | Volume 5 | Issue 4 | e1000358 Editorial Ten Simple Rules for Choosing between Industry and Academia

David B. Searls*

One of the most significant decisions we bioinformaticists were in such short supply you need a quick infusion of cash, compa- face as scientists comes at the end of our that any qualification would do. nies may offer signing bonuses, though formal education. Choosing between in- If you are an old hand and have already again these were more common when dustry and academia is easy for some, notched up a post-doc or two, take stock of bioinformatics was a rarer commodity. incredibly fraught for others. The author your star power. This unspoken but Industry offers forms of compensation has made two complete cycles between universally understood metric encompass- unavailable in academia, and you will these career destinations, including on the es such factors as whom you’ve trained need to consider how to value them one hand 16 years in academia, as grad with, where you’ve published (and how relative to your present and future needs. student (twice, in biology and in computer much), and what recent results of yours Despite recent bad press, bonus systems science), post-doc, and faculty, and on the are on everyone’s lips. If you are fortunate are often part of the equation, and other hand 19 years in two different enough to have significant capital in this depending on your entry point they may industries (computer and pharmaceutical). department, then the world may be your constitute a significant percentage of total The following rules reflect that experience, oyster, but you still need to consider where compensation. There is a tendency among and my own opinions. you will get the greatest leverage. While academics to discount bonus programs in your stardom may be less taken for their comparison shopping, sometimes to Rule 1: Assess Your granted in industry, my feeling is that zero, and this is a mistake. Bonuses are Qualifications academia is a better near-term choice in considered core aspects of compensation such circumstances. Consider that it was in most companies, and though they If you are a freshly minted Ph.D., you in academia that you achieved the success always have a performance-based multi- know that you will need a good post-doc you own thus far, so you obviously ‘‘get plier, the base levels have historically been or two before you can be seriously it.’’ The simple fact is that academia is fairly dependable. That said, these are considered for a junior faculty position. If rather more of a star system (as in tough times in industry, and there are no you’re impatient, you might be thinking of Hollywood) than is industry. guarantees. Your best strategy is to industry as a way to short-circuit that long Finally, if you count among your understand the reward system thoroughly, haul. You should be aware that companies qualifications a stint in industry already, ask for historical data, and avoid compar- will strongly consider your post-doctoral as an intern or perhaps as part of a ing only base salaries unless you are experience (or lack thereof) in determining collaboration, you will not only be in a extraordinarily risk-averse. your starting position and salary. While better position to compete for a perma- Share options are another matter. you may not relish extending your inden- nent job, but you will be much better While in the past these were very attrac- tured servitude in academia, any disad- prepared to make the decision facing you. tive, and fruitful in practice, most industry vantage, financial and otherwise, can Stated another way, if you are seriously types will tell you frankly that any options quickly be made up in the early years of considering industry as a career path, you they’ve received in the past decade are your career in industry. In other words, should probably have already taken ad- deep underwater and a deep disappoint- trying to get off the mark quickly is not vantage of the many opportunities out ment. Many consider pharma shares (and necessarily a good reason to choose there to dip your toes in the water. industry over academia. therefore options) to be a bargain at the moment, but that’s between you and your On the other hand, you may have Rule 2: Assess Your Needs completed an undergraduate or Master’s financial adviser to assess. In any case, it is program with a view to going to industry In taking stock of your needs, and perhaps not a short-term consideration, since all along, with never a thought of an those of your family, a decent living is options typically take several years to vest. academic career. You should still consider generally at or near the top of the list. If you are looking at biotech, however, the point of the previous paragraph. While Salaries are still higher in industry, though share options and similar ownership abbreviated ‘‘practical’’ bioinformatics the gap is not nearly so wide as it once was. If schemes need to be a key consideration, training programs can be excellent, a Ph.D. is a significant advantage in all but Citation: Searls DB (2009) Ten Simple Rules for Choosing between Industry and Academia. PLoS Comput the most IT-oriented positions in industry, Biol 5(6): e1000388. doi:10.1371/journal.pcbi.1000388 at least at the outset. This is not to discourage anyone from embarking on a Published June 26, 2009 fast-track-to-industry program if their Copyright: ß 2009 David B. Searls. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, heart is in it, but be aware that the further provided the original author and source are credited. you climb the educational ladder, the Funding: The author received no specific funding for this article. higher and faster you can start when you step across to the business ladder, and the Competing Interests: The author has declared that no competing interests exist. better you will compete for a job in the * E-mail: [email protected] first place. The days are long past when David B. Searls is an Associate Editor of PLoS Computational Biology.

PLoS Computational Biology | www.ploscompbiol.org 1 May 2009 | Volume 5 | Issue 6 | e1000388 since these are a major rationale for science, and your drivers will be to start a funding decision, etc.). If you are assuming risk—more on that below. out on your career by getting results, impatient, industry offers relatively fast- Finally, you may have more specific publishing, networking, and building your paced decision-making and constant needs to consider, such as a spouse also in reputation with a view to impressing your change. If you thrive more under struc- need of a job. The two-body problem has tenure committee. A career in industry tured expectations, academia would be always been tougher in academia than in may put more of an early emphasis on better for you, for although industry has all industry, and probably always will be. If your organizational aptitude, people skills, the trappings of long-range strategies and you are both academics, note that industry powers of persuasion, ability to strategize career planning, the highly reactive envi- often has good contacts with local univer- and execute to plan, etc.; in terms of ronment means these are more honored in sities, and can facilitate interviews. Being a growing your reputation, your audience the breach. For one thing, reorganizations star certainly helps, so don’t be afraid to will be the rather narrower community of are common, and in the extreme case negotiate. In fact, a general rule of thumb your immediate management. A some- mergers (I have experienced two) can reset is that it never hurts to make your specific what more cynical view would be that in everything, for good or ill, and devour needs known, within reason. Academia business you will spend seemingly endless many months. will try to accommodate them as a hours in meetings and writing plans and This is not to say that all is chaos— community, while on the other hand reports, while in academia you will spend industry certainly favors a goal-directed business (particularly large, diversified all that time and more in grantsmanship— personality, but with plenty of flexibility. companies) may have resources to address in this regard, you must pick your poison. On the other hand, flexibility is more the them that you wouldn’t have expected. Finally there is the elephant-in-the- hallmark of academic research, where Nobody wants to hear a peremptory room question: Do you want to make you will have the opportunity to follow demand, but if a company wants you, be money, or to help people? This is, of whereverthescienceleads,onceyouare sure to let them know anything that might course, a false dichotomy, but many running your own shop. In industry, the offer them a way to attract you. people consciously or unconsciously frame flexibility is more of the conforming sort, the decision in just this way, and you had since you won’t be able to investigate Rule 3: Assess Your Desires best deal with it. Try thinking of it not so every promising lead and change your much in terms of the profit motives of the research direction at will. In academia, There are needs, and then there are respective institutions, but in terms of the diverging from the Specific Aims of a desires. Do you want riches? Fame? A life people with whom you would spend your grant may be a problem when the time at the frontiers of knowledge? The hurly- career. You should have encountered a comes to renew, but the risk is yours, as burly of the business world? How do you good sampling of scientists from industry is the reward. In industry, you can make really feel about teaching, publishing, during meetings, internships, collabora- the case for a new program of research, managing, interacting, traveling, negotiat- tions, interviews, etc. (or in any case you but the decision is management’s and ing, collaborating, presenting, reporting, should certainly try to do so before making will be guided by business consider- reviewing, fundraising, deal-making, and judgments). If you are left in any doubt as ations. The ‘‘lone wolf’’ or ‘‘one-person on and on? Though it may seem obvious, to their ethics or sincere desire to relieve band’’ may be increasingly rare in this is a good time to decide what really human suffering as efficiently as possible, academia in an age of collaboration, drives you. or if you feel these are somehow trumped but it is unheard of in industry, where First, the obvious. Do you want to by the corporate milieu, then by all means being able to work in teams with teach? If lecturing is in your blood, your choose academia—but only after applying specialized division of labor is essential. decision is made, although if a smattering analogous tests to the academics you It should be apparent, as well, that will suffice you may have the option from already know well. In my experience, mavericks and quirky personalities tend within industry of an adjunct academic business doesn’t have a monopoly on to do better in academia. appointment. (By the same token, if you greed, nor are humanitarian impulses The pecking order in industry is deeper are not so enchanted with lecturing, restricted to academia. That said, in the and more pyramidal than in academia, grading, tutoring, etc., there are often final analysis you must be comfortable and you might end up languishing in a pay options for research track professorships with your role in the social order and not grade (or feel like you are), but there are that minimize teaching duties.) Do you finesse the question. usually plenty of opportunities for lateral want to publish? While it will always be moves and a variety of experiences—not ‘‘publish or perish’’ in academia, it is Rule 4: Assess Your Personality to mention that it’s easier to switch certainly possible to grow your CV in companies than colleges. In industry, one industry, and it can even enhance your Not surprisingly, some personality types does need to be able to thrive in a career, depending on the company. How- are better-suited to one environment or hierarchy; you will always answer to ever, it might be largely on your own time, the other. Raw ambition can be viewed as someone, though the degree to which and you will likely encounter restrictions in unseemly in either case, but there is more you are monitored will vary. By the same proprietary matters, though in practice latitude for it in industry, and greater token, if your personality is such that you can generally find ways to work within likelihood of being recognized and re- climbing a management ladder and as- them. Ask about publication at the warded sooner if you are ‘‘on the go.’’ In suming steadily greater responsibility suits interview, both policies and attitudes, fact, one of the clearest differences be- you, industry is built for that, and plenty of and watch out for any defensiveness. tween academia and industry are their management training is on offer in larger An important question, surprisingly respective time constants. Although the companies. Learning to manage is much often overlooked, is how you want to pace of academia may have quickened of more hit-or-miss in academia; opportuni- actually spend your time, day by day and late, it is still stately by comparison with ties to lead large organizations are rare hour by hour. In academia, you will industry, and much more scheduled (so (and to manage them actively rather than immediately be plunged into hands-on many years to tenure, so many months to by consensus, rarer still).

PLoS Computational Biology | www.ploscompbiol.org 2 May 2009 | Volume 5 | Issue 6 | e1000388 If your personality type is that of a risk- other journals at the same scientific career in pharma rather less so, in the taker, biotechs and/or startups may fit you meetings you attend. The same is true of opinion of the author. to a tee. These are the wild and wooly end government agencies such as the NIH, of the industry spectrum, and the risks and NSA, DOE, and so forth, where grants Rule 7: Plan for the Long Term rewards are well-known. You will work administration is very actively tied to longer hours than in large pharma, and research trends and can be an entre´e into Having noted the current situation in maybe even more than in academia. You the world of science policy. There are Rule 6, it’s important also to say that a will most likely share more in ownership, many more such positions when founda- career decision should be made with the and learn entrepreneurial skills that will tions, interest groups, and other private long haul in mind. The business cycle will serve you well, once the bug has bitten. funding bodies are included. If you have a eventually reverse itself, and while the Bear in mind the very common pattern of knack for business, many management business model may need to change faculty spinning off startups or otherwise consulting firms have scientific and tech- irrevocably, the aging population alone participating in boards and the like, not to nical consulting arms that value Ph.D.s dictates that healthcare will be an increas- ing global priority. Likewise, history shows mention staking out intellectual property and offer intensive training opportunities, that growth in government funding for (shared with their university); thus, you and, though it may not be attractive at the science waxes and wanes, with a time may well be able to scratch this itch from moment, a career as a financial analyst constant somewhat longer than a decade. the vantage of academia as well. specializing in biotech is yet another Trying to optimize a career decision based A final word about politics. Whether possibility. on current conditions is a bit like trying to you are an enthusiastically political ani- time the stock market—you are sure to be mal, or abhor this aspect of the human Rule 6: Consider the Timing overtaken by events. condition, you will encounter plenty of One approach is to choose some politics in both academia and industry. The current business environment can- reasonably long time frame, perhaps a The flavors differ, to be sure. As a student not help but be among your consider- decade, and ask yourself whether you’d be you doubtless heard the cliche´s about ations. Pharma has certainly been con- content to have lived through the average tedious academic committees and under- tributing to the unemployment rolls of ups and downs you’d experience in a given handed deans, but you have probably had late. Corporate strategies, which used to job over that period. In academia, that more exposure to the realities behind those be very similar across the sector, have would include a tenure decision (rate your stories than the corresponding ones about started to diverge, so that some companies chances), a lot of grant applications with the dog-eat-dog corporate world. Compa- are divesting bioinformatics at the same mixed success at best, and maybe some ny politics, I would hazard to say, are time that others are hiring computational great students and really significant scien- more transparent—the maneuvering more types disproportionately as they place tific contributions. In pharma or large open and the motives more apparent. The more of an emphasis on mathematical biotech, it would encompass a couple of results are often more life-altering, unbuf- modeling, systems approaches, pharmaco- promotions, your own group and maybe a fered by tenure and academic convention. genomics, drug repurposing, and the like. Overall, though, the industry trend has department, at least one merger or other Again, it is a matter of taste, but in my big disruption, and several rounds of opinion the differences are overblown, for been to shrink R&D, and this may well continue through a round of consolida- layoffs. In small business, it might include the simple reason that people are the same a failed startup (or two, or three), an IPO if tion, with several mega-mergers now everywhere, in both environments gov- you’re lucky, and a lucrative exit strategy under way. As noted above, mergers are erned by an underlying sense of fair play, or long-term growth if you’re really lucky. times of upheaval, carrying both risk and but also occasional opportunism. If you game these scenarios with various opportunity, and usually a period in limbo probabilities, and use your imagination, it as well. At the same time, it is worth Rule 5: Consider the just might become clear which ones you bearing in mind that a corollary of Alternatives have no stomach for, and which ones downsizing is outsourcing, so that there really hold your interest. As I’ve suggested, the choice you face is may be new opportunities for startups and far more fine-grained than simply that even individual consultants. Rule 8: Keep Your Options Open between industry and academia. Industry For much of the last decade, academia is a spectrum, from large pharma to has also been in the doldrums, as NIH Job-hopping is much more prevalent mature biotech to startup. By the same budgets have effectively contracted. As I now than in days of yore, and you should token, the academic side has at one write this, things are definitely looking up, consider this in your scenarios. In industry, extreme the research powerhouses, where with prospects for renewed funding of there is little stigma attached to changing you will be judged by volume of grants, science and even near-term benefits to the employers, and if you can tolerate the and at the other the teaching institutions, NIH and NSA from the Obama stimulus relocation and/or want to see the world, it which may not even have graduate package. Whether universities will respond is a more or less standard way to advance departments. Unless you are very sure of proportionately with faculty hiring, given your career by larger-than-usual incre- yourself, you’d be well-advised to consider the losses in their endowment funds and ments. This stratagem is far from un- the full range, given the competition you cutbacks in salaries and discretionary known in academia, but perhaps a bit may face. spending, remains to be seen. There is a trickier to execute, though of course it is de Also, don’t neglect other careers that lot of slack to be taken up, and in rigueur if you fail to get tenure. may value your training. If you love the particular a backlog of meritorious grant Of greater interest is the question of language, consider science journalism, applications that are now being reconsid- moving between academia and industry. either writing or editing—Science and ered. Nevertheless, on balance, an aca- From the former to the latter is fairly easy, Nature have large staffs, and you will often demic career has to be somewhat more but the reverse is not as common, for a encounter them and representatives of promising today than a year ago, and a variety of reasons. Superstar academics in

PLoS Computational Biology | www.ploscompbiol.org 3 May 2009 | Volume 5 | Issue 6 | e1000388 relevant areas are in great demand in Rule 9: Be Analytic classic advice to ‘‘make a list of pros and industry, to which they are often exposed cons,’’ which always makes one feel a little through consulting or scientific advisory Approach the decision with the analytic more in control. boards. There are multiple examples of skills you’ve learned to apply to scientific senior academics taking over major R&D questions. Gather data from all available Rule 10: Be Honest with sources and organize it systematically. organizations in industry, sometimes or- Yourself ders of magnitude larger than anything When you interview, don’t just impress, they managed in academia, and you might but get impressions; record everything Another homily: Now, if ever, is the even consider this well-trod path as a down to your gut feelings. Do some time to be honest with yourself. Take a career goal from the outset. bibliometric or even social network anal- hard look at your qualifications, with as It is not impossible to return to yses of your potential colleagues. Check much objectivity as you can muster, and academia from industry, particularly if the industry newsletters and blogs, albeit use these rules to decide where you would you were already quite prominent when with a grain of salt, to get a sense of the be best-suited and positioned for success. you left, but if you start your career in mood around R&D units (not to be But even more importantly, deal with your industry you may be at a disadvantage confused with manufacturing, sales and emotional responses to industry and aca- unless you go to great lengths to maintain marketing, or other divisions, which may demia. If something is nagging at you, an academic-style publication record and have completely different cultures within tease it out into the open, and try to decide CV. Important exceptions would be if the the same company). if it is well-founded or not; if you can’t work that you did in industry was You might even try out some decision decide, then you have to acknowledge it, particularly novel and/or high-profile, or theoretic methodologies, such as decision and realize that it may not go away in the if your business experience is valued in the matrices and Bayesian decision trees, or future either. post you seek. Examples of the latter might run simulations on the scenarios of Rule 7. Finally, try to keep some perspective. be faculty positions with a prominent I recommend taking a look at expected Your career choice is important, but not management component (centers, insti- utility theory and prospect theory, for an irrevocable, and there are more conse- tutes, core facilities, and the like), or an interesting quantitative excursion. But quential things in life. Don’t let the interface role back to industry, or perhaps honestly, these suggestions are just a more decision process ruin what should be an a joint business school appointment. sophisticated informatics version of the exciting time for you.

