Jump Off the Page Researchers Are Learning to Embrace Online Lab Notebooks, but Not Without Growing Pains

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RESEARCH TOOLS Jump off the page Researchers are learning to embrace online lab notebooks, but not without growing pains.

BY AMANDA MASCARELLI is followed by the open-science community. contain much more information than will Viewers can find the notebook through the ever be published in an academic paper. They wo years into his PhD, Carl Boettiger wiki’s RSS feed and links on social media as can be used as evidence for securing patents, needed a better way to organize his data well as in Google searches, and can post com- to settle legal issues or to pass a project from and synthesize his ideas. Fishing around ments. He soon started to receive suggestions one researcher to another. Industry labs almost Tonline, he stumbled across chemist Cameron about, and valuable feedback on, his research always require their researchers to maintain Neylon’s open electronic lab notebook. Boet- and methods from other scientists — mostly such records, as do many academic principal tiger, who was studying mathematical ecology, followers of open science from outside his field investigators, and until very recently the infor- liked what he saw. Neylon, now advocacy — and some even led to collaborations. mation would be kept securely under wraps in director at the Public Library of Science in San Four years on, Boettiger, now a theoretical the lab until it was published. Francisco, California, had pulled back the cur- ecologist at the University of California, Santa Open electronic notebooks are a radical tain on the steps and thought processes behind Cruz, is a leader in the use of the open note- departure from this ethos. Data and methods his protocols and research. His data collection, book. He is convinced of its value, and he is not are no longer cloistered in books or tucked protocols and results were linked together and alone — the idea is steadily gaining traction in away on private hard drives. Instead, they can available online, making the concepts easy to some (but not all) scientific circles. be shared online for all to see. Some scientists reference and explore. Whether on paper or in digital form, lab might shudder at the thought of anyone but Inspired, Boettiger created his own electronic notebooks are meant to document exactly lab mates and close collaborators knowing the notebook, reporting online about his day-to- what, when and why experiments were done detailed logic and steps behind their research day research in a publicly available wiki that (see ‘Record of achievement’) and usually projects before publication. But open

science is becoming more widely accepted The problem is mainly down to a lack of allow me to explore alternative ideas in a as technologies change and as younger genera- training. Undergraduates turn in detailed structured and documented way without dis- tions of researchers discover alternative tools notebooks for relatively simple experiments, rupting my existing work,” says Karthik Ram, and approaches. but as the complexity of their work increases a computational ecologist at the University of when they become graduate students, they California, Berkeley. EMBRACE THE OPENNESS may struggle to document these larger exper- Between 2009 and 2011, Ram was a post- Boettiger readily admits that having his entire iments. Many labs do not have formalized doc at the University of California, Santa scientific process exposed online at each step notebook-writing Cruz, studying the impacts of climate change of the way carries a risk. But “you have to take conventions in place. on large mammals in Yellowstone National risks to be successful”, he points out. “The Strasser says that her Park in Wyoming. He needed to incorporate idea that there’s a risk-free way of getting your approach as a PhD decades of data from multiple sources — on science out there and understood and engag- student in marine the natural history of herbivores and on how ing collaborators is a myth.” He posts updates biology was makeshift migratory behaviour has changed over time, to his work throughout the day, as if scrib- — cutting and pasting for example — and link it all to long-term STRASSER CARLY bling notes in a conventional notebook, but computer printouts climate data and changes in snowpack and publishes synthesized analyses and summa- into a paper note- vegetation. Because he uses existing data and ries several times a week or month. Boettiger book, storing data in models to answer questions, he often needs still has some concerns about being scooped “chaotic heaps” on to understand intermediate steps along the (see Nature 493, 711; 2013), but says that those her computer and “There are just way, such as the statistical methods used. Ram reservations are mostly offset by the many ben- using the comment a lot of moving found it time-consuming and difficult to tease efits of making his science open and accessible feature in Excel to apart other researchers’ data sets so that he — such as providing another way to attract col- describe results. parts. Scientists could build on them. Workflow platforms such laborators and to gain recognition in his field. don’t ever really as R and IPython (see ‘Taming the workflow’) The gradual acceptance of open science in GO WITH THE FLOW learn how to are now making this type of work much more fields such as chemistry, mathematics, neu- As researchers move capture the manageable, he says. Other platforms include roscience and ecology is highlighting the beyond simply docu- process.” Projects (developed by Digital Science, a sister information-management challenges that menting their daily Carly Strasser company of Nature Publishing Group). scientists face. “Now that science has become tasks, they are turn- Once a workflow system is populated with more complicated and not all of the details ing to electronic lab notebooks that have the nitty-gritty of the project, scientists can and data fit in the papers we publish, we’re at myriad bells and whistles and offer ‘workflow’ take advantage of Internet tools, such as wikis a loss,” says Boettiger. “How do we communi- capabilities. These software packages aim to and social media, to post and share their work. cate exactly what we’re doing? How do we keep capture the entire scientific process — from Jean-Claude Bradley, an organic chemist at science replicable?” study design to data analysis and visualization Drexel University in Philadelphia, Penn- Scientists collect, store and analyse data in — in close to real time, and enable colleagues sylvania, has several projects in his lab that different ways and with a growing array of to review and replicate the work. Users can rely on wikis. Any raw data a project obtains, tools. That makes it difficult to compare one share data and methods as they develop, or including pictures, videos and spectroscopy researcher’s results with another’s, and even choose to wait until publication. results, are quickly shared among team mem- harder to know how to reproduce their results, A piece of software called R, for example, bers, usually within a day. Lab members also says Carly Strasser, a data-curation and open- is widely used in the ecology community. use the wikis to share their findings. One wiki science specialist at the California Digital With it, researchers can weave together text, page represents one page in a lab notebook, Library in Oakland. “We still have paper note- programming code and data analysis into a with sections, objectives, methods and other books, we still have Post-it notes, we still have narrative. The steps leading to a published components. phone calls that we don’t transcribe and a ton of paper no longer need to be impenetrable to All these tools help to create what open- e-mails going back and forth,” she says. “There other researchers — anyone can access any notebook aficionados call a living paper, are just a lot of moving parts. Scientists don’t step along the way and reproduce it, or take which contains all components of the ever really learn how to capture the process.” the work in other directions. “These tools research, from e-mails to conference chatter

