OpenWetWare:PLoS community page

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Revision as of 15:00, 17 October 2007 by Reshma P. Shetty (Talk | contribs)
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See Jason and Sri's version

See Reshma and Austin's previous version

Article

In the face of expensive printing and distribution costs, scientists and publishers built the current publication system to optimize the exchange of the most critical information among researchers: results. Communities were established to celebrate sound and notable results. The peer-review system was developed to evaluate results. And infrastructure was built to distribute journals of results to scientists around the world. The success of the current system is reflected in the health of the scientific community today. However, given the dramatic decline in publishing costs with the advent of the internet, this focus on sharing primarily research products rather than the entire research process makes less sense. For example, information regarding protocol development, equipment operation, raw data and new research directions is not shared in a broad or timely way. The consequences of not sharing such information slow the pace of science, create barriers of entry to researchers coming from different fields, reduce collaboration and inhibit the replication of results. OpenWetWare is an experiment to establish a new ecosystem (infrastructure, process and community) that fosters information sharing throughout the research process in biology and biological engineering.

Need to rework below some.

Infrastructure

OpenWetWare (http://openwetware.org) is a website that uses the same wiki software that runs Wikipedia. It is our first attempt at providing the necessary infrastructure to capture and share biological knowledge as it is generated. The wiki allows for instantaneous distribution of information with few constraints on format or structure. Simple, quick and easy-to-use mechanisms for sharing information are essential if we expect scientists to share the many details underlying the research process. The flexible wiki format has proven effective at accommodating the breadth of information communicated by scientists (see box 1).

Process

The existing process for communicating results involves manuscript writing, peer review and evaluations by journal editors and reviewers to establish importance. We expect a very different process to support the exchange of information throughout research projects. Formal peer review will be less critical as information will be judged by its immediate usefulness and repeatability. It will be more important to provide mechanisms for providing feedback on shared information than to provide peer review pre-publication. We are also attempting to embed information capture in the research process by supporting electronic lab notebooks and online protocol collections. Authors currently omit much of the information generated during research, such as alternative hypotheses, failed experiments, protocol details and raw data, simply because it wasn’t captured in a form that is amenable to easy distribution.

  • Reshma 13:32, 16 October 2007 (CDT): I think this is ambiguous right now. By process, are we talking about the process of sharing or the process of research (and embedding sharing in it)? Should we rename this from process or processes to something else?

Need to rework above some.

Community

The current publication system is not based on infrastructure and process alone. It only works because the scientific community ties career rewards (promotion, grant support, awards etc.) to dissemination of research results via the current publishing system. Similarly, OpenWetWare's success to date is not a result of the wiki alone but of the OpenWetWare communities that encourage and value information sharing throughout the research process. We find that users often post information on OpenWetWare not because they wish to publish it for strangers to see but because they want to share it with their lab members. By sharing this information openly, they often receive unintended benefits like additional feedback and new collaborations. Thus, OpenWetWare has helped to foster the growth of these communities by encouraging global publication of local sharing. To date there are few communities that value the dissemination of information about the research process itself; however, the success of OpenWetWare suggests that we can grow new communities that celebrate the sharing of this information.

Today 3200 researchers representing over 100 laboratories around the world contribute to OpenWetWare in a variety of ways (see box 1). Two salient features of contributions to OpenWetWare point to its uniqueness. First, the breadth of content on OpenWetWare highlights information sources that are not well represented anywhere else. For example, information on operating common laboratory equipment, new research ideas or the details of protocols that led to the latest research results are rarely disseminated widely. Second, the depth of information sources on OpenWetWare is also unlike that found elsewhere. For example, there are several examples of detailed laboratory notebooks. In particular, teams of undergraduates participating in the international Genetically Engineered Machines competition (http://igem.org) like the 2006 team from Imperial College London used OpenWetWare daily to document and coordinate their research project.