PLoS Computational Biology | www.ploscompbiol.org 4 May 2009 | Volume 5 | Issue 6 | e1000388 Editorial Ten Simple Rules for Chairing a Scientific Session

Alex Bateman1, Philip E. Bourne2* 1 Wellcome Trust Sanger Institute, Cambridge, United Kingdom, 2 Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, California, United States of America

Chairing a session at a scientific confer- It is your job to excite people at the session Rule 7: Don’t Be Afraid to Move ence is a thankless task. If you get it right, and have them stay in the auditorium. on Without Questions no one is likely to notice. But there are Regarding the speakers, introduce each many ways to get it wrong and a little one before they begin, providing their A good scientific session is characterized preparation goes a long way to making the background and highlighting their major by a lively question and answer session. In session a success. Here are a few pointers accomplishments. Speakers love to be fact, some speakers believe it is their right that we have picked up over the years. properly introduced and the audience likes to expect to answer questions even after to feel they know the person speaking. But their allotted time is up. If you are running Rule 1: Don’t Let Things for the sake of both the timing of the session over time, you should not be afraid to Overrun and your speakers, do keep it brief. Are you move on to the next talk without ques- expected to give any housekeeping messages tions. You will be more confident in Probably the main role of the session or to remind people to switch off their enforcing this principle if you have warned chair is to keep the meeting running on phones? Allow time for that if so. the speaker beforehand that running over time. Time is a strange and elastic concept will require foregoing taking questions at when people are under pressure. Some Rule 4: Write Down the Actual that time. You can stay on schedule by speakers will talk much faster than normal Start Times of the Speakers diplomatically saying that the speaker will and finish a talk in half the expected time. be happy to take questions at the break. Others will ramble on without knowing If you don’t know what time a speaker that time is running out and they have started, it is difficult to know when to ask Rule 8: Get to the Venue Early only just finished their introduction. Tim- them to stop. So always write down the and Be Audiovisually Aware ing is important to ensure that a meeting start and finish times of speakers through- runs smoothly. Delegates should leave the out the session. Make sure to know where everything is, session at just the right time so that like pointers, microphones, projectors, and lunches are still fresh, bars still open, etc. Rule 5: Do Have a Watch computers and who to turn to if it all goes Timing is particularly acute if there are wrong. It is worth checking that all these multiple parallel sessions and delegates It sounds obvious, but it is very difficult things work so that you can swiftly fix would want to switch between talks in to chair a session if you don’t have a watch them yourself. Knowing ahead of time any different sessions. and don’t know the time. Yes, one of us unusual requests from speakers to show has done this! It is embarrassing to have to movies and sound clips requiring special Rule 2: Let Your Speakers Know ask your neighbor for a watch. Actually, it attention. Be sure the venue supports the the Rules is probably best to have two watches, just needs of speakers. If not, let them know in case. before they get to the venue. If each A session will run more smoothly if you speaker is expected to load their presenta- let all the speakers know how you plan to Rule 6: Communicate How tion on a single computer associated with run your session. This could be done by e- Much Time is Left to the the podium, allow time for that and have mail before the event or you might want to Speaker the speaker run through their slides to be gather up the speakers just before the sure everything is working properly. session. Reminding them how much time Letting the speaker know their time is they have to speak, how much time to up is crucial in keeping time. A simple sign Rule 9: Prepare Some Questions allow for questions, and how you will let held up at the right time is usually fine. in Advance them know time is up will stop confusion Have one saying, ‘‘5 minutes to go’’ and later on. Beyond the rules, encourage another saying ‘‘time is up’’. Beyond that It can take an audience a few seconds to speakers to review what others in the time, standing up on the stage is a good digest the contents of a talk and think of session will say. The less redundancy, the sign that the speaker should wrap up. questions. So it is always good to have one better the session will be for everyone, including the chair. Citation: Bateman A, Bourne PE (2009) Ten Simple Rules for Chairing a Scientific Session. PLoS Comput Biol 5(9): e1000517. doi:10.1371/journal.pcbi.1000517 Rule 3: Be Prepared to Give a Editor: Burkhard Rost, Columbia University, United States of America Short Introduction Published September 25, 2009 Be prepared to give a short introduction Copyright: ß 2009 Bateman, Bourne. This is an open-access article distributed under the terms of the to the session, and, of course, introduce Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any yourself as well. Be sure to review the medium, provided the original author and source are credited. abstracts of the talks and then give a Competing Interests: The authors have declared that no competing interests exist. succinct summary of what will be presented. * E-mail: [email protected]

PLoS Computational Biology | www.ploscompbiol.org 1 September 2009 | Volume 5 | Issue 9 | e1000517 or two ready to ask. These can be Rule 10: Keep Control of the questioner are getting into a long-winded, prepared beforehand from the abstracts Question and Answer Sessions technical discussion. and supplemented from ones that occur to Hopefully with a bit of preparation and you during the talk. This is a very good It is difficult for the session chair to keep a little luck, you will get through the ordeal reason for paying attention during the talk. things on time if the speaker is in control of of chairing a scientific session unscathed. Also, it is worth thinking of one or two taking questions. Make sure you are the And remember, if no one thanks you, you general purpose questions such as ‘‘What one who selects the next questioner. Also, have probably done an excellent job. do you plan to do next?’’ be prepared to step in if the speaker and

PLoS Computational Biology | www.ploscompbiol.org 2 September 2009 | Volume 5 | Issue 9 | e1000517 Editorial Ten Simple Rules for Organizing a Virtual Conference—Anywhere

Nelson N. Gichora1,2, Segun A. Fatumo3, Mtakai V. Ngara1,2, Noura Chelbat4,5, Kavisha Ramdayal6, Kenneth B. Opap7, Geoffrey H. Siwo8, Marion O. Adebiyi3, Amina El Gonnouni5, Denis Zofou9, Amal A. M. Maurady5, Ezekiel F. Adebiyi3, Etienne P. de Villiers10,11, Daniel K. Masiga12, Jeffrey W. Bizzaro13, Prashanth Suravajhala13,14, Sheila C. Ommeh10*, Winston Hide6,15 1 International Institute of Tropical Agriculture, Nairobi, Kenya, 2 Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom, 3 Department of Computer and Information Sciences, Covenant University, Ota, Nigeria, 4 Institute of Bioinformatics, Johannes Kepler University, Linz, Austria, 5 Moroccan Society for Bioinformatics Institute, Morocco, 6 South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa, 7 University of Cape Town, Cape Town, South Africa, 8 University of Notre Dame, South Bend, Indiana, United States of America, 9 Biotechnology Unit, University of Buea, Buea, South West Region, Cameroon, 10 International Livestock Research Institute, Nairobi, Kenya, 11 Biosciences Eastern and Central Africa, Nairobi, Kenya, 12 International Center of Insect Physiology and Ecology, Nairobi, Kenya, 13 Bioinformatics Organization, Hudson, Massachusetts, United States of America, 14 Bioinformatics Team, Center for Development of Advanced Computing, Pune University Campus, Pune, India, 15 Harvard School of Public Health, Boston, Massachusetts, United States of America

The First African Virtual Conference on retaining the key benefits presented by an used in both developed and undeveloped Bioinformatics 2009 (AFBIX09) [1], organized on-site conference, such as learning op- environments. by the Bioinformatics Organization [2] and portunities, sharing of ideas, and network- The conference was set up as a series of the International Society for Computa- ing. The use of inexpensive ‘‘commodity virtual hubs defined as a group of ten or tional Biology Student Council’s Regional off-the-shelf’’ (COTS) technologies permit more persons in one location. Each hub Student Groups of Africa and Morocco anyone with an Internet connection, Web consisted of a computer attached to a Web (ISCBSC RSG-Africa and RSG-Morocco) cam, and headset to give and/or attend a cam and speakers with a stable Internet [3] received support from the African presentation. According to Andrew Sage, connection. The hub activities and the Society for Bioinformatics and Computa- Cisco Systems’ vice president for market- interaction with other hubs were coordi- tional Biology (ASBCB) [4]. The aim was to ing, virtual conferences ‘‘can live on long nated by persons within the locality. provide students and scientists in the after the physical booths have been torn Speakers within faculty and industry bioinformatics and computational biology down,’’ while content continues to be were identified on the basis of their fields a chance to network through a unique viewed in a dedicated virtual environment expertise or involvement and relevance platform conceptualized as ‘‘hubs.’’ These by many people, even after the conclusion to the research topics covered by the hubs then gave participants the opportunity of the event [5]. virtual conference. There were a total of to foster both physical and virtual interac- At the Fall Joint Computer Conference 16 speakers and out of these, four were tions as well as develop collaborations, on December 9, 1968, Douglas Engelbart keynotes divided between 2 days and four irrespective of geographical location. presented, among other innovations, a sessions. In addition, there were five Virtual conferencing may prove to be virtual conferencing system that utilized invited speakers and three oral presenta- an effective low-cost strategy for conveying the broadcast of computer monitor video as tions selected from 12 submitted abstracts. bioinformatics and computational biology well as presenter audio and video [6]. This The rest of the abstracts were presented as education to African scientists who other- ‘‘expensive approach’’ has involved tradi- posters during break sessions. There were wise would be deprived of the opportunity. tional video conferencing and technologies tutorials, relevant discussions from senior Unlike conventional conferences, virtual such as the Access Grid [7], which have faculties, as well as welcome and closing conferencing permits the involvement of a been viable options for the most affluent statements from AFBIX09 organizers. greater number of participants who would regions of the world, but the approaches The conference was 19 hours long and otherwise be unable to participate in mentioned here are broad enough to be was held over 2 days. The first day consisted events of this breadth owing to (1) limited travel fellowships, if any; (2) lack of time to travel to distant conference locations; and Citation: Gichora NN, Fatumo SA, Ngara MV, Chelbat N, Ramdayal K, et al. (2010) Ten Simple Rules for (3) insufficient accommodation and subsis- Organizing a Virtual Conference—Anywhere. PLoS Comput Biol 6(2): e1000650. doi:10.1371/journal. tence funds. These factors apply in general pcbi.1000650 to the post-/undergraduate student com- Editor: Philip E. Bourne, University of California San Diego, United States of America munity and especially to the target audi- Published February 26, 2010 ences that reside in developing countries. Copyright: ß 2010 Gichora et al. This is an open-access article distributed under the terms of the Creative Minimizing the requirement to travel also Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, means that the availability of invited provided the original author and source are credited. speakers is greatly increased, improving Funding: SANBI hub was funded in part by the South African Medical Research Council (WAH). ILRI hub was funded in part by the International Livestock Research Institute and the Biosciences Eastern and Central Africa the chances of attracting highly relevant under a SIDA (Swedish) grant. Covenant University hub was funded by a special grant from the Covenant and high-impact presenters. University Center for Research and Development (CUCERD). University of Notredame hub was supported by Through the use of video conferencing the Eck Institute for Global Health and the Notre Dame Bioinformatics Core. The funders had no role in study software, virtual conferences are able to design, data collection and analysis, decision to publish, or preparation of the manuscript. provide an accessible and cost-effective Competing Interests: The authors have declared that no competing interests exist. alternative to real time conferences while * E-mail: [email protected]

PLoS Computational Biology | www.ploscompbiol.org 1 February 2010 | Volume 6 | Issue 2 | e1000650 of 8 hours, tailored to accommodate time cation/device, such as a VoIP service, in WebEx, Netviewer, Adobe Connect, etc.), zone differences between each of the place to ensure synchronous coordination however all available Internet systems are participating hubs. This was inclusive of of the proceedings with other participating subject to bandwidth limitations and 100 minutes of break time divided between hubs. resulting congestion. It is therefore advis- two 20-minute coffee sessions concurrently As an illustration, the last point was able that presentations be prerecorded spent on poster presentations, with an hour particularly useful in an instance where and in no less than 2 weeks before the on a lunch break and 20-minute welcome two of the participating hubs during the conference, in order to permit time for the speech. The second day consisted of an 11- conference experienced network down- recordings to be edited or redone, if hour program including one 20-minute time, cutting off real-time presentations. necessary. Prerecorded presentations can coffee and poster session, 40-minute lunch Before the restoration of network connec- then be hosted via the conference Web break, and 30-minute vote of thanks and tion, the respective hub coordinators had sites, making them available to the partic- closing remarks. to inform the other hubs of their downtime ipating groups in an agreeable video The following ten simple rules are and continually synchronize conference format and in good time to conduct/ derived from experiences gained while activities. resolve software compatibility concerns. organizing AFBIX09. We propose these as Moreover, this allows the participants a reference material to those intending to plan Rule 3: Manage bandwidth chance to become familiar with the for similar events, with particular emphasis usage: to safeguard against conference content and to play back presentations containing key concepts/ on resource-constrained communities. conference interruptions. information. The use of prerecorded Rule 1: Address time zone It is critical and advisable to make sure presentations compensates for slow and differences: timing is your organizations’ IT personnel are able unreliable networks and even intermittent electrical outages (e.g., when two of the everything. to allocate sufficient bandwidth to the virtual conference, to avoid disruptions of aforementioned hubs experienced connec- Allow between 6 to 9 months before the live presentations (especially in organiza- tivity problems, they resorted to projecting conference to permit (1) administrators in tions where network resources are shared). prerecorded presentations to the partici- the respective virtual hubs a sufficient Alternatively, if a group of 10 or more pants in their respective hubs, and when amount of time to finalize their decisions participants are registered for the confer- this was resolved they were able to join the regarding presentation and/or attendance ence, it is advisable that these individuals live Q&A sessions). Alternatively, if the time slots (relative to time zones) and (2) form an independent virtual hub to save network problems are not restored in time, IT departments’ confirmation for the on bandwidth usage. This approach will the narrator can then appear online after provision of necessary support, amongst reduce the number of Internet connections the prerecorded presentation to answer other logistics, for the designated event being used and thus the potential compli- questions in real time or to take questions times. The organizing committee should cations for your virtual conference while via a text-based chat system. agree on a conference schedule that will be allowing other users an equally reliable suitable for the time zones of all partici- functioning network. Rule 6: Allocate time for pating groups. presenter orientation: to ensure It is effective to create a proposed Rule 4: The concept of virtual glitch-free schedule conference program for all participating hubs: makes registration and compliance. groups in their local time zones to avoid participation simpler. confusion. Once established, it is then Keynote and invited presenters should crucial to conduct tests of the proposed Distribute the virtual conference regis- become familiar with the designated times precisely as scheduled, weeks before tration fee across all participating hubs software, preferably a month before the the actual event, to ensure the reliability of and participants [8–12]. Cumulative hub conference. This will enable them to get the conference program and to identify payments ensure a reduced registration fee acquainted with the software while allow- problems that could arise. for the individual participant. Hubs pro- ing them to prerecord their own presen- vide local expertise and relevant local tation at their convenience. Recorded Rule 2: Test the available advertising for the conference. These presentations should then be sent to the resources: to ensure that you ‘‘front porch’’ gathering sites compensate conference host, who should test and archive all recordings before use if/when are able to host the conference. for some of the personal interaction that can be missing from virtual conferences. the scheduled presenter is absent at the Ensure the availability of (1) a stable The use of virtual hubs as ‘‘conference time of his/her presentation. Internet connection; (2) a computer in- nodes’’ tends to increase impact by stalled with the required video-conferenc- providing access for those without the Rule 7: Establish dedicated ing software; (3) reliable audio speakers equipment and also traditional face-to face virtual interaction rooms that have been tested for audio clarity; (4) interaction. Hub participants can also (e-lobbies): to ensure a practical adequate screen resolution for the capa- share traditional meeting activities such platform for participant Q&A bilities of the network; and (5) a public- as enjoying a meal together. and networking. address system (i.e., video camera and projector connections). There should be Rule 5: Prerecord presentations: Each participating hub should have at adequate lighting for the conference hall to gear-up if streaming video least one person responsible for the to avoid glare or other aspects of poor fails for any reason. collection and consolidation of all partic- visibility. Another useful resource is a ipant questions or answers from that hub. standby computer assigned to the hub- There is a wide range of software This consolidation avoids redundancy coordinator with a communication appli- available to get connected virtually (e.g., while saving time and kilobytes. Alterna-

