ISMB 2008 Toronto

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Citation Linial, Michal, Jill P. Mesirov, B. J. Morrison McKay, and . 2008. ISMB 2008 Toronto. PLoS Computational Biology 4(6): e1000094.

Published Version doi:10.1371/journal.pcbi.1000094

Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:11213310

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Michal Linial1,2, Jill P. Mesirov1,3, BJ Morrison McKay1*, Burkhard Rost1,4 1 International Society for Computational Biology (ISCB), University of California San Diego, La Jolla, California, United States of America, 2 Sudarsky Center, The Hebrew University of Jerusalem, Jerusalem, Israel, 3 Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America, 4 Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America

the integration of students, and for the of ISMB. One meeting in South Asia support of young leaders in the field. (InCoB; http://incob.binfo.org.tw/) has ISMB has also become a forum for already been sponsored by ISCB, and reviewing the state of the art in the many another one in North Asia is going to fields of this growing discipline, for follow. ISMB itself has also been held in introducing new directions, and for an- Australia (2003) and Brazil (2006). nouncing technological breakthroughs. Multi-tracking in response to The International Society for Computa- ISMB and ISCB are contributing to the challenges posed by merging fields. tional Biology (ISCB) presents the Six- advance of biology, and to helping to build ISMB/ECCB 2007 considerably expanded teenth International Conference on Intel- bridges and understanding between dedi- the breadth of the meeting. ISMB 2008 in ligent Systems for cated and passionate groups of scholars Toronto builds on its successful predecessor (ISMB 2008), to be held in Toronto, from an unusual variety of backgrounds. by keeping what worked, and by providing Canada, July 19–23, 2008. Now in the ISMB 1993–2008. The ISMB more open time for spontaneous exchange final phases of scheduling selected presen- conference series began in 1993, the and meetings. The main goal of ISMB is to tations, demonstrations, and posters, the result of the vision of David Searls contribute toward the success and enjoy- organizers are preparing what will likely (GlaxoSmithKline), Jude Shavlik (Univer- ment of science. In fact, scientific process is be recognized as the premier conference sity of Wisconsin Madison), and Larry highly dependent on good communication on computational biology in 2008. ISMB Hunter (University of Colorado). A few of results and nascent ideas. Creating outlets 2008 (http://www.iscb.org/ismb2008/) years later, ISMB had established itself as for such communication is therefore an will follow the road paved by the ISMB/ a primary event for the computational important catalyst for the advancement of ECCB 2007 (http://www.iscb.org/ biology community and triggered the computational biology. ismbeccb2007/) in Vienna in the attempt founding of ISCB, the International The major challenge for this interdisci- to specifically encourage increased partic- Society for Computational Biology plinary field is that two cultures with very ipation from previously under-represented (http://www.iscb.org/). ISCB has been different ways of publishing intersect. On disciplines of computational biology. This organizing the ISMB conference series the one hand, computational sciences conference will feature the best of the since 1998. While ISCB evolved into the publish their most important results in computer and life sciences through a only society representing computational rigorously reviewed proceedings of meet- variety of core sessions running in multiple biology globally, its flagship conference ings; the lower the ratio between accept- parallel tracks, along with single-tracked has become the largest annual worldwide ed/submitted papers, the more valued the Keynote Presentations, posters on display forum focused on computational biology. publication. Publications in conference throughout the duration of the conference, In January 2007, the ISCB came to an proceedings are often more highly regard- and an extensive commercial exposition. agreement with the European Conference ed than those in peer-reviewed scientific The first day (July 18) of the meeting is on Computational Biology (ECCB) to journals. In contrast, the life sciences reserved for two-day Special Interest Group organize a joint meeting in Europe every publish their best work in peer-reviewed (SIG) and Satellite meetings, the second day other year. This led to the ISMB/ECCB journals with the highest possible impact; (July 19) runs SIGs for the first time in in Vienna in 2007 that set the standard for journals with higher impact are ranked parallel with Tutorials and the Student a large-scale integrative forum for all those higher, and publications are not coupled Council Symposium, and for the first time with interest in subjects related to to presentations at any meeting. Open two SIGs are running in parallel with the computational biology. access publications attach value to the main ISMB meeting (July 20–23). ISCB is now focusing on expanding individual publication rather than to the participation beyond North America and specific vehicle. Thus, they may ultimately Introduction Europe, which has accounted for the offer a way to bring these two publication majority of participants during the history cultures together. However, this approach A considerable fraction of all the major scholars in computational biology fre- quently participate in ISMB. Consistent Citation: Linial M, Mesirov JP, Morrison McKay BJ, Rost B (2008) ISMB 2008 Toronto. PLoS Comput Biol 4(6): with this leading role in representation, e1000094. doi:10.1371/journal.pcbi.1000094 ISMB has become a major outlet for Published June 27, 2008 increasing the visibility of this extremely Copyright: ß 2008 Linial et al. This is an open-access article distributed under the terms of the Creative dynamic new discipline, and for maintain- Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, ing and elevating its scientific standards. It provided the original author and source are credited. has become the vehicle for the education Competing Interests: The authors have declared that no competing interests exist. of scholars at all stages of their careers, for * E-mail: [email protected]