RECORD OF ACHIEVEMENT A glossary of electronic notebooks

There are many ways to build a twenty-first- ●●Workflow software Platforms such as R and progress and then share it with others. For century electronic notebook — and to make IPython integrate all the pieces of research into example, a site called OpenWetWare allows work accessible to others. a single system. They capture data collection researchers to build a notebook wiki. and analyses in near real time and these can ●●Electronic notebook (open or closed) then be shared with colleagues for review or ●●Living paper A term coined by researchers A digital version of the conventional collaboration simply by clicking a button. to describe the concept of archiving the paper lab notebook in which the entire entire scientific process, from phone calls scientific process can be captured. Unlike ●●Wiki Web tools that serve as platforms for and Twitter conversations to methods and conventional notebooks, which are difficult electronic notebooks. Wikipedia, the online analysis, in a way that is openly accessible. for others to access, electronic notebooks encyclopaedia, is one example of a wiki. A It allows other researchers to view the steps make it easier for researchers to organize, wiki can be made accessible and modifiable leading up to the final products and even manage and share the many components of by others. Many researchers who practice to build on or derive ideas from the original their work. open science use wikis to record their work. A.M.

GRANTS TAMING THE WORKFLOW Gender differences The open-access platform IPython Women are less successful than men in getting grants from Research Councils In 2001, as a final-year PhD student working in the fields of biology, physics UK (RCUK), according to an 11 March in theoretical physics, Fernando Perez and neuroscience. It functions like a report from the umbrella body for the UK started on a side project. For his word processor, with normal text and government’s research councils. RCUK’s research on quantum field theory, he formatting, but also enables users to first such analysis compared the annual needed to bring together his hotchpotch insert programming language and rich success rate during 2010–13 of grant of computer code and data-analysis graphics and data analyses, and easily go applications from women and men in tools. Using a programming language back and forth between them. “It’s like eight age groups. Across all age and grant called Python, he created IPython having a very powerful calculator in the categories, women averaged a 25% success (ipython.org), an open-source, integrated middle of your word processor that can rate, compared with men’s 29%. Iain platform that allowed him to type code, do anything programming language can Cameron, head of research careers and run his analyses, plot and visualize his do,” says Perez. diversity at RCUK, says that the reason for data and add rich graphics within a Researchers have even begun to women’s lower success is not clear. One single system. publish papers directly from IPython, council is launching unconscious-bias “When I started working on IPython says Perez. The University of California, training for peer reviewers, and RCUK I told myself and my adviser that this Berkeley, offers courses in IPython, and may do a follow-up analysis. “The point of was just going to be an afternoon hack Harvard University and the Massachusetts publishing these data is to expose them,” and that I would get back to ‘real work’ Institute of Technology in Cambridge, and Cameron says. very soon,” he says. Some 13 years later, Columbia University in New York, among Perez is a computational scientist at the others, have adopted it. Brain Imaging Center at the University The National Center for Ecological MOBILITY of California, Berkeley, and he develops Analysis and Synthesis at the University IPython for computational science, of California, Santa Barbara, runs Swiss frozen out publication and education across domain workshops on collaborative synthesis and Early-career researchers in Switzerland disciplines as his full-time