PLoS Computational Biology | www.ploscompbiol.org 2 February 2010 | Volume 6 | Issue 2 | e1000650 tively, the designated person could verbal- online educational system operated at nent. The African Virtual Conference on ly relay the questions to the presenters on Bioinformatics.Org could be utilized for Bioinformatics (AFBIX), which was a behalf of the hub to ensure clarity. This that in the future. hybrid between a normal and virtual approach is especially applicable in cases conference, has had a large impact in where one of the hubs is in a country Valuable Lessons the field and consequently there are plans where the language of instruction is not to hold it biennially. This has impacted the one adopted for the conference. The Overall, what worked included prere- greatly on ISCB Regional students groups availability of ‘‘e-lobbies’’ will permit the cording the presentations, which were of (see below) as well as other spin-off confe- comfortable virtual interaction of partici- great assistance when streaming video rences such as the Indian Virtual Confer- pants with similar research interests during failed. Use of a chat facility (e.g., Skype) ence on Bioinformatics (Inbix10, http:// virtual poster sessions and/or coffee was key in coordinating hub activities www.bioinformatics.org/wiki/Inbix10). breaks. during the course of the conference as In terms of participants, the Regional some of the participating hubs experi- Student Group (RSG)-Moroccan hub had enced connectivity problems and had to Rule 8: Troubleshoot technical a total of 12 attendees for the AFBIX09, synchronize their prerecorded presenta- which enabled RSG-Morocco to develop glitches: to equip yourself for tion with the live presentations being any foreseeable challenges. a working relationship/collaboration with viewed by other hubs. the Institut Pasteur de Tunis in Tunisia. What didn’t work included disruption in Identify at least one person per hub to The presentations made during the con- the streaming video, which was a major coordinate the technical set-up of the ference sparked discussions between stu- drawback, and resulted in most hub conference venue and to ensure, well in dents and scientists touching on the coordinators relying on prerecorded vid- advance, that all technical equipment and various topics covered, leading to the eos of the conference presentations. Vir- relevant software are available and func- forging of new ideas on possible bioinfor- tual interaction rooms (e-lobbies) were not tioning properly. matics projects to undertake. effectively utilized as earlier anticipated; The RSG-Africa-Southern Africa hub this was in contrast to the hub level where attracted on average ten attendees for the Rule 9: Get motivated… It’s the participants were able to effectively inter- 2 days. The hub was faced with technical key to your success. act. It would be useful to set up subcom- issues that affected the quality of the mittees in order to deal with conference It is crucial to be able to set and meet presentations. Although overall, the at- requirements as they arise. These include your deadlines/milestones through ade- tendees benefited greatly and called for technical committees, fundraising commit- quate time management, hub organiza- improvement of future conferences. tees, and scientific committees among tion, etc. Besides this, involve people who The RSG-Africa-Eastern Africa hub others. It is also important for all commit- are inspired, willing, and passionate to attracted a total of 25 attendees as a result tee members to meet regularly with the organize the conference. Encourage par- of a collaborative effort between the frequency of meetings increasing as the ticipants in different hubs to take photos Biosciences East and Central Africa (BecA), conference start date draws near. throughout the event. The effects of team who funded all of the students, and the building last long after the conference, and International Livestock Research Institute encouraging participation results in lead- Impact on Science in Africa (ILRI), who provided conferencing facilities ership development. Plus, the managerial The novel idea of virtual hubs through gratis. The success of AFBIX09 prompted skills developed play an enormous part in e-conferencing was pioneered in AF- members to come up with plans to start the success of the conference. BIX09. With a stable Internet connec- collaborative bioinformatics projects be- tion, the maximum number of partici- tween RSG-Africa-Eastern Africa and oth- Rule 10: Participant feedback: pants at any conference is dependent on er RSGs, organizations, or institutes that useful for future reference. whether future conferences will adopt the will enable greater collaborations in re- concept of virtual hubs. This means that search and training. The hub also estab- At the conclusion of the conference, be the audio-visual facilities in each hub and lished contacts with RSG-India, which has sure to request feedback from the partic- sitting space should dictate the maxi- experience in virtual collaborative bioinfor- ipants to be able to identify any faults or mum number of persons in one hub as matics projects. errors that can then be addressed in future compared to the single user participation The RSG-Africa-Western Africa hub events. Make sure to have all questions option. Depending on the choice of the had a total of 17 attendees. The confer- that were raised during the presentations video-conferencing software and the max- ence provided a platform for forging and their corresponding answers available imum number of connections it can allow collaboration between the biological sci- online to all participants including photos at a given time, this value can be tran- ences and computer science departments taken during the event. Aside from having slated to hubs. Therefore the number of at Covenant University, which acted as this information on record, it will help participants that can attend a virtual the hub for the conference. The confer- sustain communication even after the meeting will depend on the number of ence attracted key administrators in their virtual conference has been concluded. formed hubs and consequently, the max- institute, including the vice chancellor, The recorded videos and presentations imum capacity of each hub, which may and this was a great boost for the students’ have been made available through Bioin- translate to thousands of participants. A group of West Africa. formatics.Org and hyperlinked on the wiki new high bandwidth optical fiber cable is The University of Notre Dame had an page at http://www.bioinformatics.org/ being laid around the coast of Africa with average range of eight to 20 attendees.In wiki/Afbix09. Bioinformatics.Org seeks bandwidth improvements of 10–100 times addition, three other faculties participated the opinions of the community via online expected around most places in Africa. in the conference. This was a sure venue polls. Blogging was not implemented in This development should greatly affect to foster collaboration with other students this conference, but we envisage that the future virtual activities within the conti- in developing countries.

PLoS Computational Biology | www.ploscompbiol.org 3 February 2010 | Volume 6 | Issue 2 | e1000650 The total number of participants, in- Acknowledgments Bioinformatics Institute (SANBI) MRC/UWC/ cluding speakers, organizers, and single SANBI Bioinformatics Capacity Development user participants was close to 100. In We acknowledge the contributions made by all Unit, University of the Western Cape, South participating institutions and organizations: The Africa [6]; Moroccan Society for Bioinformatics conclusion, although several challenges Regional Student Group of Africa (RSG-Africa) Institute (SMBI), Morocco [7]; Covenant Uni- were experienced, AFBIX09 has estab- and Regional Student Group of Morocco (RSG- versity, Nigeria [8]; University of Notre Dame, lished a foundation for future virtual Morocco), both of which are affiliates of the USA [9] and the Bioinformatics Organization, conferences. International Society for Computational Biology USA [1] as the host. We thank Sonal Patel (ILRI) Student Council (ISCBSC). The five independent and Dale Gibbs and Mario Jonas (SANBI) for virtual hubs: International Livestock Research their kind voluntary assistance. Institute/Biosciences East and Central Africa (ILRI/BecA), Kenya [5]; South African National

References 1. African Virtual Conference on Bioinformatics 2009 5. Link to ‘‘Virtual conferences home advantage’’ in tion. 2nd edition. San Francisco: Morgan Kauf- (AFBIX09). Available: http://wiki.bioinformatics. BusinessWeek. Available: http://www.businessweek. man. pp 513–532. org/Afbix09. com/technology/content/may2008/tc2008054_ 8. International Livestock Research Institute (ILRI). 2. Bioinformatics Organization. Available: http:// 560356.htm. Available: http://www.ilri.org/. www.bioinformatics.org/. 6. Engelbart D, English W (1968) A research center 9. South African National Bioinformatics Institute 3. International Society for Computational Biology, for augmenting human intellect. AFIPS Confer- (SANBI). Available: http://www.sanbi.ac.za/. Student Counci. Available: http://www.iscbsc. ence Proceedings of the 1968 Fall Joint Computer 10. Covenant University. Available: http://www. org/. Conference; December 1968; San Francisco. covenantuniversity.com/. 4. African Society for Bioinformatics and Compu- Volume 33. pp 395–410. 11. University of Notre Dame. Available: http:// tational Biology (ASBCB). Available: http:// 7. Reed D, Mendes C, Lu C, Foster I, Kesselman K www.nd.edu/. www.asbcb.org/. (2003) The Grid 2: blueprint for a new computing 12. Moroccan Society for Bioinformatics Institute infrastructure-Application Tuning and adapta- (SMBI). Available: http://www.smbi.ma/.

PLoS Computational Biology | www.ploscompbiol.org 4 February 2010 | Volume 6 | Issue 2 | e1000650 Editorial Ten Simple Rules for Editing Wikipedia

Darren W. Logan1, Massimo Sandal2, Paul P. Gardner1, Magnus Manske1, Alex Bateman1* 1 Wellcome Trust Sanger Institute, Cambridge, United Kingdom, 2 Department of Chemistry, University of Cambridge, Cambridge, United Kingdom

Wikipedia is the world’s most successful you can build a record of good edits, and it depends on the regular contributions of online encyclopedia, now containing over is easier to communicate and collaborate tens of thousands of volunteers. Therefore, 3.3 million English language articles. It is with others if you have a fixed, reputable Wikipedia urges all users to be bold: if you probably the largest collection of knowl- identity. Finally, registering an account spot an error, correct it. If you can edge ever assembled, and is certainly the provides access to enhanced editing fea- improve an article, please do so. It is most widely accessible. Wikipedia can be tures, including a ‘‘watchlist’’ for monitor- important, however, to distinguish bold- edited by anyone with Internet access that ing articles you have edited previously. ness from recklessness. Start off small. chooses to, but does it provide reliable Begin by making minor modifications to information? A 2005 study by Nature found Rule 2: Learn the Five Pillars existing articles before attempting a com- that a selection of Wikipedia articles on plete rewrite of History of science. scientific subjects were comparable to a There are some broad principles— Many new editors feel intimidated professionally edited encyclopedia [1], known as the ‘‘five pillars’’—all editors about contributing to Wikipedia at first, suggesting a community of volunteers are expected to adhere to when contrib- fearing they may a mistake. Such reticence can generate and sustain surprisingly uting to Wikipedia. Perhaps most impor- is understandable but unfounded. The accurate content. tant for scientists is the appreciation that worst that can happen is your first edits For better or worse, people are guided Wikipedia is not a publisher of original are deemed not to be an improvement and to Wikipedia when searching the Web for thought or research [9]. Accordingly, it is they get reverted. If this does occur, treat it biomedical information [2]. So there is an not an appropriate venue to promote your as a positive learning experience and ask increasing need for the scientific commu- pet theory or share unpublished results. It the reverting editor for advice. nity to engage with Wikipedia to ensure is also not a soapbox on which to expound that the information it contains is accurate your personal theories or a battleground to Rule 4: Know Your Audience and current. For scientists, contributing to debate controversial issues. In this respect, Wikipedia is an excellent way of fulfilling Wikipedia fundamentally differs from oth- Wikipedia is not primarily aimed at public engagement responsibilities and er types of new media, such as blogs, that experts; therefore, the level of technical sharing expertise. For example, some encourage editorializing. detail in its articles must be balanced Wikipedian scientists have successfully Contributing to Wikipedia is something against the ability of non-experts to integrated biological data with Wikipedia to enjoy; a natural extension of your understand those details. When contribut- to promote community annotation [3,4]. enthusiasm for science. But differences of ing scientific content, imagine you have This, in turn, encourages wider access to opinion inevitably arise, particularly on been tasked with writing a comprehensive the linked data via Wikipedia. Others have pages provided for discussion on how to scientific review for a high school audi- used the wiki model to develop their own improve articles. Treat other editors as ence. It can be surprisingly challenging specialist, collaborative databases [5–8]. collaborators and maintain a respectful and explaining complex ideas in an accessible, Taking your first steps into Wikipedia can civil manner, even in disagreement [10]. If jargon-free manner. But it is worth the be daunting, but here we provide some you begin to find a particular interaction perseverance. You will reap the benefits tips that should make the editing process stressful, simply log off and come back when it comes to writing your next go smoothly. another time. Unlike most scientific enter- manuscript or teaching an undergraduate prises, Wikipedia has no deadlines. class. Rule 1: Register an Account Rule 3: Be Bold, but Not Rule 5: Do Not Infringe Although any visitor can edit Wikipe- dia, creating a user account offers a Reckless Copyright number of benefits. Firstly, it offers you The survival and growth of any wiki With certain conditions, almost all of privacy and security. Though counterin- requires participation. Wikipedia is un- Wikipedia’s content is free for anyone to tuitive, editors registered under a pseu- matched in size, but its continuing success reuse, adapt, and distribute. Consequently, donymous username actually have greater anonymity than those who edit ‘‘anony- mously’’. A few of us have chosen to associate our accounts with our real Citation: Logan DW, Sandal M, Gardner PP, Manske M, Bateman A (2010) Ten Simple Rules for Editing identities. Should you choose to forgo Wikipedia. PLoS Comput Biol 6(9): e1000941. doi:10.1371/journal.pcbi.1000941 pseudonymity on Wikipedia, your entire Published September 30, 2010 editing history will be open to indefinite Copyright: ß 2010 Logan et al. This is an open-access article distributed under the terms of the Creative scrutiny by curious Web searchers, includ- Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ing future colleagues, students, or employ- ers. Do not forget this. Funding: The authors received no specific funding for this article. As in academic circles, a good reputa- Competing Interests: The authors have declared that no competing interests exist. tion helps your wiki career. By logging in * E-mail: [email protected]

PLoS Computational Biology | www.ploscompbiol.org 1 September 2010 | Volume 6 | Issue 9 | e1000941 it does not accept non-free material under unlike a personal Web page, your Wiki- will be rightly challenged irrespective of copyright restriction. Some journals, in- pedia biography is not yours to control. A how many degrees you hold. cluding those from the Public Library of lovingly crafted hagiography extolling Science, publish material under an open- your many virtues can rapidly accumulate Rule 9: Write Neutrally and with access license that is compatible with use in information you would rather not be pub- Wikipedia if properly attributed. Most do licized. You may already have a Wikipedia Due Weight not. Therefore, although it may be tempt- biography, but it contains factual inaccu- All articles in Wikipedia should be ing, avoid copying text or figures from racies that you wish to correct. How do impartial in tone and content [13]. When your latest review article (or anyone else’s) you do this without breaking the rules? writing, do state facts and facts about into Wikipedia. It will quickly be identified Wikipedia’s guidelines encourage you to notable opinions, but do not offer your as a copyright violation and flagged for provide information about yourself on the opinion as fact. Many newcomers to immediate deletion. associated discussion page, but please Wikipedia gravitate to articles on contro- You can give Wikipedia permission to permit other editors to add it to the article versial issues about which people hold use material you own, but this process is itself. strong opposing viewpoints. Avoid these non-reversible and can be time consum- Think twice, also, before writing about until familiar with Wikipedia’s policies (see ing. It is often better to rewrite the text in your mentors, colleagues, competitors, in- Rule 3), and instead focus on articles that simpler language or redraw the figure to ventions, or projects. Doing so places you are much easier to remain dispassionate make it more accessible. This will also in a conflict of interest and inclines you about. ensure it is more suitable for Wikipedia’s towards unintentional bias [12]. If you Many scientists who contribute to non-expert readership (see Rule 4). have a personal or financial interest in the Wikipedia fail to appreciate that a neutral subject of any article you choose to edit, point of view is not the same as the declare it on the associated discussion page Rule 6: Cite, Cite, Cite mainstream scientific point of view. When and heed the advice of other editors who writing about complex issues, try to cover To maintain the highest standards can offer a more objective perspective. all significant viewpoints and afford each possible, Wikipedia has a strict inclusion with due weight, but not equal weight. For policy that demands verifiability [11]. This Rule 8: Share Your Expertise, example, an article on a scientific contro- is best established by attributing each but Don’t Argue from Authority versy should describe both the scientific statement in Wikipedia to a reliable, pub- consensus and significant fringe theories, lished source (but see Rules 7 and 8 on Writing about a subject about which but not in the same depth or in a manner excessive self-citing). Most scientists are in you have academic expertise is not a suggesting these viewpoints are equally the fortunate position of having access to a conflict of interest [12]; indeed, this is held. wide body of literature, and experience in where we can contribute to Wikipedia using inline citations to support their most effectively. Jimmy Wales, co-founder writing. Since unverified content may be of Wikipedia, told Nature that experts have Rule 10: Ask for Help removed from Wikipedia at any time, the ability to ‘‘write specifics in a nuanced Wikipedia can be a confusing place for provide supporting citations for every way’’, thereby significantly improving the inexperienced editor. Learning Wiki statement that might be challenged by article quality [1]. When writing in your markup—the syntax that instructs the another editor at some point in the future. area of expertise, referencing material you software how to render the page—may Whenever possible, give preference to have published in peer-reviewed journals appear daunting at first, though the recent secondary sources (such as reviews or is permitted if it is genuinely notable, but implementation of a new editing toolbar book chapters) that survey the relevant use common sense (and revisit Rule 7). For primary research over research articles example, if you have an obscure, never- has made this easier, and usability devel- themselves. been-cited article in the Journal of New opment is ongoing. The intersecting Wikipedia’s accessibility makes each of Zealand Dairy Research discussing the RNA guidelines and policies (and the annoying its scientific articles an excellent entry content of cow milk, then referencing this tendency of experienced editors to use an point for laypeople seeking specialist in- in the introductory paragraph of the alphabet soup of acronyms to reference formation. By also providing direct hyper- Wikipedia articles on ‘‘RNA’’, ‘‘Milk’’, them) can also be tricky to comprehend. links to reliable, freely accessible online ‘‘Cow’’, and ‘‘Evolution of mammals’’ is Thankfully, the Wikipedia community resources with your citations (biological not a good idea. puts great stock in welcoming new edi- databases or open-access journals, for Occasionally you may interact with tors. Guidance is available through a example), other editors can quickly verify another editor who clearly does not share number of avenues, including help desks, your content and readers have immediate your expertise on the subject of an article. a specific IRC channel, and an Adopt-a- access to authoritative sources that address This can often prove frustrating for experts User mentorship program. You can even the subject in greater detail. and is the basis of much academic angst summon help using a special template— on Wikipedia [1]. On such occasions, {{helpme}}—and, as if by magic, a friendly Wikipedian will appear to offer Rule 7: Avoid Shameless remember that you are assessed only on one-on-one assistance. Self-Promotion your contributions to Wikipedia, not who you are, your qualifications, or what you Many people are tempted to write or have achieved in your career. Your Acknowledgments edit Wikipedia articles about themselves. specialist knowledge should enable you to We thank Philip Bourne for insightful com- Resist that urge. If you are sufficiently write in a neutral manner and produce ments and gratefully acknowledge the contribu- notable to merit inclusion in an encyclo- reliable, independent sources to support tions of the many Wikipedians who collectively pedia, eventually someone else will write each assertion you make. If you do not developed the policies and guidelines that an article about you. Remember that provide verification, your contributions inspired these rules.

