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

CAREERS GRANTS Success rate for UK government SALARIES Faculty pay up more at US public NATUREJOBS For the latest career funding is lower for women p.525 universities than at private p.525 listings and advice www.naturejobs.com SERGEV NIVENS/SHUTTERSTOCK 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 27 MARCH 2014 | VOL 507 | NATURE | 523 © 2014 Macmillan Publishers Limited. All rights reserved CAREERS 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.

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