job. data-sharing for graduate students and will have limited access to the Erasmus In 2011, he, along with collaborator postdocs. And short, on-site workshops Plus student-exchange programme and Brian Granger at California Polytechnic by a worldwide volunteer group called other European research funds for the State University in San Luis Obispo and Software Carpentry offer hands-on next academic year. Switzerland lost its their colleagues, added in a web-enabled training in Python, R, GitHub and other status as an Erasmus Plus programme notebook, which has been rapidly data-synthesis programs at various country after it voted to impose quotas on adopted by computational scientists locations. A.M. immigrants from European Union (EU) countries that restrict the free movement of people from Croatia, the newest EU on Twitter, and links them together in an popularity and if that happens, the record member. The change means that Swiss openly accessible, easily updatable, digital can languish unseen, or potentially even nationals who wish to study in the EU will workflow. “A living paper is alive in that be lost. FriendFeed, for example, a hybrid no longer be eligible for Erasmus grants it gets updated and it reflects the ongoing between Twitter and Facebook, had a healthy and that students from eligible countries process,” says Boettiger. It allows scientists researcher following in 2010 but now has will not be able to obtain an Erasmus to document their entire scientific process, substantially fewer users. Phillip Lord, a bio- grant to study in Switzerland. Erasmus which they — and whomever they choose informatician and a collaborator of Andras, funds around 7,000 exchanges a year to share it with — can add to and derive new says that for security he archives digital files between Switzerland and other countries. ideas from, says Matthew Jones, an expert in through both archive.org, a general web informatics at the National Center for Eco- repository, and an initiative at the British logical Analysis and Synthesis at the Univer- Library in London. Archiving services act as SALARIES sity of California, Santa Barbara. networks of libraries, storing data in multiple places to ensure that if one copy were lost or Public boost PRESERVED FOR POSTERITY destroyed, it could be retrieved elsewhere. Pay rises were slightly higher for faculty All these records must be stored, and archiv- Such challenges make it difficult to main- members at US public institutions (2.2%) ing not only data and computations, but also tain electronic and open notebooks — but than at private institutions (2.0%) for the intellectual discussions, presents challenges. they are unlikely to stop their increasing first time since 2009, finds the College Boettiger links his Twitter feed to his open adoption. “We’re moving away from the and University Professional Association notebook, and generates a running online science that we can document with a pen and for Human Resources (CUPA-HR) tab of his reading and notes through the paper to the science that we do in six different in Knoxville, Tennessee. The change Mendeley reference manager. “Our lit- venues on instruments and with GPSs and suggests an overall strengthening of erature has expanded so rapidly that other laptops and paper and pen,” says Strasser. state economies, says Andy Brantley, people are often our best sources of being “How do we capture that? It’s super hard.” CUPA-HR president. CUPA-HR’s poll able to figure out what to read,” he says. Even so, the advantages are hard to ignore. of 792 institutions and 180,000 faculty Peter Andras, a computer scientist at New- “The days of paper lab books,” Lord says, “are members also showed that compensation castle University, UK, also logs his reading well past their best.” ■ for tenure-track and tenured faculty through Mendeley and encourages his stu- members across both university categories dents to do the same. Amanda Mascarelli is a freelance writer rose by an average of 2.1% this academic But web-based resources often decline in based in Denver, Colorado. year, the same increase as the year before.