PLoS Computational Biology | www.ploscompbiol.org 2 September 2010 | Volume 6 | Issue 9 | e1000941 References 1. Giles J (2005) Internet encyclopaedias go head to a million minds for community annotation in wikipedia.org/wiki/Wikipedia:Civility. Accessed head. Nature 438: 900–901. WikiProteins. Genome Biol 9: R89. 26 July 2010. 2. Laurent MR, Vickers TJ (2009) Seeking health 7. Pico AR, Kelder T, van Iersel MP, Hanspers K, 11. Wikipedia contributors (2010) Verifiability. Wiki- information online: does Wikipedia matter? J Am Conklin BR, et al. (2008) WikiPathways: pathway pedia, the Free Encyclopedia. Available: http:// Med Inform Assoc 16: 471–479. editing for the people. PLoS Biol 6: e184. en.wikipedia.org/wiki/Wikipedia:Verifiability. 3. Daub J, Gardner PP, Tate J, Ramskold D, doi:10.1371/journal.pbio.0060184. Accessed 26 July 2010. Manske M, et al. (2008) The RNA WikiProject: 8. Hodis E, Prilusky J, Martz E, Silman I, Moult J, 12. Wikipedia contributors (2010) Conflict of interest. community annotation of RNA families. RNA 14: et al. (2008) Proteopedia - a scientific ‘wiki’ Wikipedia, the Free Encyclopedia. Available: 2462–2464. bridging the rift between three-dimensional http://en.wikipedia.org/wiki/Wikipedia:Conflict 4. Huss JW, 3rd, Orozco C, Goodale J, Wu C, structure and function of biomacromolecules. _of_interest. Accessed 26 July 2010. Batalov S, et al. (2008) A gene wiki for community Genome Biol 9: R121. 13. Wikipedia contributors (2010) Neutral point of annotation of gene function. PLoS Biol 6: e175. 9. Wikipedia contributors (2010) No original re- view. Wikipedia, the Free Encyclopedia. Avail- doi:10.1371/journal.pbio.0060175. search. Wikipedia, the Free Encyclopedia. Avail- able: http://en.wikipedia.org/wiki/Wikipedia: 5. Hoffmann R (2008) A wiki for the life sciences able: http://en.wikipedia.org/wiki/Wikipedia: Neutral_point_of_view. Accessed 26 July 2010. where authorship matters. Nat Genet 40: >

PLoS Computational Biology | www.ploscompbiol.org 3 September 2010 | Volume 6 | Issue 9 | e1000941 Editorial Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia

Philip E. Bourne* Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, California, United States of America

Getting a promotion or a new position the paper is not valuable in a narrow field. software, publications that cite the soft- are important parts of the scientific career Tell the committee why it has significant ware, and the impact of those citations. process. Ironically, a committee whose impact in that field. There are also other For software that is modular, include the membership has limited ability to truly less likely sources of support that can help. diversity of applications to which those judge your scholarly standing is often Coverage by the Faculty of 1000, press methods and/or software have been charged with making these decisions. Here releases, blogs, and any positive commen- applied. Describe what it took to develop are ten simple rules from my own experi- tary on the paper by others are also the methods and/or software and what ences, in both getting promoted and serving valuable indicators of impact. impact that has on the community. Many on such committees, for how you might reviewers will not appreciate what it takes maximize your chances of getting ahead Rule 2: Quantify and Convince to develop and maintain methods and/or under such circumstances. The rules focus software for the community. Do what you Reviewers may not be that familiar with on what might be added to a CV, research can to help the reviewer with details of the concept of article-level metrics and statement, personal statement, or cover your time and resources, and that of what they say about your science—where letter, depending on the format of the others, in maintaining the software for requested promotion materials. In part, the applicable, convince them in your appli- cation. Let me use an example. The very the good of the community. Educate the rules suggest that you educate the commit- committee on what open source implies, tee members, who have a range of first article I wrote in this series was titled ‘‘Ten Simple Rules for Getting Published’’ assuming your software is open source. expertise, on what they should find impor- Indicate as best you can how your efforts tant in the promotion application provided [1]. It has been downloaded over 65,000 times, which is about 35 times per day in software and methods bring credit to by a computational biologist. Further, the institution. while some rules are generally applicable, since it was published 5 years ago. At the the focus here is on promotion in an same time, according to Google Scholar it Rule 4: Make Web Sites Count academic setting. Having said that, in such has been cited 30 times and according to ISI Web of Knowledge 11 times. The a setting teaching and community service This follows from Rule 3, but applies implication is that it has had some are obviously important, but barely specifically to Web sites where Google scholarly impact that is not reflected by touched upon here. Rather, the focus is Analytics, AWStats, and other tools can be the more traditional citation metric. In this on how to maximize the appreciation of used to quantify the impact your work has case, the scholarly impact is mainly your research-related activities. As a final had and present those statistics to review- pedagogical in that it assists in professional thought before we get started on the rules, ers. Another irony is that papers about development. This is easily overlooked by this is not just about you, but an opportu- Web sites are rarely read, but they are a promotion committee, but of some value nity to educate a broad committee on what highly cited if your resource is useful. is important in our field. Use that oppor- in academic promotion. Metrics may not tell the whole story, for instance, in work Hence, they can be used to enhance your tunity well, for it will serve future genera- standing. Good professional conduct tions of computational biologists. that is relatively new. Use your application to inform the reviewers why you believe should dictate that you only write such your work is significant. papers when you have something substan- Rule 1: Emphasize Publication tively new to report regarding improve- Impact, Not Journal Impact Rule 3: Make Methods and ments to the Web site. Spreading citations over multiple papers just to enhance your Reviewers who do not know your work Software Count H-factor while not adding anything sub- well, unless told otherwise, will often judge that work primarily by the journals in Keep statistics on software and methods stantively new speaks poorly of you and to which it appears. If the majority of your use. For example, keep statistics on the the value system we use to evaluate papers are in Nature and Science, then let the number and diversity of users of the scholars. system continue to fool the reviewer. For the rest of us, it is important to emphasize Citation: Bourne PE (2011) Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia. PLoS that the impact of the journal does not Comput Biol 7(1): e1002001. doi:10.1371/journal.pcbi.1002001 necessarily reflect the impact of your Published January 6, 2011 paper. Include any data that reflect the Copyright: ß 2011 Philip E. Bourne. This is an open-access article distributed under the terms of the Creative value of your work regardless of the Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, journal. The number of times the paper provided the original author and source are credited. has been cited and the download statistics Funding: The author received no specific funding for this article. for that paper are obvious metrics, but Competing Interests: The author is Co-founder of SciVee Inc., which works with Thomson Reuters on should be put in context. A few citations products. At this time, these products are not related to those outlined in this article. and downloads do not necessarily mean * E-mail: [email protected]

PLoS Computational Biology | www.ploscompbiol.org 1 January 2011 | Volume 7 | Issue 1 | e1002001 Rule 5: Make Data Deposition, some other allowable personal statement. a significant undertaking when done well. Curation, and Other Related Items on that list should include, where They will thank you for it. You might even Activities Count appropriate: published and accepted papers, include information they would appreci- pending and funded grants, including the ate, that the committee would not—for Maintain records on your data-related amount coming to your institution, summa- example, specific details of research if you activities, namely public accessibility, how rized accomplishments in software, data, and and the reviewer are in the same field. much curation and other effort went into methodsasperRules3,4,and5,students providing these data, and how much these mentored and in what capacity, courses Rule 10: Do Not Oversell data are used. Currently, there is no way to offered and their standing, other educational Yourself quantify the impact your public contribu- and outreach activities, company involve- tions of data have had on science; therefore, ment, professional activities (e.g., editorial This may be obvious, but have an try to ensure that such contributions have an boards,scientificadvisoryboards),invitedlec- impartial third party look over your associated publication. Contact data re- tures, and awards. The idea is not to provide application and have them give you a sources to see if they can provide metrics details here—your CV should do that—just candid opinion; perhaps a senior member for how frequently data you have contrib- numbers for easy and quick comprehension. of your institution not on your committee. uted has been accessed and include that Don’t oversell yourself with flowery adjec- information in your list of accomplishments. Rule 8: Make the Reviewers’ Job tives. Show, don’t tell; that means, enu- Easy merate facts. If you head a laboratory, even Rule 6: Use Modern Tools to though it is your file under consideration, it Emphasize/Quantify Your Often, one or more of the reviewers is really the work of the collective you are Academic Standing looking at your application are going to be highlighting—be clear and fair about that. responsible for writing a summary of why, Just state the facts—if you have done well, Increasingly, tools are available to impart or why not, your advancement was grant- you will do well. It is as simple as that. to reviewers your scholarly standing. For ed. Again, unless the reviewers are very I have placed significant emphasis on example, ResearcherID from Thomson familiar with your work they will appreciate what to include in a cover letter or personal Reuters [2] will provide graphs on the total a candid, quantitative and honest discus- statement that accompanies your CV, number of citations per year, average sion of your accomplishments. But take research statement, and perhaps other number of citations per article, and so on. heed of Rule 10. Where such a discussion materials, such as teaching evaluations. I However, these are only for publications should be included depends on the form of have not discussed preparing a good CV found in ISI databases, which can be limited your application—usually as a cover letter since such information is available on the for a multidisciplinary researcher. PubNet or part of your personal statement is Internet and elsewhere already. What has [3] will provide your collaborative network appropriate. Whatever the form, it should not been covered before, as far as I am from PubMed where each node on the be brief and highlight, in a way that can be aware, is how a computational biologist in network is a researcher you have published understood by a non-expert, what was done academia might maximize their chances of with and the thickness of edges reflects the and why it is of high impact and, if being promoted by a committee that is not number of times you have published available, how others have followed up on fully appreciative of the field. together. BioMedExperts [4] provides sim- the accomplishments. These highlights As always, we welcome your comments. ilar data. Again, this can be somewhat should be peppered with citations and I would particularly like to hear addition- limiting for multidisciplinary researchers. quantitative data that a reviewer can easily al/alternative advice from those like my- Bolster these statistics by indicating the full reference should they choose to do so. self who have been through this process a range of your scholarly activities not covered More often than not the reviewer will number of times. In closing, I can only by the tools. Adding papers manually to the appreciate this summation and it will be offer an example of such materials that I tracking resource can often help as well. reflected in the letter they write. think helped me get promoted last time around (see Text S1). Rule 7: Make an Easily Rule 9: Make the Job of Your Digestible Quantified Summary References Easy Supporting Information of Your Accomplishments Often your application will include Text S1 Example support letter. Reviewers are often faced with many letters of support from external references, Found at: doi:10.1371/journal.pcbi. applications for promotion to review, and some chosen by you, others chosen by the 1002001.s001 (PDF) your accomplishments are easily lost in a long reviewers. For the ones you choose, send CV.Thisisparticularlytrueiftherevieweris those references the same summary you Acknowledgments trying to sort out what you have accom- provide the reviewers (Rule 8). The Thanks to my fellow Editors Barbara Bryant plished in a specific time frame, as would reviewers will likely know your work well, and Steven Brenner as well as previous Ten often be the case when considering a promo- which is why they were chosen. Notwith- Simple Rules co-authors Jenny Gu, Quentin tion. One way to summarize accomplish- standing, a good factual summary can help Vicens, and Iddo Friedberg for their important mentsisasabulletedlistinacoverletteror in their writing a reference letter, which is input.

References 1. Bourne PE (2005) Ten simple rules for getting 3. Douglas SM, Montelione GT, Gerstein M (2005) published. PLoS Comp Biol 1: e57. doi:10.1371/ PubNet: a flexible system for visualizing literature journal.pcbi.0010057. derived networks. Genome Biol 6: R80. 2. Thomson Reuters (2010) ResearcherID home 4. Collexis (2010) BioMedExperts home page. page. Available: http://www.researcherid.com/. Available: http://www.biomedexperts.com/. Ac- Accessed 1 December 2010. cessed 1 December 2010.

PLoS Computational Biology | www.ploscompbiol.org 2 January 2011 | Volume 7 | Issue 1 | e1002001 Editorial Ten Simple Rules for Providing a Scientific Web Resource

Sebastian J. Schultheiss* Machine Learning in Biology Research Group, Friedrich Miescher Laboratory of the Max Planck Society, Tu¨bingen, Germany

Many projects in computational biology from a command-line interface or a whole student leaves. As the senior author, lead to the creation of a small application framework for large-scale analysis? How solving such issues are your responsibility. program or collection of scripts that can be will users be able to access it? Read more Feel free to direct students towards using a of use to other scientists. A natural about these options and how to make good certain software framework; creating such progression is to make this tool available use of the infrastructure available to you in lab rules limits responsibility in a good via a Web site or by creating a service for Rule 4. way. You can even think of creating an it, from now on collectively called ‘‘Web Throughout the life of your resource, intergenerational treaty for software main- resource.’’ there may be many different people tenance among students in different years. We conducted a survey among provid- involved in developing and maintaining If your resource is used by collaborators ers and users of scientific Web resources, it. Documentation is important for both and they think your program is valuable as well as a study on availability. The developers and users of the resource. A enough, you could convince them to take following rules reflect the experiences and scientific Web resource should be offered it over. The same is true for one of the opinions of over 250 scientists who have as open source software. Making your following institutions: If your resource has answered our questions and who use Web resource a software project at SourceFor- a high impact and is useful to many resources regularly, as well as our own ge.net, for instance, greatly facilitates people, you may be able to convince experience. The study of availability development and maintenance. This also someone at the European Bioinformatics allows us to draw objective conclusions lets you keep an open channel of commu- Institute (EBI), National Center for Bio- about the characteristics of those Web nications with your users, tell them about technology Information (NCBI), Nether- resources that are still available and any major changes, and get their feedback lands Bioinformatics Centre (NBIC), or correlate the features that distinguish them to shape future developments. the PSU Galaxy instance to take over. from disappeared or nonfunctional ones. Eventually, the resource may have Early decisions about the framework used These ten simple rules aid you in designing outlived its usefulness. Read Rule 10 to can have a big impact later on. and maintaining a scientific Web resource find out when and how to shut down that is available to anyone interested in operations. Rule 3: Know Your User Base using it. Rule 2: Discuss Responsibilities The most important component to Rule 1: Plan Your Resource consider is the Web resource audience. More than 58% of resources are Come up with a use case: when and how As soon as you are seriously thinking developed entirely by researchers without will another researcher want to use what about offering a Web resource to the a permanent position who will eventually you are offering? When you know who general public, it is a good idea to lay move to another institution. you are developing for, many decisions down some ground rules. Clarify respon- As a graduate student, involve your become very straightforward. In our sibilities in the processes of developing and advisors early when you consider provid- survey, we determined that 36% of Web maintaining the resource. Discuss these ing a Web resource. Chances are, they resource providers think that only re- issues with the senior author or principal already know a way to share the work searchers with programming experience investigator, who is ultimately responsible load. Discuss the issue of software main- use their resource. If your audience can for the availability of the resource. Read tenance, both for the time the original manage to run your application on their more about some ideas to manage respon- developers are still on site and for the time own computer, let them. It’s harder to sibility in Rule 2. they have moved on. Do you want to take integrate a Web resource into a scripted Try to think of a good name that is not your work with you or leave it behind? workflow. already taken and can be easily remem- As an advisor, remember that this issue On the flip side, 64% of resources are bered. Changing the Web address of an could come up, at the latest when your also used by researchers without program- existing resource is hard to do; it’s better to start off with your own Internet domain Citation: Schultheiss SJ (2011) Ten Simple Rules for Providing a Scientific Web Resource. PLoS Comput name or a persistent URL. For the latter, Biol 7(5): e1001126. doi:10.1371/journal.pcbi.1001126 the Online Computer Library Center Editor: Philip E. Bourne, University of California San Diego, United States of America offers a Persistent Uniform Resource Published May 26, 2011 Locator (PURL) for a changing Web address (for an overview, see [1]). It is Copyright: ß 2011 Sebastian J. Schultheiss. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any essentially a transparent link to wherever medium, provided the original author and source are credited. your resource is currently hosted; its Funding: This work was funded by the TL Stiftung Tuebingen, Germany: http://www.tl-stiftung.de/ destination can be updated accordingly. foerderpreise.php. The author holds a position at the Max Planck Society, Germany: http://fml.mpg.de. The Some decisions early on can greatly funders had no role in study design, data collection and analysis, decision to publish, or preparation of the impact the resource over its whole life manuscript. cycle. Consider the level of service you Competing Interests: The author has declared that no competing interests exist. want to offer. Is it a simple tool one step up * E-mail: [email protected]