PLoS Computational Biology | www.ploscompbiol.org 1 June 2008 | Volume 4 | Issue 6 | e1000094 does not address the needs of all members criteria for a Highlights talk is that the tational biology through research, educa- of a Society rooted firmly in both cultures. designated presenter has strong present- tion, service, or a combination of the Accepting this complex challenge al- ation skills. Thus, most presenters are three. This year’s Overton prize goes to ready implies the need for at least four already well-known in the community. An (Broad Institute of MIT and parallel tracks: two for presentations from important body of work is typically the Harvard, Cambridge, Massachusetts, proceedings (Proceedings Tracks), two for prerequisite for invitation for a Keynote United States), and the Senior Scientist presentations from high-profile work pub- Presentation by an accomplished researcher. award goes to (University lished in refereed journals (Highlights Finally, the Special Sessions are ways to expose of California Santa Cruz and Howard Tracks). Further expansion may offer even the field to areas and novelties that are not Hughes Medical Institute, Santa Cruz, greater opportunities to include new and already integrated into the community. The California, United States). The awards will relevant areas of research into the scien- extension of what was previously a track for be presented along with the accompanying tific program. software demonstrations to a more inclusive Keynote addresses. In fact, the Senior Events in light of a scientific Technology Track now includes investigators Scientist will conclude the scientific pre- career. One way of drawing the from all scientific career stages. sentations of ISMB on the afternoon of dividing line between the multiple events Keynotes. The Keynote Presentations Wednesday, July 23. Claire M. Fraser- (Figure 1) is with respect to the stage of the (http://www.iscb.org/ismb2008/keynotes. Liggett (Institute for Genome Sciences, participant in their scientific career. php) are run in a single track with no other University of Maryland, Baltimore, Mary- Young participants (students, postdocs, competing session and typically attract land, United States will kick off the main and young faculty) typically present most participants. In Toronto we will meeting with her talk on Microbial Posters that may combine published and continue our pursuit of several missions Communities in Health and Disease. unpublished material and may represent for these talks: to make the marriage The five other Keynotes will be given by very recent work. If the work has matured between computational and experimental (in alphabetical order): David Jaffe (Broad to the publication stage, the investigator biology more beneficial for biology, to Institute of MIT and Harvard, Cam- may consider submitting to the Proceedings present outstanding, exciting, and bridge, Massachusetts, United States), Track for novel, original research work. thought-provoking jewels of the biological (Hebrew University, Jer- (We note that the acceptance rate is sciences, and to celebrate the marvels usalem, Israel), Eugene M. Myers (Ho- typically below 17%, i.e., more restrictive uniquely represented in the world by ISCB. ward Hughes Medical Institute, Ashburn, than most peer-reviewed journals and Two Keynote Presentations feature the Virginia, United States), Bernhard Ø. most computer science conferences). winners of the annual ISCB awards—the Palsson (University of California San Most papers accepted in past ISMB Overton Prize, in memory of Chris Over- Diego, La Jolla, California, United States), proceedings were by investigators who ton, for outstanding investigators early in and Morag Park (McGill University, were already established in the commu- their career, and the Accomplishment by a Montreal, Canada). These lectures will nity. Published work with a track record of Senior Scientist Award given to those at review recent outstanding results in areas being a highlight in the field finds a home the zenith of their career who have made such as Oncology, Metabolic modeling in the Highlights Track. One of the selection major contributions to the field of compu- and reconstruction, transcriptional regula-

Figure 1. Sketch of Program for ISMB 2008 in Toronto. doi:10.1371/journal.pcbi.1000094.g001