Challenges for the future

Moving forward, many challenges remain. To what extent can we address competitive concerns of publishing information early, without undercutting the very idea of getting information in the open? Are their explicit reward structures that we can incorporate into such systems that will encourage the sharing of such tacit knowledge? Can we continue to take advantage of the software tools to make information contribution even easier? How do we ensure that researchers can quickly find the information that is relevant to them, particularly as we relax the filters provided by traditional peer-review publications?

The OpenWetWare Steering Committee, a volunteer group of OpenWetWare users, is charged with addressing such questions on the site. We invite all researchers in biology and biological engineering to join the OpenWetWare community and help to establish a new norm of sharing. To begin contributing, please visit http://openwetware.org/wiki/Join and request an account.

Acknowledgments

OpenWetWare's past and continued success is entirely due to the efforts and passion of the entire OpenWetWare community. We thank them for their invaluable ideas, contributions and support.

Funding. The authors acknowledge funding from the U.S. National Science Foundation Biological Databases and Informatics program award 0640709 to Drew Endy, Department of Biological Engineering, MIT.

Box 1

Needs to be shortened!

Lab webpages

A lab's webpage ideally communicates the ongoing research of the lab to the outside world. In reality, maintaining a lab's webpage usually falls to one person and the content quickly goes stale. OpenWetWare provides labs with an easy way of generating a "normal" non-wiki lab webpage from the wiki. This permits all lab members to easily edit the lab's webpage, improving the chances that the webpage reflects the current lab research.

Protocols

Detailed experimental protocols are critical for reproducing results. Yet with journal space limitations, materials and methods sections are often the first to get shortened. In addition, scientists do not publish failed protocols or the process by which a particular protocol was decided upon. This information are both important for understanding the scientific process. By providing a low barrier to not only posting finished protocols but also protocols in development and discussions about protocols, OpenWetWare captures knowledge that would otherwise never be shared or digitized.

Lab notebooks

The lab notebook is the most detailed record of what a researcher does and what they learn. Therefore, the lab notebook is central to capturing knowledge from the research process. Rather than allowing information to languish in paper lab notebooks, we encourage users to document their work digitally online so that the work is computer searchable. OpenWetWare-based lab notebooks have gained the most traction with the teams of undergraduate students participating in the international Genetically Engineered Machines (iGEM) competition [1]. For example, the 2007 Imperial College London iGEM used OpenWetWare to describe their work as they were doing the research. This information included their brainstorming session, their chosen team projects, their daily lab notebooks, their cloned DNA constructs, modeling results and more [2]. The Imperial team's notebook is a complete, digital, online record of their research project complete with timestamps and author attribution. It is a model for how sharing research and digitization of biological knowledge should work.

Courses

MIT has published virtually all of its course materials online via OpenCourseWare. Inspired by OpenCourseWare's example, we have also encouraged professors to host their courses on OpenWetWare. OpenCourseWare is similar to a journal article in representing a final published version whereas OpenWetWare provides a place for pre-publication and constantly updated content. For example, MIT's Department of Biological Engineering runs its introductory lab techniques course on OpenWetWare [3]. All background material, protocols and homework assignments are posted on OpenWetWare. As students follow the protocols in lab, they can correct any errors or points of confusion in the lab manual. They can also post their results online to share with their classmates. Running the course on OpenWetWare engages the students more directly in the course and increases the communication between instructors and students.

Collaboration

The wiki has proven to be an excellent platform for collaboration, whether it be between instructors and students, students and advisors, researchers in the same lab, or groups physically far apart. Articles, such as this one, can be written collaboratively on the wiki [4]. Brainstorming ideas and discussions work especially well. For example, the top hit on google for "science 2.0" is a discussion page on OpenWetWare [5].

Initiatives in development

We have several projects in development to further lower the technical barriers to sharing research. We have launched an initiative to compose review articles on OpenWetWare [6]. Wiki-based reviews should enable communities to collaboratively summarize and document the latest work in their field. For an example, see the review on directed evolution [7]. We are also piloting the introduction of OpenWetWare blogs for those who prefer a more diary-like interface for expressing their work [8]. Finally, we are also working on developing curated consensus protocols [9].


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