PLoS Computational Biology | www.ploscompbiol.org 1 May 2011 | Volume 7 | Issue 5 | e1001126 ming experience. They will appreciate a source, so users are paying for their own compute cloud. However, it is still advis- graphical user interface. If you know your computing time. Providing your own able to provide information on how to set users personally, they can give you ideas large-scale computing infrastructure can up your program from scratch. Together about how to make the interface fit their be very costly. with source code comments and a high- needs. Just watching collaborators or You will have to think about a user level user manual, these three layers of students use your software or programs interface for your resource. Here, an documentation will ensure portability. like it will tell you a lot. Get users involved existing framework can save you a lot of early and include them in the development time. Examples include Taverna [2], Rule 6: Create an Open Source process. As long as the Web resource is in where you provide a description of the Project use, you can solicit feedback from users input and output in the Web resource and see if their needs have evolved (cf. description language. Your resource is Your source code should be public if the Rule 7). accessed from a client workbench, in results are used in scientific publications. Constant monitoring of usage patterns which users can connect your program’s This is needed for reproducibility (read and access statistics can be achieved by output to others to create workflows. It still more about this in Rule 8). tracking who visits the Web resource page. runs on your own servers and you have to To make your life easier, it is a good If your institution is not already collecting provide the necessary software infrastruc- idea to place your source code in a these data from visitors, you can set up a ture for that. repository such as SourceForge.net [4] or free Web analytics tool within minutes. Galaxy [3] is a customizable workbench Bioinformatics.org [5]. Then you don’t Most scientists will come to your Web that you can download and run on your have to take care of version control and site via a search engine. Use the indexing own Web server. It lets you integrate any release issues and it’s easier for collabora- power of the search engine spiders by command-line tool with a few lines of tors to work together over distance. Most putting, for example, the paper title, XML; moreover, it even lets you connect of these open source software project sites abstract, and keywords on the page. When your own tools with the pre-packaged ones provide developers a means of communi- you follow the tips about naming your to create transparent workflows for your cation both with each other and with end resource in Rule 1, it should be easy to users. You don’t need to think about file users. You can choose between mailing find. management and pretty user interfaces, lists (with an online archive), a Web site and for those time-intensive jobs, you can forum, or an FAQ page. Rule 4: Use Services Available easily connect your Galaxy instance to a Many scientists develop programs for to You during Development compute cluster or even run it in the one of the proprietary mathematical cloud. environments that require expensive li- The finest way out of much of the strife If you want to build an interface from censes to run. If you are still in the with hosting and availability is to find scratch, there are also frameworks that planning stage, consider switching to an someone else to take care of it. If you work make this task easier. Aside from the open source alternative. Your funding on a larger campus or cooperate with classic Apache, SQL, and PHP combina- body may not be willing to pay for a score someone at an institution that already runs tion, there are a few more modern of licenses just for the users of your Web several scientific Web resources, get in alternatives: take a look at Ruby on Rails, resource. touch with the administrators to set up Tomcat, Pyjamas, or CherryPy. Using open source software, good your tool on an established server. Such source code documentation, and standard decisions can greatly influence the soft- Rule 5: Ensure Portability file formats will go a long way in making ware development process. Be aware of your software able to run on other the Web address you use to publish your Make sure that you can still install and computers (cf. Rules 5 and 7). resource. It’s best to use a persistent URL run the software on another machine. If or your own domain name for the you want your software to be available Rule 7: Provide Ample resource to make sure it is always available three years from now, consider this Documentation and Listen to under the published address (cf. Rule 1). strongly. Chances are that the server you Feedback Estimate the number of potential simul- are developing on will be replaced or taneous users. Together with the memory software is updated, which often breaks A good first impression is very impor- and compute time requirements, this will the functionality. Ensuring portability also tant for Web resources, too. It is crucial tell you about the kind of infrastructure makes it easier for computational biolo- that first-time users feel welcome on your you will have to provide to make the gists to install your software locally. Ask a site. Provide good documentation and resource usable even with many queries colleague to install the resource from some short info about parameter settings, coming in at the same time. In an age of scratch on another computer and you’ll that is, accepted ranges and optional high-throughput experiments, this can be see where the pitfalls are. settings. Ideally, there is a one-click testing a lot. To get an estimate on the number of A brute-force approach to portability is possibility with meaningful but easily simultaneous queries your setup can creating a virtual machine (VM). If you understood example data. If the output handle, you can perform a stress test, have a server where your resource runs of the example is well-defined, set it up to sending a high number of requests with a just fine, back up its hard disk and restore run periodically as a functional test, for script from an external source. it in a VM like VirtualBox. That way, you instance during the build process. If your requirements seem enormous, have a running version of your server in a Nothing teaches you about parameter consider optimizing your program further single file. The VM approach is a settings, file formats, and the general and finding redundancies between indi- steamroller tactic for resources with very purpose of a resource like a well-crafted vidual queries that can be pre-computed intricate dependencies. This is a way to demonstration of what it can do, for and stored. You can also offer an interface provide users with the necessary disk instance, in a video or screen cast. Many to a cloud-computing on-demand re- image to run your resource on the of these points are part of journals’

PLoS Computational Biology | www.ploscompbiol.org 2 May 2011 | Volume 7 | Issue 5 | e1001126 instructions to authors and therefore provide users with details about the change the Web resource’s address. If your required when submitting a research parameter settings they used, the version resource has been published in a journal, article about your Web resource. number, and information about the input try contacting them and ask to have the A main complaint of the interviewed data. link to your resource updated. Some scientists about working resources was lack Everything to run the analysis again journals may require a formal correction. of documentation (41%). Beyond the should be available to reviewers and Get your previous institution to link or reference to the paper to be cited when readers. This includes the source code of forward to the new address from the old using the resource, you should include a the Web resource itself (cf. Rule 6). page for as long as possible. If you used a brief overview of the resource’s purpose, It is good practice to make available persistent URL, all you need to do is for what kinds of data it is applicable, and older versions of the resource for purposes update the link (cf. Rule 1). pointers to common pitfalls or preprocess- of reproducing results; at least boldly ing steps that are not so obvious. The display the Web resource’s current version Rule 10: Switch off an Unused latter is hard to imagine beforehand, so number on the site and hints about how Resource find out from users what they consider changes may affect the output. difficult. If you change the server’s behavior, During our study, we determined that, It will be worth your while to set up a your users have to know. Even if it is while a surprising number of Web re- channel of communication with your merely a bug fix, be sure to report it sources are still available after a long time, users. Many source code repositories publicly in a place that will be noticed they may not always work any longer. For provide such functions (cf. Rule 6), which when using the server. Keep in mind that users, this can be even more frustrating will save you a lot of time responding to some users, for example, may have book- than an unavailable page. frequent questions users ask about the marked the data submission page. If your resource is no longer under resource. You can post announcements active development, chances are that it has about maintenance, updates, and bug Rule 9: Plan Ahead: Long-Term outlived its usefulness after some years. fixes, and best of all, experienced users Maintenance After that, check to see if there is anyone often will be there to answer recurring still using it or if the original publication questions raised by newbies, or you can You will probably move to another has been cited recently. This should be refer them to the collective wisdom of the place during your career. If you leave easy when you followed the advice about archives. It is also common practice to behind a Web resource, try to make the collecting statistics in Rule 3. If no one is provide an e-mail address where the transition to the new maintainer as using your resource any longer, release the authors can be reached. smoothly as possible. Ideally, a protocol source code one last time, and you’re Make your life easier by providing a has already been established during the done. comprehensive error report option that planning phase (cf. Rule 1). In our survey, If the resource is still useful to some users can click on when something fails, we found that more than 24% of Web researchers, try posting a notice on the site thereby e-mailing you all the information resources will not be maintained after the asking for someone to take over (cf. Rule you need to find out what went wrong. original developers leave. Ultimately, it is 9). If all of that seems like too much work There are two more layers of documen- the responsibility of the senior author of a and the source code alone won’t help tation: in addition to the high-level help publication to make sure that this does not anyone, consider creating a VM that runs for end users, installation instructions will happen, but it is a very important the resource. When you still have access to ensure portability, and good source code consideration for all authors of a Web the server, this can be done in a matter of comments enable you to hand over resource publication. hours. maintenance responsibility to another Documentation of the source code and By following these rules, your resource developer, maybe even from the user the installation process will greatly facili- will have a long and productive life. community (cf. Rule 9). tate the transition to new maintainers. If there is no one in your old lab to take over, Acknowledgments Rule 8: Facilitate but the resource is still heavily used, you Reproducibility may be able to convince a current user or The author would like to thank David J. Engel, a collaborator to take over maintaining the Verena A. Kottler, Christoph U. Malisi, Reproducibility is always a topic of resource. This will be even easier if the Gunnar Ra¨tsch, and Eva-Maria Willing for discussion in computational biology. program is an open source software critically reading the manuscript, and Jonas When a user analyzes data with your project, where a new developer can join Behr, Regina Bohnert, Philipp Drewe, Andre Kahles, Vipin Thankam Sreedharan, and Web resource, the results may end up in a at any time. Christian Widmer for discussions. The com- research article. Therefore, all the steps You may want to take your software ments from Philip E. Bourne and the anony- needed to reproduce these results have to with you and find a new home for it. In mous reviewers were greatly appreciated and be documented entirely. In your output, some circumstances, this requires you to very helpful in improving this manuscript.

References 1. Simonson J, Berleant D, Zhang X, Xie M, Vo H building and running workflows of services. 4. Geeknet, Inc (2010) SourceForge.net: open (1998) Version augmented URIs for reference Nucleic Acids Res 34: 729–732. source software development. Available: http:// permanencevia an Apache module design. Com- 3. Goecks J, Nekrutenko A, Taylor J, The Galaxy sourceforge.net/. Accessed 8 April 2011. puter Networks and ISDN Systems 30: 337– Team (2010) Galaxy: a comprehensive approachfor 5. Bioinformatics Organization (2010) Collaborative 345. supporting accessible, reproducible, and transparent development environment. Available: http:// 2. Hull D, Wolstencroft K, Stevens R, Goble C, computational research in the life sciences. Genome www.bioinformatics.org/wiki/Hosting. Accessed Pocock MR, et al. (2006) Taverna: a tool for Biol 11: R86. doi:10.1186/gb-2010-11-8-r86. 8 April 2011.

PLoS Computational Biology | www.ploscompbiol.org 3 May 2011 | Volume 7 | Issue 5 | e1001126 Editorial - Ten Simple Rules for Building and Maintaining a Scientific Reputation

Philip E. Bourne1*, Virginia Barbour2 1 Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, California, United States of America, 2 Public Library of Science, Cambridge, United Kingdom

While we cannot articulate exactly what plays on that human characteristic of not temptation. It will pay off over time, defines the less quantitative side of a appreciating the value of something until particularly in an era when every word you scientific reputation, we might be able to you do not have it any more. commit to a digital form is instantly con- seed a discussion. We invite you to crowd A scientific reputation is not immediate, veyed, permanently archived somewhere, source a better description and path to it is acquired over a lifetime and is akin to and can be retrieved at any time. achieving such a reputation by using the compound interest—the more you have comments feature associated with this article. the more you can acquire. It is also very Rule 2: Do Not Ignore Criticism Consider yourself challenged to contribute. easy to lose, and once gone, nearly impossible to recover. Why is this so? Whether in your eyes, criticism is The scientific grapevine is extensive and deserved or not, do not ignore it, but At a recent Public Library of Science constantly in use. Happenings go viral on respond with the knowledge of Rule 1. (PLoS) journal editors’ meeting, we were social networks now, but science has had a Failure to respond to criticism is perceived having a discussion about the work of the professional and social network for centu- either as an acknowledgement of that Committee on Publication Ethics (COPE; ries; a network of people who meet each criticism or as a lack of respect for the http://www.publicationethics.org/), a fo- other fairly regularly and, like everyone critic. Neither is good. rum for editors to discuss research and else, like to gossip. So whether it is a publication misconduct. Part of the dis- relatively new medium or a centuries-old Rule 3: Do Not Ignore People cussion centered on the impact such cases medium, good and bad happenings travel have on the scientific reputation of those quickly to a broad audience. Given this It is all too easy to respond to people in involved. We began musing: What on pervasiveness, here are some rules, some a way that is proportional to their earth is a scientific reputation anyway? intuitive, for how to build and maintain a perceived value to you. Students in Not coming up with a satisfactory answer, scientific reputation. particular can be subject to poor treat- we turned to a source of endless brain- ment. One day a number of those students power—students and other editors. Hav- Rule 1: Think Before You Act will likely have some influence over your ing posed the question to a group of career. Think about that when responding graduate students, PLoS, and other edi- Science is full of occasions whereupon you (or not responding). As hard as it is, try to tors, we got almost as many different get upset—a perceived poor review of a personally respond to mail and telephone answers as people asked, albeit with some paper, a criticism of your work during a calls from students and others, whether it common themes. They all mentioned the seminar, etc. It is so easy to immediately is a question about your work or a request explicit elements of a reputation that relate respond in a dismissive or impolite way, for a job. Even if for no other reason, you to measurables such as number of publi- particularly in e-mail or some other imper- give that person a sense of worth just by cations, H factor, overall number of sonal online medium. Don’t. Think it responding. Ignoring people can take citations etc., but they also alluded to a through, sleep on it, and get back to the other serious forms, for example in leaving variety of different, qualitative, factors that offending party (but not a broader audience deserving people off as paper authors. somehow add up to the overall sense of as it is so easy to do nowadays with, for Whether perceived or real, this can appear reputation that one scientist has for example, an e-mail cc) the next day with a that you are trying to raise your contribu- another. professional and thoughtful response, what- tion to the paper at the expense of What these students and editors identi- ever the circumstances. In other words, others—definitely not good for your rep- fied en masse is one important side of a always take the high road whatever the utation. scientific reputation that is defined by data; but they also identified a much more Citation: Bourne PE, Barbour V (2011) Ten Simple Rules for Building and Maintaining a Scientific nebulous side, that, while ill-defined, is a Reputation. PLoS Comput Biol 7(6): e1002108. doi:10.1371/journal.pcbi.1002108 vital element to nurture during one’s Published June 30, 2011 career. A side defined to include such Copyright: ß 2011 Bourne, Barbour. This is an open-access article distributed under the terms of the terms as fair play, integrity, honesty, and Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any caring. It is building and maintaining this medium, provided the original author and source are credited. kind of less tangible reputation that forms Funding: No funding was received by Philip E. Bourne for this work. Virginia Barbour is paid a salary by the the basis for these Ten Simple Rules. You Public Library of Science, and she wrote this editorial during her salaried time. might be wondering, how can you define Competing Interests: Virginia Barbour’s individual competing interests are at http://www.plosmedicine.org/ rules for developing and maintaining static/editorsInterests.action. something you cannot well describe in * E-mail: [email protected] the first place? We do not have a good Philip E. Bourne is Editor-in-Chief of PLoS Computational Biology. Virginia Barbour is Chief Editor of PLoS answer, but we would say a reputation Medicine and Secretary of COPE.