PLoS Computational Biology | www.ploscompbiol.org 2 June 2008 | Volume 4 | Issue 6 | e1000094 tion, genomics, microbiology, neuronal growing opportunities for computational 189 proposals for this track. A diverse team Imaging, and new sequencing technolo- biologists and the need for new tools and of accomplished and dedicated experts gies. methodologies. accepted 61 of those for presentation in Special Sessions Track. For the Proceedings Track. Traditionally the two Highlights Tracks in Toronto (Table 1). second year, a Special Sessions Track (http:// majoreventattheISMBmeetingsisthe Papers from high-impact journals such as www.iscb.org/ismb2008/special_sessions. presentation of original papers, which are Science and Nature,aswellastheofficialISCB php) will enable in-depth focus on emerging published in the ISMB Proceedings as a special journal, PLoS Computational Biology,were and important areas. Seven Special Sessions issue of the journal .Common submitted. In all, more than 40 journals will cover a wide spectrum of topics, practice for computer science precludes the were cited among the submissions received, including cancer research, virology, proteo- re-publication of material published in ranging from Bioinformatics to PNAS,from mics, new generations in technologies Conference Proceedings in any other peer- Cell to PLoS Biology,andfromMolecular including sequencing, mass spectrometry, reviewed journal or meeting. Thus, the Systems Biology to PLoS ONE. flow cytometry, and cell imaging. For special issue of Bioinformatics increases the Industry Track. The Industry example, the session on Health and Diseases value of these Conference Proceedings for the Track (http://www.iscb.org/ismb2008/ in our Genomes chaired by ISMB’s honorary more biology-oriented members in the field. industrytrack.php) will run for the second co-chair Thomas Hudson (Ontario Institute In 2008, we received 287 submissions to this year and is for talks that are more relevant for Cancer Research, Toronto, Canada) will track; (CNIO, Madrid, and interesting for participants from highlight the role of computational biology Spain) chaired the rigorous review process industry. Chaired by Reinhard Schneider spanning from analyzing human genome modeled on the editorial review in scientific (EMBL, Heidelberg, Germany), this track variability to understanding disease. Other journals. He and his team of Area Chairs introduces a new forum for the meeting of Special Sessions will feature the Toronto selected 48 (16.7%) original research papers academia and industry in a venue that scientific community’s efforts towards for presentation in Toronto. This highlights innovative applications and aspectsofproteomicsanddisease,e.g., acceptance rate is slightly higher than practical impact studies of Life Science Interaction Networks and Disease chaired by ISMB/ECCB 2007. Informatics. Each selected talk will and Gary Bader One problem for the reviewers is that describe a scientific problem from a (University of Toronto, Toronto, Canada) submissions have to be accepted or business perspective, including the and Structural Bioinformatics: Deciphering the rejected given the submitted material approach used to address the problem, Proteome chaired by Igor Jurisica (Ontario without the conditional acceptance pend- the current state of the project, an Cancer Center, Toronto, Canada) and ing major revisions that satisfy the authors. evaluation of the benefits, and plans for Ryan Lilien (University of Toronto, In fact, most papers accepted by journals future developments. These presentations Toronto, Canada). Imaging techniques go through revisions and are published are tailored to give attendees the opport- are introduced in Frontiers in Cell Imaging whenever ready; the Proceedings, in con- unity to view scientific approaches through chaired by Robert F. Murphy (Carnegie trast, have to be ready by May. For the an industrial lens, which may prove Mellon University, Pittsburgh, Pennsyl- first time, the mechanism of revision for especially valuable to young researchers’ vania, United States), the challenges of some of the submissions was used, by understanding of the use of Life Science tackling the interactions between organisms Alfonso Valencia and his team of experts, Informatics in the business sector. are summarized in Computational Challenges which accounted for the higher accep- Technology Track (previously Demo and Opportunities in Host–Pathogen Systems tance rate. Track). Demonstrations of software Biology chaired by T. M. Murali and Papers will be presented in two parallel have also become an integral part of the Matthew D. Dyer (Virginia Polytechnic tracks. The paper reviewing process put ISMB and ECCB conference series, and Institute, Blacksburg, Virginia, United increased weight on work that opens new are now also offered at other bioinformatics States), and the very large-scale directions and is likely to impact molecular conferences. Demos allow academic sequencing of the future is previewed in and medical biology. All papers selected institutions as well as for-profit organiza- Sequencing Thousands of Human Genomes for oral presentation will be published in tions to showcase their software and/or chaired by Francisco De La Vega the conference proceedings as part of a hardware in a hands-on format to (Applied Biosystems, Foster City, regular online issue of Bioinformatics under audiences of up to 50 participants. The California, United States) and Gabor the open-access model, i.e., will be made Demo sessions have proven to be in high Marth (Boston College, Chestnut Hill, freely available, and, as in previous years, demand, and have consistently added a Massachusetts, United States). will be fully indexed in PubMed and by valuable aspect of the conference for both Finally, a group of investigators in- the Institute of Scientific Investigation presenters and attendees alike. These volved with both ISCB and the Society’s (ISI). traditional demonstrations are currently official journal, PLoS Computational Biology, Highlights Track. For the second being selected by a team of experts present a perspective on the Future of year, there will be a Highlights Track chaired by Rodrigo Lopez (EBI, Hinxton, Scientific Publishing chaired by Scott Markel (http://www.iscb.org/ismb2008/highlights. England) and a team of experienced (ISCB Publications Committee chair, Ac- php) featuring recently published, high colleagues. celrys, San Diego, California, United impact work. Work from highly ranked For the Toronto meeting, we decided to States). This is one of the two events journals and from journals traditionally extend the concept of demonstrations by highlighting the connection between ISCB featuring more experimental biology is integrating other events that had no and PLoS Computational Biology (the other is welcome. As with the other two tracks that traditional place in the ISMB framework. a Tutorial on Professional Development given by were introduced in Vienna (Special Sessions The change in the name from Demo to Phil Bourne, the Editor-in-Chief of PLoS Track and the Industry Track, below), the Technology Track reflects the following Computational Biology). Highlights Track was very well received by extensions and novelties. Firstly, we will All Special Sessions will review the current many participants, as it increased diversity give institutions and research consortia the state of a specialized field, and will explore and added quality. This year, we received opportunity to reserve a block of slots and