PLoS Computational Biology | www.ploscompbiol.org 1 June 2011 | Volume 7 | Issue 6 | e1002108 Rule 4: Diligently Check daily newspaper. For example, we often review is small relative to writing a good Everything You Publish and agree to review a paper because we paper in the field yourself, it all adds up Take Publishing Seriously imagine we will learn from the experience. towards your overall reputation. That is fine. Where it crosses the line is Science does not progress in certain- when it could be perceived by someone Rule 9: Do Not Write References ties—that is one of its joys but also what that you are competing with the person for People Who Do Not Deserve makes it such a hard profession. Though whose work you are reviewing and have It you cannot guarantee that everything you more to gain than just general knowledge publish will, in 50 years’ time, be shown to from reviewing the work. There is a gray It is difficult to turn down writing a be correct, you can ensure that you did the area here of course, so better to turn down reference for someone who asks for one, work to the accepted standards of the time a review if not sure. Failure to properly even if you are not inclined to be their and that, whether you were the most handle conflicts will eventually impact advocate; yet, this is what you should do. junior or senior author, you diligently your reputation. The alternative is to write a reference that checked it (and checked it again…) before (a) does not put them in a good light, or (b) you submitted it for publication. As a first Rule 6: Do Your Share for the over exalts their virtues. The former will author you may well be the only one who Community lead to resentment; the latter can impact appreciates the accuracy of the work being your reputation, as once this person is undertaken, but all authors have a respon- There is often unspoken criticism of hired and comes up short, the hirer may sibility for the paper. So, however small or scientists who appear to take more than question aspects of your own abilities or big your contribution, always be upfront they give back. For example, those who motives. with your co-authors as to the quality and rarely review papers, but are always the first to ask when the review of their paper accuracy of the data you have generated. Rule 10: Never Plagiarize or When you come to be a senior author, it is will be complete; scientists who are avid so easy to take a draft manuscript at face users of public data, but are very slow to Doctor Your Data value and madly publish it and move on. put their own data into the public domain; This goes without saying, yet it needs to Both actions can come back to haunt you scientists who attend meetings, but refuse be said because it happens, and it is and lead to a perception of sloppy work, or to get involved in organizing them; and so happening more frequently. The electron- worse, deception. As first author, this on. Eventually people notice and your ic age has given us tools for handling data, mainly lets down your other authors and reputation is negatively impacted. images, and words that were unimaginable has a subtle impact on your growing even 20 years ago, and students and reputation. As the senior author of an Rule 7: Do Not Commit to Tasks postdocs are especially adept in using error-prone study, it can have a more You Cannot Complete these tools. However, the fundamental direct and long-lasting impact on your principle of the integrity of data, images, It tends to be the same scientists over reputation. In short, take publication and text remains the same as it was 100 seriously. Never accept or give undeserved and over who fail to deliver in a timely years ago. If you fiddle with any of these authorship and in addition never leave way. Over an extended period, this elements beyond what is explicitly stated anyone out who should be an author, becomes widely known and can be as acceptable (many journals have guide- however lowly. Authorship is not a gift—it perceived negatively. It is human nature lines for images, for example), you will be must be earned and being a guest or gift for high achievers to take on too much, guilty of data manipulation, image manip- author trivializes the importance of au- but for the sake of your reputation learn ulation, or plagiarism, respectively. And thorship. Never agree to be an author on a how to say no. what is more, you will likely be found out. ghostwritten paper. At best these papers The tools for finding all these unaccept- have undeclared conflicts of interest; at Rule 8: Do Not Write Poor able practices are now sophisticated and worst potential malpractice. Reviews of Grants and Papers are being applied widely. Sometimes the changes were done in good faith, for Rule 5: Always Declare Conflicts Who is a good reviewer or editor is example, the idea of changing the contrast of Interest more than just perception. Be polite, timely, constructive, and considerate and, on a digital image to highlight your point, Everyone has conflicts of interest, ideally, sign your review. But also be but one always needs to think how such a whether they are financial, professional, honest—the most valued reviewers are change will be perceived and in fact or personal. It is impossible for anyone to those who are not afraid to provide honest whether it might, even worse, give the judge for himself or herself how their own feedback, even to the most established average reader a false sense of the quality conflict will be perceived. Problems occur authors. Editors of journals rapidly devel- of that data. Unfortunately, even if done in when conflicts are hidden or mismanaged. op a sense of who does a good job and good faith, if any of these practices are Thus, when embarking on a new scientific who does not. Likewise for program found out, or even raised as a suspicion, endeavor, ranging from such tasks as being officers and grant reviews. Such percep- the impact on one’s career can be a grant reviewer, or a member of a tions will impact your reputation in subtle catastrophic. scientific advisory board, or a reviewer of ways. The short term gain may be fewer In summary, there are a number of dos a paper, carefully evaluate what others will papers or grants sent to you to review, but and don’ts for establishing a good reputa- perceive you will gain from the process. in the longer term, being a trusted tion—whatever that might be. Do not Imagine how your actions would be reviewer will reflect your perceived knowl- hesitate in giving us your thoughts on what perceived if read on the front page of a edge of the field. Although the impact of a it means to be a reputable scientist.

PLoS Computational Biology | www.ploscompbiol.org 2 June 2011 | Volume 7 | Issue 6 | e1002108 Editorial Ten Simple Rules for Getting Help from Online Scientific Communities

Giovanni M. Dall’Olio1*, Jacopo Marino2, Michael Schubert3, Kevin L. Keys1, Melanie I. Stefan4, Colin S. Gillespie5, Pierre Poulain6,7,8, Khader Shameer9,10, Robert Sugar3, Brandon M. Invergo1, Lars J. Jensen11, Jaume Bertranpetit1, Hafid Laayouni1 1 Institute of Evolutionary Biology (UPF-CSIC), Departament de Cie`ncies Experimentals i de la Salut, Barcelona, Spain, 2 Institute of Organic Chemistry Universita¨t Zurich, Zurich, Switzerland, 3 EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, United Kingdom, 4 California Institute of Technology, Biology Division, Pasadena, California, United States of America, 5 School of Mathematics & Statistics, Newcastle University, Newcastle upon Tyne, United Kingdom, 6 DSIMB, INSERM, U665, Paris, France, 7 Univ Paris Diderot, Sorbonne Paris Cite´, UMR-S665, Paris, France, 8 Institut National de la Transfusion Sanguine, Paris, France, 9 Division of Cardiovascular Diseases, Mayo Clinic, Rochester, Minnesota, United States of America, 10 National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, India, 11 NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark

Introduction ignorant or foolish. Other people worry A way to keep your questions short and about their ability to express the question concise is to systematically break down the The increasing complexity of research proficiently or with the correct grammar. problem into smaller parts. This can help requires scientists to work at the intersection Actually, asking a question in a public you to decide where to seek help, and how of multiple fields and to face problems for website is a good thing. First, the process much to seek. If you feel your problem is which their formal education has not of composing a message to explain a composed of multiple questions, then post prepared them. For example, biologists with problem is itself a great exercise. Second, as many messages as needed. You should no or little background in programming are it is a great way to learn faster, and to start a separate discussion thread for each now often using complex scripts to handle enter into contact with people from of the problems you want to solve, the results from their experiments; vice different fields. Third, and more impor- versa, programmers wishing to enter the avoiding mixing messages about different tantly, your career will be difficult if you topics together. world of bioinformatics must know about do not learn how to get help from other biochemistry, genetics, and other fields. On the other hand, you should provide people. enough details so that people can answer In this context, communication tools such As Albert Einstein once said, ‘‘The as mailing lists, web forums, and online you without having to ask you for important thing is not to stop questioning. additional explanations. Read the message communities acquire increasing importance. Curiosity has its own reason for existing’’ you wrote carefully, and think about These tools permit scientists to quickly [3]. Asking the right questions should which details you forgot to include. A contact people skilled in a specialized field. always be a priority in science, and online reader should be able to answer you just A question posed properly to the right online communities are a good place to practice. scientific community can help in solving by reading your initial message, without having to look at the rest of the discussion, difficult problems, often faster than screening Rule 2. State the Question literature or writing to publication authors. or at what other people already have said The growth of active online scientific Clearly in response. communities, such as those listed in Table The key to getting a good answer is to Some examples of non-concise ques- S1, demonstrates how these tools are ask the question in a clear and concise tions and how to improve them are shown becoming an important source of support way. If your question is too long, many in Text S1. Spend as much time as you for an increasing number of researchers. people simply will not read it. On the need in preparing your initial message: this Nevertheless, making proper use of these contrary, if your question is too short, will save time later and will lead you to resources is not easy. Adhering to the social people may interpret it incorrectly and find the best solution more easily. Many norms of World Wide Web communica- give you an erroneous answer. people are surprised to see how some- tion—loosely termed ‘‘netiquette’’—is both important and non-trivial. In this article, we take inspiration from Citation: Dall’Olio GM, Marino J, Schubert M, Keys KL, Stefan MI, et al. (2011) Ten Simple Rules for Getting Help our experience on Internet-shared scien- from Online Scientific Communities. PLoS Comput Biol 7(9): e1002202. doi:10.1371/journal.pcbi.1002202 tific knowledge, and from similar docu- Editor: Philip E. Bourne, University of California San Diego, United States of America ments such as ‘‘Asking the Questions the Published September 29, 2011 Smart Way’’ [1] and ‘‘Getting Answers’’ Copyright: ß 2011 Dall’Olio et al. This is an open-access article distributed under the terms of the Creative [2], to provide guidelines and suggestions Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, on how to use online communities to solve provided the original author and source are credited. scientific problems. Funding: GMD is supported by grants SAF-2007-63171 and BFU2010-19443 (subprogram BMC) awarded by Ministerio de Educacio´n y Ciencia (Spain), the Direccio´ General de Recerca, Generalitat de Catalunya (Grup de Recerca Consolidat 2009 SGR 1101) to JB. KLK is supported by a 2010–2011 Fulbright student research grant to Rule 1. Do Not Be Afraid to Ask Spain. LJJ is supported by a donation from the Novo Nordisk Foundation. JM is supported by funding from the University of Zurich. MIS is supported by a long-term fellowship from EMBO. The funders had no role in study a Question design, data collection and analysis, decision to publish, or preparation of the manuscript. Some people are afraid of asking a Competing Interests: The authors have declared that no competing interests exist. question in public, for fear of appearing * E-mail: [email protected]

PLoS Computational Biology | www.ploscompbiol.org 1 September 2011 | Volume 7 | Issue 9 | e1002202 times, in thinking about how to pose the Use a clear and concise title, so that of the error. This will help the other users problem, the answer reveals itself! readers can decide whether they are able to inspect your logic, to test the code on to respond to your message without having their own computers, and to easily pin- Rule 3. New to a Mailing List? to read the whole message. point the problem therein. Learn the Established Customs An approach to choosing a good title is If you ask a question about a software before Posting to think of a hypothetical web search package, make sure that the solution is not query that you would use to find a solution already answered in the user manual or A common error is to rush into a web to your problem. For example, where you the Frequently Asked Questions (FAQs) forum and start asking something without might search for ‘‘format BLAST data- before bringing your question to a forum. understanding how its web interface works base,’’ an adequate title for a forum post Also, declare that you have already and which people use the resource. could be ‘‘How do I format a BLAST checked these sources. Instead, a good habit is to spend a few database?’’ or ‘‘Formatting a BLAST If you really need another person to days, after having created an account, database.’’ More specificity, within reason, write a program or a task for you, then reading the discussions published and is preferable. explain that you are looking for a practicing with the web interface. You At the same time, it is important not to collaboration, and say how you will will see which people use the forum or waste the time of the people who are not acknowledge a correct answer. If you mailing list, which rules of netiquette are able to help you, and are not interested in explain everything well, your reputation used, which kind of questions are asked, what you are writing. Refrain from online will also improve. and how much time it takes to obtain an attempts to attract attention with titles answer. For this reason, it is a good idea to such as ‘‘Help me’’ or ‘‘Urgent.’’ People Rule 7. Proofread your Post and subscribe to a few mailing lists or forums usually do not appreciate these kinds of Write in Correct English on your topics of interest even when you titles because each forum member must do not urgently require anything from then view the post in order to understand Using correct grammar is important. them. This will show you the concrete what you are asking. If you use incorrect Readerswillbemorelikelytoanswerifthe ways in which people post messages. titles, your message may be censured or question is clear and correctly posed. Your Remember that you may have to use a closed by the moderators, and you may be grammar does not need to be academic, but different language depending on the forbidden to use the resource. it must be intelligible to a broad audience. audience you are addressing. For example, Some examples of good and bad titles Avoid slang and abbreviations as much as some technical terms may be understood are shown in Text S1. possible, to show that you have made at least in one mailing list or community but not some effort in writing a clear message. in others. People who do not study Rule 6. Do Your Homework Writing in capital letters or in unconven- genomics might not immediately know before Posting tional styles, such as that of text messages, is how to respond to questions about usually unwelcome, and in the long term can GWASs, SNPs, or STRs (genome-wide People in an online community are deteriorate your reputation online. association studies, single nucleotide poly- willing to help, but are not there to work Your message should be as concise as morphisms, and single tandem repeats, for you. You should always show that you possible. You do not need to introduce respectively). have first tried to solve your problem by yourself on every message; doing it only yourself. Explain clearly what you have once will be enough. Be careful of using Rule 4. Do Not Ask What Has done, and describe the approach that you too many adverbs and adjectives, or took. Already Been Answered unnecessary changes in verb tense, as they When asking for help to solve an may make the text difficult to understand. People in general do not like to repeat assignment, always explain how you have Also, do not be afraid of repeating their explanations. Before posting a ques- tried to solve it. Many students from technical terms more than once, as using tion, use a search engine to see if a similar bachelor programs use web forums and too many synonyms will only make the question has been asked previously. You mailing lists to copy-paste the assignments text more difficult to understand. should post a new question only if the given by their teachers, and call on other This rule may be the most difficult to answers you have found are not satisfac- people to show them how to solve them. follow for non-native English speakers. A tory. In case you decide to post a new This behavior is not well received and can good approach is to spend some time question, cite the previous answers and bring you a bad reputation. reading the messages written by other explain why they are not sufficient to solve However, you can nonetheless ask for users of the forum or the mailing list and your problem. This demonstrates that you help on how to solve an exercise if you follow their example. Search for a question have already researched the answer on demonstrate that you have made some similar to what you want to ask, and use it your own. Most discussion forums or effort in solving it. Show what you have as a model; you may even copy and paste mailing lists also have a searchable ar- done so far, and why you think it is not some portions of the text if it helps you to chive, which should be consulted before correct. Ask other people to check your formulate a correct question. posting a question. solution, not to give the solution to you. When asking about a programming Rule 8. Be Courteous to Other Rule 5. Always Use a Good Title issue, do not expect other people to write Forum Members a whole program for you: rather, post an People like to quickly skim through example of the code that you have written Members of a discussion forum are titles, looking for questions within their and where you are stuck. Include an usually unpaid volunteers who offer their expertise that they are able to answer. So, example of the input and the expected time and expertise by volition and not by you will have to be good at catching the output of your program. If you receive obligation. They are therefore not obliged attention of the readers that can help you. error messages, also include the full output to answer any questions at all.

PLoS Computational Biology | www.ploscompbiol.org 2 September 2011 | Volume 7 | Issue 9 | e1002202 Maintaining civil and polite conversa- avoid spreading embargoed information; your previous position. Most online com- tions fosters an environment that encour- and if possible, use your academic/corpo- munities are very welcoming to new ages people to contribute. You must rate email address when registering, to keep members, as they alleviate the work of remember that forums are as human as your private life separated from your work. more experienced ones. Also, as a new their users, and you may sometimes receive Nevertheless, most of the time it is possible contributor, you might be able to see a perfect answer written in an unfriendly to make use of online communities without problems from a beginner’s point of view. tone. This can happen for various reasons: breaking any of your employer’s rules. In You do not have to contribute to the perhaps the same question was asked these cases, the fact that an archive of the community by answering questions, as some previously, or maybe the author was in a discussion remains publicly accessible is communities have a ‘‘wiki-style’’ interface bad mood when writing. For your career, it positive, as it becomes a useful resource for where you can contribute by editing, is crucial that you not permit the discussion people searching for solutions to similar tagging, or flagging questions. In any case, to degenerate into an argument. Even if problems. Several knowledge archives are following at least a few science-related you receive an impolite answer, stay calm actively saving bioinformatics-related ques- mailing lists and contributing actively to and answer as gently as you can [4]. And tions from open source projects. For example, them is a great way to come into contact remember the golden rule: treat other questions about BioPerl [5] are kept in the with researchers working in your field, and forum members as you wish to be treated. GMANE (http://news.gmane.org/gmane. over time can lead you to new collabora- One of the most impolite behaviors comp.lang.perl.bio.general) and Nabble ar- tions and new opportunities for your career. toward an online community is asking a chives (http://old.nabble.com/BioPerl-f135 question in multiple places at the same 96.html). Supporting Information time. ‘‘Cross-posting’’, as this practice is Since an archive of the discussions called, can make two distinct online remains available on Internet, it is good Table S1 List of bioinformatics- and communities work through a solution for practice to conclude the discussion by biology-related mailing lists and commu- you when only one is needed; this is an indicating the correct solution to the nities. abuse of forum members’ time. If you problem exposed or by summarizing the (DOC) have not received an answer and you suggestions received. If some of the answers Text S1 Examples of poorly posed believe that asking it in another place that you received have proven to be wrong, would get you one, provide a link back to do not be afraid of writing it in the online questions, and how to improve them. the original discussion. Similarly, if you discussion: this will help other people avoid (DOC) receive an answer in a different forum, trying an erroneous solution. Even if you report the answer to the original forum. did not receive any useful answers, sacrifice Acknowledgments Then, the people who helped you will a bit of your time to thank the people who This article has been written collaboratively as know what the correct solution is and that tried to help you and to explain that you an open initiative based on the WikiGenes you are no longer looking for it. were not able to find a solution. platform, at the address http://tinyurl.com/ tenrules-onlinecommunities. We would like to Rule 9. Remember That the Rule 10. Give Back to the thank Robert Hoffmann from the Computer Archive of Your Discussion Can Science and Artificial Intelligence Laboratory, Community Massachusetts Institute of Technology, Cam- Be Useful to Other People Have you found your answer? Great! As bridge, Massachusetts, for making available the Messages in a mailing list or forum time progresses and you get more experi- WikiGenes platform and for the support. We would also like to acknowledge Nelson Ndegwa remain archived on the Internet. In certain enced in the respective field in which you from EMBL-EBI and Daniel Mietchen from situations, this can be a source of trouble: asked your question, you might want to start University of Jena for contributions to the draft check the policy of your university or contributing the knowledge that you have of the manuscript. employer regarding posting on the Internet; gained by helping people that are now in

References 1. Raymond ES, Moen R (2006) How to ask questions 3. Miller W (2 May 1955) LIFE magazine. 5. Stajich JE, Block D, Boulez K, Brenner SE, the smart way. Available: http://catb.org/esr/ 4. Bourne PE, Barbour V (2011) Ten simple rules for Chervitz S, et al. (2002) The Bioperl toolkit: Perl faqs/smart-questions.html. Accessed 31 May 2011. building and maintaining a scientific reputation. modules for the life sciences. Genome Res 12: 2. Ash M (2006) Getting answers. Available: http:// PLoS Comput Biol 7: e1002108. doi:10.1371/ 1611–1618. www.mikeash.com/getting_answers.html. Ac- journal.pcbi.1002108. cessed 31 May 2011.

PLoS Computational Biology | www.ploscompbiol.org 3 September 2011 | Volume 7 | Issue 9 | e1002202 Editorial Ten Simple Rules for Getting Involved in Your Scientific Community

Magali Michaut* The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada

A scientific community consists of scien- volunteers often have to take initiative and idea. In addition, you can search on the tists working in a particular field of science take things into their own hands. That is the Internet and look for information about and, most importantly, of their relation- context in which these rules should be of societies or associations you are interested ships and interactions. Beyond the tradi- particular interest. in, if they exist. If they don’t, it can also be tional publication of research projects, I have been involved in the Student good to create something new, but that is discussions occurring during conferences, Council of the International Society for more challenging and may not be appro- seminars, and even online through social Computational Biology for five years, priate for a first experience. networks or blogs enable ideas to spread progressively taking on more responsibili- more efficiently and are essential for ties, in particular in the organization of Rule 2: Define What You Want building a lively and dynamic community. conferences (co-chair of the symposium in and Expect Activities such as organizing conferences Boston in 2010 and chair of the first and workshops, answering questions and European symposium in Ghent in 2010), It is important to know why you are discussing scientific ideas online, contribut- but also more generally in the Student getting involved and to define a clear goal. ing to a scientific blog, or participating in Council (I was secretary—one of the This will help you keep the motivation. open source software projects are typically elected leaders—of the Student Council For instance, you want to be part of a thought of as outside classic research in 2009). In addition, I created the French team of international students to improve activity. Having scientists involved in those Regional Student Group (RSG-France), your communication skills, or you want to activities, however, is very important for the which I chaired for two years. This paper learn how you can raise funds and contact community to be dynamic and to promote is based on my experience in the bioinfor- sponsors. Maybe you want to get experi- fruitful discussions and collaborations. Sci- matics community, but also on associative ence in organizing a conference or simply entific associations have an important role involvement I had outside science. Most meet new colleagues all around the world. in enabling science by bringing people examples are taken from the bioinfor- Defining what you will get or expect to get together and giving them a voice. More- matics community, but I believe the rules from the involvement is certainly a good over, being involved in such activities is are rather general and apply for other idea. You might realize afterwards that individually very rewarding because it communities. you actually got very different benefits enables scientists to acquire new skills not from what you were expecting, but it is typically taught and to expand their Rule 1: Collect Information good to think about it at first. network and interactions. Maybe you are not sure whether you For those reasons, I encourage young Rule 3: Define Your Boundaries want to get involved or not and which kind scientists to get involved in their scientific of involvement is possible and would be To keep the balance between your community. However, it should be noted interesting for you. The first thing to do is activities you need to define clear bound- that this involvement takes time during certainly to ask people around you about aries, in particular to what extent you want which you are not directly contributing to their experience in various associations to get involved. If you don’t know what your research projects and publications. It and committees, should it be in your you are doing, you don’t know when to is thus essential to balance those activities. scientific community or other communi- stop. This is true for the daily work when The purpose of this paper is twofold: i) ties. You can ask them about the kind of you are wasting a lot of time simply illustrate some of the benefits of being involvement they have or had and what because the task is not clear. But it is also involved and, most importantly, discuss they like or dislike about it. Which were valid for the duration of your involvement. how to get there; and ii) give some the benefits? Which were the problems? It may be a good idea to decide before- concrete advice and rules to keep this Would they do it again? All these ques- hand when you want to stop. Do you plan involvement as effective and controlled as tions can help you get a more concrete to be involved two years? Three years? possible in order to serve the community and receive benefits in return without hampering your research activity. Citation: Michaut M (2011) Ten Simple Rules for Getting Involved in Your Scientific Community. PLoS Comput Biol 7(10): e1002232. doi:10.1371/journal.pcbi.1002232 In scientific societies or associations, many tasks are accomplished by individuals Editor: Philip E. Bourne, University of California San Diego, United States of America who volunteer their time. Even tasks that Published October 27, 2011 appear to be merely administrative or Copyright: ß 2011 Magali Michaut. This is an open-access article distributed under the terms of the Creative clerical are essential for the scientific Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. community and will make a difference in your field. In those volunteer organizations, Funding: The author received no specific funding for this article. projects are often driven by a single person Competing Interests: The author has declared that no competing interests exist. or a very small team. Consequently, * E-mail: [email protected]

PLoS Computational Biology | www.ploscompbiol.org 1 October 2011 | Volume 7 | Issue 10 | e1002232 Until you get your PhD? Until you finish involved. But if you can’t deliver what you you need to distribute the work, delegate your postdoc or any other project? It may signed up for, you penalize the team and some tasks to others, and ask for help be easier to get involved after you have the work of other people. You can think of when you need it. In general it is good to settled in your current place and project, it as a soccer team—if you commit for a assign a single responsible person and a as opposed to during phases of transition. game and don’t show up, the team is stuck. deadline for each task. Working with other people is also an interesting way to get Rule 4: Jump into the Pool and Rule 6: Dedicate Regular Time feedback on your work and ideas. Even Get Involved though it usually takes more time, it is a It is extremely important to work good idea to suggest a discussion and take Now you want to get involved, you regularly even when you are busy. It is the opportunity to get comments on your know why, and you have a goal and indeed very likely that your research will ideas, actions, and concerns. That is what boundaries. But how can you actually take up all the time that is not firmly teamwork is about. Finally, this is probably start? Keep in mind that it may be enough reserved for other activities. Thus, if you more geared towards leaders, but it is to simply be open to any good opportunity don’t take your involvement as seriously as extremely important to be able to get the that can unexpectedly happen. Haven’t your research, you will never get anything best out of a group of different and you been asked already to help out with done. When you feel overwhelmed, post- complementary volunteers. Identify the the organization of an event or the poning everything for later when you strengths and weaknesses of your team reviewing of some abstracts? Otherwise, expect to have more time is generally not workers and help everybody achieve their you will need to be proactive to get a good strategy, because you will always be best based on their interests and skills. involved, and there are many ways to busy. It is often the case that 10 or Identify and respect the differences of the start. For instance, you can send an e-mail 15 minutes on a project can be enough people in the team. In particular, in to a committee chair or the society chair to get the next step done. Think about international associations you will likely asking questions about how it works or where you are and what is the next step. be interacting with people from all over how you could help. You can even Maybe you just need to send an e-mail to the world who may have cultural differ- indicate your interest if you have some ask about the quotes Jack had to get, or ences in work styles, expectations, and ideas or know what you would like to do, remind this keynote speaker about the ways to communicate. In line with this, it but it is certainly not required. Don’t picture he has to send. However, we still may be useful to provide an action item list hesitate to contact people and just ask if have some periods when it is more difficult with concrete tasks that allows people to there is anything you can do to help. Help than usual to dedicate the smallest amount find where they can help in the project. is often needed and very appreciated. You of time. In that case, be clear about it and can also attend the annual meeting of the try to give your expected schedule and deadlines in advance so that other people Rule 9: Encourage Others to Get society, join a committee, or participate in Involved mailing list discussions. Even when you are on the team can adjust. already involved you can be proactive Don’t hesitate to let your colleagues about taking on more responsibilities. If Rule 7: Organize Your Time know about your involvement. The point would like to do more, or change what you Since you can’t spend all your time on is not to show them how great you are are working on, let people know and offer your community involvement and want to doing and that they should do the same. to do something different or new. It is maintain a balance with the activities But it is very likely that many people are always very motivating for the team to see directly related to your research projects, not aware of this kind of involvement and that volunteers want more responsibilities. it is essential to get organized. You can don’t realize how useful it is for the decide in advance how much time you community and for you. Explain the work Rule 5: Let Other People Know want to dedicate and track the time you you are doing and what you get from it. What You Want to Do actually spend on your various activities. You can encourage your colleagues to play You might realize that some tasks take an active role in the scientific community. Everybody has different interests and it much more time than you were expecting If you think that someone would be is key to know them to build a team as or, conversely, are much faster to perform effective in some specific task, tell him or effective as possible. If Joe hates contacting than you initially thought. The more you her so. Sometimes people don’t realize potential sponsors but likes writing meet- do it, the more accurate you become in that they are good in specific tasks that ing reports, he will be happy to know that your time estimates. This will enable you seem complicated for others. For instance, William would rather be part of the to know precisely which responsibilities you can ask Averell, who has very good fundraising effort and hates writing re- and tasks you are able to handle and to be graphical skills, to work on the design of ports. Thus, be clear about your interests reliable in your commitments. As part of various documents, flyers, or posters. for the benefit of everybody. Following this your schedule, you also want to define Since the organization is composed of idea, it is important to be clear with realistic milestones and deadlines, and volunteers, it is often the case that people yourself and with others about what you stick to them. have to step down from their position can or can’t do. You have to realize that when their job situation changes. Thus, it you are part of a team. The point is not to Rule 8: Work in a Team is important to have other volunteers who do everything, or to take as many tasks or can take over. But it is also important to responsibilities as possible to show you are Unless you are really working on a get new people to bring fresh ideas, new very much involved. The point is to project alone, you will likely be part of a perspectives, and different ways to work. commit to what you can do and to do it team and you should take advantage of it. When you start to know people and have (and do it as well as you can). If you have Thus, don’t take all the work for you, and experience working with them, for exam- some more time, you can always ask for remember that you are not alone. Keep in ple, in organizing a conference, you can be more, help on other tasks, and get more mind, particularly if you lead a team, that very effective doing similar tasks again.

PLoS Computational Biology | www.ploscompbiol.org 2 October 2011 | Volume 7 | Issue 10 | e1002232 Nevertheless, it is rewarding to get new doing it and if you enjoy it, you will take of course different, and I would be glad to people involved and to have new com- the time to do it, and you will do it well. hear about your experience, should it be ments from outside, even if it seems more And if you don’t like it anymore or get similar or very different. It is possible that complicated and takes more time. Last but bored, then finish your commitments and you will have a bad experience or that not least, you should guide interested discontinue that activity. Of course, I something you try will not work out. In people to get involved. Many people should emphasize here that you have to that case, don’t be discouraged and try would be happy to help but don’t take something else. Your experience can also finish your commitments first (see team- the time to actually start, or don’t feel simply be different from what you were work comments above)! confident enough. If you mentor them in expecting, but in the end, it is always a I hope I managed to illustrate that the beginning, it might be enough for good experience. After all, experience is getting involved in your scientific commu- them to get into it. what you get when you didn’t get what nity is not only extremely rewarding for you wanted. Rule 10: Enjoy as Much as you, but also possible for everybody, and Possible that simple rules can help you balance your activities. There is a lot to do, various Acknowledgments What you like, you will do great without tasks for various people and at different I would like to thank Nils Gehlenborg for specific effort. If you know why you are levels of involvement. Every experience is detailed and insightful comments on this paper.

PLoS Computational Biology | www.ploscompbiol.org 3 October 2011 | Volume 7 | Issue 10 | e1002232 Editorial Ten Simple Rules for Teaching Bioinformatics at the High School Level

David Form1, Fran Lewitter2* 1 Science Department, Nashoba Regional High School, Bolton, Massachusetts, United States of America, 2 Bioinformatics and Research Computing, Whitehead Institute, Cambridge, Massachusetts, United States of America

Given the availability of free, online students is likely to contain too much teins. Students can utilize 3-D protein genomic databases and tools for the information for them to digest during one models to compare the structures of analysis of biological data, it is now lesson. Focus on one or a few items. proteins with very different functions, such feasible to teach bioinformatics in the high as collagen, the estrogen receptor, and school classroom [1]. There are a number Rule 2: Familiarity: Use alpha amylase. of reasons why it is appropriate and Activities to Explore Examples desirable to introduce bioinformatics at That Are Familiar to Students Rule 4: Develop Activities That the high school level. Students can engage Build on Each Other in inquiry-based activities that involve Familiarity breeds relevance. Much of approaching real-world problems using the information presented to students will More complex tasks and skills can be 21st century skills, while being tailored to be new to them. It will make it easier to done successfully if they are broken down high school biology frameworks. Many understand new concepts or information if into small pieces that are taught separately tools, such as 3-D protein visualization they are linked to something that is and then combined in a stepwise fashion. software, allow for differentiated and already familiar to them. High school Students can focus on learning one skill or highly interactive instruction. The fore- students are particularly interested in concept at a time. most reason may be that students can topics that they can relate to their develop a research toolkit that they will be immediate personal or social lives. Choose Rule 5: Use Activities to Build able to use subsequently during college genes, proteins, or processes that relate to Skills and to Provide and beyond. disease, development, or other aspects of As a high school science teacher for the Information through Inquiry- human physiology and behavior. Obesity, Based Research past 23 years, I (DF) have had the diabetes, and developmental disorders are opportunity to incorporate bioinformatics some examples that have worked well. Students learn best when the work has into my courses to enrich the teaching of meaning and when they are actively concepts of molecular biology, human Rule 3: Link Activities to pursuing a goal. For example, a student biology, genetics, and evolution, providing who was asked to find the mRNA increased opportunities for effective differ- Preexisting Science Curricula sequence for the gene involved in a disease entiated instruction and individual student Bioinformatics exercises are more likely that she was researching was wondering research. This past experience has inspired to be used if they are related to the why there were several mRNA sequences the creation of this set of Ten Simple curriculum that is already being taught. In for what she thought was a single gene. Rules. a biology class, a lesson using 3-D protein After an explanation of alternative tran- It is important to distinguish between models is more likely to be utilized if the scripts and the roles of introns and exons curricula designed to teach the fundamen- proteins studied relate to concepts in the in generating these transcripts, she was tals of bioinformatics and those that utilize curriculum. For example, analysis of excited about her ‘‘discovery’’ and pro- bioinformatics as a teaching tool. Exam- hemoglobin structure can be part of units ceeded to explain this to her classmate/ ples of both types of successful teaching on the circulatory system and genetics friend. She found the concept of RNA can be found in Text S1, Text S2, and (sickle cell disease). The use of 3-D models editing to be fairly easy because she Text S3. can be used to help introduce students to actively discovered the process as part of structure–function relationships in pro- her research. Rule 1: Keep It Simple Set one, or a very few, objectives for Citation: Form D, Lewitter F (2011) Ten Simple Rules for Teaching Bioinformatics at the High School Level. PLoS each activity. Begin with a few, limited, Comput Biol 7(10): e1002243. doi:10.1371/journal.pcbi.1002243 straightforward goals. For example, an activity may require students to find a Editor: Philip E. Bourne, University of California San Diego, United States of America limited set of specific information in a Published October 27, 2011 GenBank file, such as the coding sequence Copyright: ß 2011 Form, Lewitter. This is an open-access article distributed under the terms of the Creative for a gene, and print it out in FASTA Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. format. You can link these objectives to other, more complicated, concepts in later Funding: The authors were supported by institutional funds. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. lessons. An activity will be more effective if Competing Interests: The authors have declared that no competing interests exist. extraneous information is kept to a Fran Lewitter is Education Editor of PLoS Computational Biology. minimum. The output provided to the * E-mail: [email protected]

PLoS Computational Biology | www.ploscompbiol.org 1 October 2011 | Volume 7 | Issue 10 | e1002243 Rule 6: Provide Opportunities Rule 9: Model Processes Using ary school students. One is for for Individualization Pen and Paper before Using the bioinformatics activities to incorporate in Computer an introductory biology course. The Students will often become more in- second is for a course ‘‘Models for volved if they feel a sense of ownership for Computers can handle large amounts of Disease’’ and is offered to Accelerated/ their work. Have individual students, or data and make complex manipulation of Honors level students after completing a student groups, each research their own this data in a short period of time—that’s first course in biology. gene or protein. For example, each why we use them in bioinformatics. (DOC) student in a class can be asked to identify However, this can often hide the processes the gene and protein associated with a from the students. Have the students run Text S2 Example term project for unique genetic disorder. Make sure that through a simplified mock-up of the data ‘‘Models of Disease’’ class. For the the level of difficulty is appropriate for the analysis using pencil and paper. For ‘‘Model for Disease’’ course, students are level and age of the students. example, have them compare protein required to complete a term project that sequences and come up with a ‘‘score’’ of uses bioinformatics tools to study a disease. Rule 7: Address Multiple relatedness before using a program, such Here we provide an example presentation Learning Styles as BLAST (through the NCBI website). given by a student based on their term Have them find and highlight appropriate project. Student abilities and learning styles will data in a printed form of a BLAST (PDF) vary among the class. Make use of the readout before they analyze a BLAST Text S3 Tips for developing curric- multiple ways that information is present- readout online by themselves. ed. For example, the output of BLAST ulum. The materials presented here were also presented as part of a tutorial makes use of a colorful graphical interface, Rule 10: Produce a Product a ‘‘hit list’’ in chart format, and sequence ‘‘Teaching Bioinformatics in High School alignments. Using all of these will help Have the students use the results of their Biology Courses’’ held at the International students to understand a BLAST output. activity to produce a ‘‘product’’ they can Society for Computational Biology’s an- present to the class. If they are researching nual meeting (ISMB) held in Boston, Rule 8: Empower Students the structure and function of a protein, Massachusetts, in July of 2010. have them design a product that uses this (PDF) Students like solving problems and dis- protein. For example, in researching leptin covering new information. Allow students to they can design an obesity pill. Acknowledgments discover the concept or information that you We wish to thank Curtis Huttenhower for want them to learn. This plays to a real Supporting Information strength of bioinformatics as a teaching tool. helpful discussions. Set up activities so that students can follow Text S1 Examples of model curric- up and extend their knowledge on their own, ulum. Here we provide example curric- using the skills that they have developed. ulum for two types of courses for second-

Reference 1. Wefer SH, Sheppard K (2008) Bioinformatics in high school biology curricula: a study of state science standards. CBE Life Sci Educ 7: 155–162.