PLoS Computational Biology | www.ploscompbiol.org 3 June 2008 | Volume 4 | Issue 6 | e1000094 Table 1. ISMB/ECCB History.

Papers Papers Highlight Highlight Posters Special Year Location Attendees Accepted Submitted Accepted Submitted Keynotes Accepted Tutorials SIG Sessions

1999 Heidelberg, Germany 655 34 91 8 139 10 2 2000 San Diego, US 1272 42 141 7 275 14 1 2001 Copenhagen, Denmark 1251 38 180 6 345 14 6 2002 Edmonton, Canada 1624 42 207 8 494 15 6 2003 Brisbane, Australia 927 48 342 8 414 16 5 2004 Glasgow, UK * 2136 67 496 8 952 14 8 2005 Detroit, US 1731 56 426 8 622 14 8 2006 Fortaleza, Brazil 880 67 407 8 556 12 4 2007 Vienna, Austria * 1752 63 418 63 215 10 1096 14 8 7 2008 Toronto, Canada 48 287 61 189 8 10 8

*Meetings organized jointly by ISCB and ECCB, with their data in italics. doi:10.1371/journal.pcbi.1000094.t001 use this to evolve the concept of a meetings that accompany the main event, ISMB Expo has consistently proven to be demonstration into a series of synchro- namely the Satellite and Special Interest highly successful for the exhibiting nized demonstrations. The second is Group Meetings (SIGs; http://www.iscb. companies featuring products and another Toronto pilot: in addition to the org/ismb2008/sigs.php). For Toronto, the services of specific value to the traditional tutorials, we will introduce event is coordinated by a group of experts computational biology community. interactive, hands-on workshops for freely chaired by Hershel Safer (Weizmann Similarly, ISMB attendees take full available software tools and methods. The Institute, Rehovot, Israel). Five meetings advantage of the opportunity to meet ones chosen for the pilot reflect the wide will run for two days (July 18–19) and four one-on-one with the conference sponsors range of popular packages and the range for one day. The two-day meetings are: and exhibitors to catch the latest updates of activity in Computational and Systems 3Dsig: Structural Bioinformatics & Computational and information on valuable software, Biology. These workshops will be more Biophysics, the Bioinformatics Open Source hardware, publications, and tools of the comprehensive than the current ‘‘demos’’ Conference (BOSC), BioPathways, Alternative trade. Overall, the Expo is another avenue and give attendees an opportunity to bring Splicing, and the Joint AFP-Biosapiens SIG. focused on the importance of industry in their own data, laptops, and problems for Two of the one-day meetings will precede science, and many of the exhibitors practical learning. the main meeting: BioLink (July 18) and Next present talks in the Industry Track to detail Posters: Continuous Display. For Generation Sequencing (July 19). Two others the problems, applications, benefits, and the second time, all Posters (http://www.iscb. will occur during the main meeting: Bio- future plans being addressed within their org/ismb2008/posters.php) accepted for Ontologies (July 20), and Genome-Scale Pattern companies. presentation will be on exhibit for the Analysis in the Post-ENCODE era (July 21). More than just science. Attendees entire meeting. Over the years, ISMB has From the beginning, an integral part of traveling with family members and/or grown to a size that has made it impossible ISMB has been the Tutorials (http://www. children will find this year’s event offers to display all accepted posters during the iscb.org/ismb2008/tutorials.php) that ran a variety of optional tours and activities entire conference. Yet, posters bring the day before the main meeting. Janet during the meeting, and extended tours on enormous value to the conference. The Kelso (MPI for Evolutionary Anthropolo- dates surrounding the conference. Metro Toronto Convention Center hosting gy, Leipzig, Germany) chairs this event. In Specifically for those traveling with ISMB 2008 has the capacity to the attempt to shorten the overall meeting, children, we are working on providing accommodate more than 