PLoS Computational Biology | www.ploscompbiol.org 2 October 2011 | Volume 7 | Issue 10 | e1002243 Editorial Ten Simple Rules for Developing a Short Bioinformatics Training Course

Allegra Via1, Javier De Las Rivas2, Teresa K. Attwood3, David Landsman4, Michelle D. Brazas5, Jack A. M. Leunissen6, Anna Tramontano1, Maria Victoria Schneider7* 1 Biocomputing Group, Department of Physics, Sapienza University of Rome, Rome, Italy, 2 Bioinformatics & Functional Genomics Research Group, Cancer Research Center (IBMCC, CSIC/USAL), Salamanca, Spain, 3 Faculty of Life Sciences and School of Computer Science, University of Manchester, Manchester, United Kingdom, 4 Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Maryland, United States of America, 5 Informatics and Bio-computing, Ontario Institute for Cancer Research, MaRS Centre, Toronto, Canada, 6 Laboratory of Bioinformatics, Wageningen University, Wageningen, The Netherlands, 7 Outreach and Training Team, EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom

Introduction paring effective materials (slides, notes, better oriented to the expected outcomes references, etc.) entails a huge effort that and are more likely to be satisfied with the This paper considers what makes a would be enormously facilitated if course course. As most training sessions are based short course in bioinformatics successful. developers could start from a body of on slide presentations, dedicate at least In today’s research environment, expo- available materials, for example if they one slide (preferably, while providing the sure to bioinformatics training is some- could gain access to repositories of session overview) to the learning objec- thing that anyone embarking on life materials deposited by trainers of other tives, and mention how these will be sciences research is likely to need at some courses. This was one of the reasons achieved, using specific examples whenev- point. Furthermore, as research technol- motivating the Bioinformatics Training er possible; if appropriate, also mention ogies evolve, this need will continue to Network (BTN) to set up the BTN web- how the knowledge gained and skill set(s) grow. In fact, as a consequence of the site (http://www.biotnet.org/), which has will be useful for trainees’ work environ- introduction of high-throughput technol- been planned as a vessel for the training ments. Stating what participants will not ogies, there has already been an increase community to share and disseminate learn to do (e.g., to avoid over-estimation in demand for training relating to the use course information and materials. Course of the depth of analysis that can be of computational resources and tools developers are warmly welcome to sub- achieved in a short course) is also impor- designed for high-throughput data stor- scribe to the site and make available their tant for tempering their expectations. age, retrieval, and analysis. Biologists and materials to the community [2]. computational scientists alike are seeking Rule 2: Verify That Trainees’ postgraduate learning opportunities in various bioinformatics topics that meet Rule 1: Set Practical and Expectations Match Course the needs and time restrictions of their Realistic Expectations Scope schedules. Short, intensive bioinformatics It is critical to explicitly identify the Verify that trainees’ expectations match courses (typically from a couple of days to training objectives and expected outcomes what will be delivered. The most effective a week in length, and covering a variety from the outset. Begin by devising the title mechanism to ensure that expectations are of topics) are available throughout the of your course and specifying the target well matched is to collect information from world, and more continue to be devel- audience (e.g., laboratory biologists, com- trainees prior to the training session itself oped to meet the growing training needs. putational scientists). This information is (e.g., via a questionnaire), or by discussions The challenges, however, when planning, not only useful for trainers to help with trainees at the start of the course. organising, and delivering such courses, appropriately focus and weight the con- Obtaining such information early on are not trivial [1], especially considering tents of their training sessions, but is also allows time to alter course materials to the heterogeneous backgrounds of partic- vital for participants. By explicitly stating better meet participant expectations, for ipants. Here, we address such challenges the course objectives up front, trainees are example by adjusting case studies and and present a consensus of rules derived from the shared expertise of several bioinformatics trainers. While the rules Citation: Via A, De Las Rivas J, Attwood TK, Landsman D, Brazas MD, et al. (2011) Ten Simple Rules for Developing a Short Bioinformatics Training Course. PLoS Comput Biol 7(10): e1002245. doi:10.1371/ apply broadly to bioinformatics training, journal.pcbi.1002245 aspects addressing specific audiences are Editor: Philip E. Bourne, University of California San Diego, United States of America also discussed in order to make these rules pragmatic and applicable to a wide range Published October 27, 2011 of readers. Delivering bioinformatics This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under training is both crucial to facilitate the the Creative Commons CC0 public domain dedication use of, and to exploit the investment in, Funding: This work was partly supported by the Intramural Research Program of the NIH, NLM, NCBI, and by bioinformatics tools and resources, and an funds awarded to the EMBL-European Bioinformatics Institute by the European Commission under SLING, grant excellent opportunity to solicit user eval- agreement number 226073 (Integrating Activity) within Research Infrastructures of the FP7 Capacities Specific uation and feedback to improve them. Programme EMBL-EBI. The funders had no role in study design, data collection and analysis, decision to One point of crucial interest to the publish, or preparation of the manuscript. training course community concerns ma- Competing Interests: The authors have declared that no competing interests exist. terial preparation and distribution. Pre- * E-mail: [email protected]

PLoS Computational Biology | www.ploscompbiol.org 1 October 2011 | Volume 7 | Issue 10 | e1002245 examples to reflect the audience’s interests. Rule 4: Ensure Computational this can be beneficial for trainees to Furthermore, this will make you aware of Equipment Preparedness and witness—you might even want to explore the trainees’ different backgrounds. Read, Hands-On Support Availability such situations extensively, to convey the or listen to, and evaluate all responses, idea that resources and tools are dynamic. both to discern whether the course content Ensure (or rather, insist) that worksta- matches participant expectations and to tions (Linux, Mac, or PC) have all the Rule 6: Balance Concepts with learn what the trainees’ needs are. Such necessary software installed to allow train- Practical Outcomes information will also allow you to detect ees to complete the course. Make sure that clusters of trainees: e.g., those working the venue provides each trainee (or, at Bioinformatics training encompasses a with a particular model organism, those most, each pair of trainees) with one vast amount of learned skills. Acquiring more interested in DNA than in proteins, computer. Where trainees are required to these skills is a bit like learning to ride a or more plant than animal scientists. bring their own workstation (e.g., laptop), bicycle, where it is best to just start Useful information to collect includes their provide enough instruction and test com- pedalling, because watching others will research backgrounds and computational mands to ensure that software and depen- not help you learn the process! Of course, skill sets, their current projects relevant to dencies have been properly set up ahead it is important to provide trainees with the course, and their expectations of the of time. Request that a system support the fundamental concepts and theoretical training (e.g., what reasons led them to technologist be available, and in the room, background to ensure that they can use apply for this particular course?). Also when starting your sessions, to ensure the bioinformatics tools and resources mean- solicit information from trainees about the functionality of the classroom workstations ingfully. Nevertheless, it is a good rule to biological problems they wish to solve by and/or of the participants’ personal com- provide a balance between the theoreti- participating in the course. puters. cal/technical and contextual aspects. For Do not underestimate the trainer/train- example, many trainees may not value ee ratio, especially in consideration of the information on flat-files, relational sche- Rule 3: Plan Exercises and trainees’ diverse backgrounds. Be pre- mas, APIs, and web services, but will be Activities and Test Resources pared to provide extra hands-on support more concerned about knowing which before Delivery while trainees become familiar with new tools and resources to use for their specific interfaces, tools, and resources. Such needs, and why, and how to interpret their Plan the course in independent units/ support may be provided by trainers of outputs (just as the average cyclist is not modules, each with an introduction, set of other modules, tutorial assistants, past interested in the internal workings of the aims, list of actions, and potential difficul- trainees, or even current trainees who gearbox, as long as they know how and ties. When a new module is introduced, are familiar with the tool/resource basics. when to shift gear!). Discuss the limitations recall the achievements of the previous of the methods without getting carried module, and state what tasks participants Rule 5: Use the Dynamic World away by the intricacies of the algorithms will be able to additionally accomplish at or the minutiae of a tool’s capabilities. the end of the new module. of Bioinformatics Resources and Tools as a Learning Ensure that you cover not only those If you, the trainer, are also responsible questions that bioinformatics approaches Opportunity for the resource/tool being presented, you can answer, but also the limitations of are likely to be able to handle unexpected Provide time references for the infor- bioinformatics, explicitly illustrating exam- queries or problems. However, many mation you deliver, as bioinformatics ples that cannot be answered. trainers deliver sessions on resources/tools resources and tools, and stored data, Avoid long sessions of browsing around built and maintained somewhere else by evolve continuously. Place emphasis on web interfaces or showing one screenshot someone else, using someone else’s data. the ‘‘official’’ sites, as these are most likely after another. Trainees will be eager to try Regardless, always prepare an alternative to remain stable reference points for tools themselves and will benefit far more plan in anticipation of unforeseen difficul- trainees. When creating your materials from a well-planned session, with ade- ties. For example, at short notice, you and exercises, as much as possible, avoid quate time allocated to an exercise or might not be able to use live queries, so screen-shots, as these date quickly—oth- simple exploration, than from merely ensure that you have sufficient back-up erwise, you risk spending substantial watching someone else explore for them. material (e.g., animations, videos, etc.) to amounts of time updating outdated slides When giving a demonstration, try to get allow you nevertheless to deliver your rather than concentrating on developing participants to follow along with you. To training session effectively. suitable case studies and examples relevant compensate for the likely diversity in To appear as prepared and experienced to your audience. Describe the essence of speed and computer-ease of your audience, as possible, try your practical exercises data that can be retrieved from a partic- when possible, pair trainees of different beforehand. In cases where the query or ular resource and the principles governing backgrounds together and progress activ- task required to a bioinformatics server a tool, rather than sticking to specific ities at a speed that will allow all trainees to takes a long time, or is too demanding on releases, web interfaces, or, for example, to keep pace. Once you have completed a the service provider, either begin with tables of ranked results, which are likely task, confirm that everyone has achieved smaller query datasets, or provide the task to differ from day to day, as new data the result, and recapitulate the scope of results after trainees have prepared the become available in the databases. Take the actions to reinforce the meaning and query set-up, so that they still gain the into account that new data may have been significance of the session. If you allow experience of performing the task and added to the databases you are planning to trainees to work by themselves on specific class time is used more efficiently. It is use, and hence the outputs of the queries tasks, conclude with what you expected important to note that some service might be different from those you planned them to have achieved and how! Also providers will often hold query results for to demonstrate. As this occurrence is consider providing this summary of steps 48 hours. actually an integral part of bioinformatics, and expected outcomes in an electronic/

PLoS Computational Biology | www.ploscompbiol.org 2 October 2011 | Volume 7 | Issue 10 | e1002245 paper version as an addendum, as trainees is available, use it. Appreciate that a plant together, asking trainees for ideas and might want, and would certainly benefit biologist will not have a need for human- alternative ways to resolve particular from being able, to review the task again, on centric examples, nor will they find them biological questions. Group sessions like their own time. Furthermore, trainees will comparable. The more relevant you make this, where trainees are encouraged to often be eager to share what they have learnt the examples for the trainees, the more share their thoughts and views with the when they return to their work environ- likely they are to retain their interest and whole class, can help both to identify ments, so having a set of good course develop their skills! Furthermore, encour- common issues and aspects to be explored, manuals/practical exercises is essential to age trainees to explore the tools and and to highlight any trainee limitations enable them to do so. Absolutely avoid resources presented during the course not and/or mismatched expectations. More- spending 80% of the session talking and then only with the carefully prepared examples over, incorporating such group discussions rushing through the last 20% of the practical provided, but also from the perspective of directly into training sessions can often aspects. Moreover, try to avoid telling their own research interests: nothing help to instil a greater level of understand- trainees to finish later (on their own) motivates as much as the need to solve ing than when trainees are left to passively whatever they did not complete, as they will one’s own problems! explore set examples (or to copy and paste probably not do so, will feel resentful The use of tools and resources from the scripts with no explanation of what these because what they really wanted to do was perspective of personal research interests, might achieve). Exploit such brainstorm- not done and, more importantly, they will will lead new users to take a fresh critical ing sessions to demonstrate how bioinfor- have lost the important recap and reinforce- look at them. From this perspective, matics tools and resources can help to ment that you can provide. trainees might be able to provide a special address, and sometimes solve, complex assessment of the tools and resources problems. Rule 7: Reinforce Learning with introduced in the course which would be Depending on the time available, in- different and complementary to the one Contextual and ‘‘Real World clude quizzes and/or problem-solving that experienced users can provide. Train- Experience’’ Examples tasks and open discussion sessions in which ers can gain an understanding of how participants can reflect on the skills they’ve Wherever possible, provide appropriate easy (or hard) exploring web interfaces or learned and how these might be used to biological context: examples without rele- programmatically access and parse re- address questions of interest to them. vant context lack meaning and fail to sources is, and specific comments on what Provide trainees (perhaps in pairs or engage trainees. After introducing a new is intuitive or not to trainees can be groups) with a brief set of questions prior concept, allow time to put the concept captured informally or formally (e.g., immediately into action. Begin hands-on through surveys). In this regard, you may to, and after, the training course. Ques- exercises with a short worked example explain to trainees that evaluation and tions that probe their knowledge and where everyone can complete contextual feedback collected during the actual train- understanding of bioinformatics are useful learning on a common dataset. Follow this ing course or in a final feedback survey both for trainers (to verify that the course with time for further exploration: here, can aid significantly to improve bioinfor- has been pitched correctly and to establish you might either provide a second data- matics resources. what knowledge has been gained) and for set or, if relevant or practicable, invite trainees. Furthermore, by asking trainees trainees to use their own. If appropriate, Rule 9: Allow for Interactivity to think about, and answer, a series of course-relevant questions, you ensure ad- illustrate examples taken from your real and Provide Time for Reflection, equate time for concept and content world research experience. For instance, Individual Analysis, and outline biological problems that you tack- digestion and reflection. Exploration led with bioinformatics and describe resources and tools that you adopted to Ensure interactivity and time for reflec- Rule 10: Encourage solve them and to achieve your findings tion. Provide time for trainees to acquaint Independent Thinking and and how. themselves with the interfaces of the tools/ Problem Solving resources, and to understand their con- Rule 8: Ensure the Methods/ tents: allowing trainees to explore a tool or Finally, teach to fish rather than give Tools Have Relevance to the resource on their own tends to promote fish! In other words, try to develop Trainee Experience and greater retention of concepts. independent thinking rather than simply spoon-feeding trainees with slides and Scientific Research Needs Schedule 10–15 minutes at the end of each module to review the presented step-by-step tutorials: it is more important Design your materials such that the concepts, and to stimulate questions from to learn how to tackle research questions examples you provide illustrate the con- the trainees, who will probably have only with bioinformatics, and to know where/ cepts you wish to convey and, at the same just started processing the information. how to search for solutions, than it is to time, are relevant to the research interests Do not simply rely on a set of slides and learn about the minutiae of every available of at least some of the trainees. Whenever step-by-step tutorials to teach concepts. tool and resource. prior information about trainees’ interests Make use of flip-charts to brainstorm

References 1. Schneider MV, Watson J, Attwood T, Rother K, 2. Schneider MV, Walter P, Blatter MC, Watson J, Budd A, et al. (2010) Bioinformatics training: a Brazas B, et al. (2011) Bioinformatics Training review of challenges, actions and support require- Network (BTN): a community resource for ments. Brief Bioinform 11: 544–551. bioinformatics trainers. Brief Bioinform. In press.

PLoS Computational Biology | www.ploscompbiol.org 3 October 2011 | Volume 7 | Issue 10 | e1002245