1,000 Posters on the Tutorials will be given in parallel with childcare options and information that display at the same time. Therefore, we are some of the SIGs on July 19. would enable parents to attend the especially pleased to ease the viewing of For the first time, the ISCB Student meeting while children are safely Posters by allowing all attendees the Council Symposium (SCS4; http://www. entertained. opportunity to view and absorb this iscb.org/ismb2008/scs4.php) on July 18 Two other Toronto novelties try to abundance of research in a single venue. chaired by Lucia Peixoto (University of expand into different realms: The first is Two Poster Author Sessions,carvedoutofthe Pennsylvania, Philadelphia, US) and Amr Visual Reflections on Science (http://www. evening program, will provide an Abuzeid (Queen’s University, Toronto, iscb.org/ismb2008/vrs.php) organized by opportunity to further explore posters of Canada), will run in parallel with the first the ISCB Student Council (ISCBSC; specific interest to any attendee: one evening day of two-day SIGs preceding ISMB. http://www.iscbsc.org/) and chaired by for even- and one for odd-numbered Posters Each of these pre-conference meetings Milana Frenkel-Morgenstern (Weizmann will be available. Marco Punta (Columbia offers additional opportunities to learn Institute, Rehovot, Israel). A space has University, New York, US) chairs the and network with a specific group of peers been set aside for the presentation of ideas selection of Posters in Toronto. of similar interests and goals. that reflect upon science from a very Tutorials, SIGs, and Students’ ISMB Expo. Another pillar of ISMB different perspective—perhaps more art Symposium. An increasingly important is the Exposition that runs through the than science. Finally, we will celebrate the aspect of ISMB is the series of smaller entire main meeting (July 20–23). The 16th ISMB with an Off-Site Dinner

PLoS Computational Biology | www.ploscompbiol.org 4 June 2008 | Volume 4 | Issue 6 | e1000094 Figure 2. Increasing Breadth of ISMB. doi:10.1371/journal.pcbi.1000094.g002 followed by the high energy Matrix Party; same time small enough to foster informal part in the world’s largest and most this event will happen in Toronto’s Liberty communication and a more intimate feel. scientifically comprehensive bioinformatics Grand (http://www.libertygrand.com/) en- While many countries have venues that meeting of the year. ISCB members gain tertainment complex. would allow meetings of between 1,000 significant ISMB 2008 Registration (http:// Challenges of numbers. Many of us and 5,000 participants, such venues often www.iscb.org/ismb2008/registration.php) may remember our first ISMB and our do not permit the level of full-scale discounts, while non-members are offered surprise at how many colleagues we parallelism that ISMB has grown into a complimentary one-year-membership as wished to connect with attended the (e.g., since we cannot tell upfront which part of their higher non-member fees. The meeting. ISMB connects an interdiscipli- track will be most visited, we currently early bird registration discount period nary scientific community through a need to reserve seven rooms each of which ended June 4 for all registration categories, single, international point of contact. can seat more than 700 participants). The although registration will remain open ISMB has been growing in terms of its Metro Convention Center in Toronto is through the conference dates. breadth of coverage and the number of one of the few sites that appear to be ideal We hope to welcome all of you in presentations (Figure 2). for the goals of ISMB. Toronto. At our current size, it becomes extreme- ISMB 2008 is expected to draw more ly challenging to identify venues that are than 1,400 attendees to Toronto to take big enough to host meetings and at the

PLoS Computational Biology | www.ploscompbiol.org 5 June 2008 | Volume 4 | Issue 6 | e1000094