OpenWetWare:PLoS community page: Difference between revisions

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(trying a new version that merges the AC/RS and JK/SK versions; work in progress)
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<font color=red>This is the Jason and Sri version.  Needs box 1.</font>
See [http://openwetware.org/index.php?title=OpenWetWare:PLoS_community_page&oldid=158761 Jason and Sri's version]


In the face of expensive publishing and distribution costs, scientists and publishers built the current peer-reviewed publication ecosystem to optimize the exchange of the most critical information among researchers: results. Communities were established that celebrated good results, peer-review processes were developed to evaluate results, and infrastructure was built to distribute journals of results to scientists around the world. The success of this system is reflected in the health of the scientific community today, however a significant flaw in the system is the amount of tacit knowledge and pre-publication research activities that remain unshared in any broad or timely way.  For example, information regarding laboratory protocols, equipment operation, current research directions, etc., remains generally unavailable.  The consequences of not sharing such information impinge on the pace of science, creating barriers of entry to researchers coming from different fields, reducing collaboration, and preventing the replication of results.  OpenWetWare is an experiment to establish a new ecosystem (infrastructure, processes, and community) that fosters the sharing of this tacit knowledge and pre-publication materials within biology and biological engineering. 
See [http://openwetware.org/index.php?title=OpenWetWare:PLoS_community_page&oldid=155377 Reshma and Austin's previous version]


===Infrastructure===
=Article=
Openwetware.org is a website based on the same wiki software that runs Wikipedia, and is our first attempt at providing the necessary infrastructure to capture and share tacit information between scientists.  The wiki allows for instantaneous distribution of information with few constraints on the publication format.  Simple, fast mechanisms for sharing information are essential if we expect scientists to share the many details underlying the research process.  The flexible format has proven effective at accommodating the breath of information communicated by scientists (see box 1).


===Processes===
OpenWetWare (http://openwetware.org) is an effort to facilitate the open communication of scientific information including methods, results, educational materials, discussions and publications. In research, the traditional mechanisms for sharing work are reference books, journal papers, personal communications via conferences and invited talks. OpenWetWare seeks to address limitations in these communication methods, by decentralizing and lowering the barriers to information exchange among all researchers, be they professors, students or research scientists. In addition, the goal is to foster a culture in which researchers openly share their experiences thereby reducing needless duplication of effort and increasing the pace of scientific discovery and technology development.
The existing processes for communicating results involve writing manuscripts, peer reviewing, and editorial decisions by journals to establish importance. We expect very different processes to support the exchange of information about the research process outside of the publication of results.  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 published 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.


===Community===
==Problems with the current publication system==
The peer-review system for distributing results is not based on infrastructure and processes alone – it rests on a foundation of career rewards that value results dissemination and general community norms of scholarship.  Likewise, OpenWetWare’s success thus-far is not a result of the wiki alone, but of the various individual communities that encourage and support the exchange of tacit knowledge.  We have helped foster the growth of these communities by encouraging global publication of local sharing.  OpenWetWare members often publish information primarily for it to be viewed by members of their lab, however by sharing this information openly they often receive unintended benefits (feedback, recruitment, new collaborations, etc).  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 OWW highlight information sources that are not well represented anywhere else.  For example, information on operating common laboratory equipment or the genotypes of common laboratory E. coli strians are often written down, but are rarely disseminated widely.  Second, the depth of information sources on OWW is also unlike that found elsewhere.  For example, there are several examples of detailed laboratory notebooks. [I think we can be more specific here; as in the AC/RS version].
There currently exist huge inefficiencies in the process of dissemination of research.  Here we describe a few of the problems with the current publication system that OpenWetWare seeks to address.


===Journal articles fail to capture much of the information generated during the research process.===
Journal articles are the most common way that researchers disseminate their work. Yet these articles are only written once a project is near completion and are, by necessity, limited in length. As a result, authors omit much of the information generated during research, such as alternative hypotheses, failed experiments, protocol details and raw data. Either these details are forgotten during the writing process or there is no space for them in the final article. Hence, much of the knowledge from a research project never finds its way into a formal publication medium and is easily lost forever.  Instead, this work remains buried in lab notebooks or is passed on as collective wisdom between successive generations of students in a lab. Even within a lab, there exists the challenge of maintaining knowledge as people leave and enter the group. These gaps in published information creates barriers for other researchers to replicate a result.
===Information sharing in research is slow and limited.===
The lag time from final experimental result to appearance online of the finished publication can easily be months or years. Personal communications are faster at spreading results than publications. However, they are inefficient at disseminating information widely and fail to take advantage of the democratic and decentralized forms of communication made possible by the Internet. For many students and research scientists below the principal investigator level, there are scarce opportunities to discuss their work with a broad audience.  Because of time constraints, a principal investigator necessarily cannot discuss the results of every lab member during talks and personal interactions. As a result, information is shared inefficiently and many potential opportunities for collaboration are lost.
==OpenWetWare's solution==
OpenWetWare provides efficient means for researchers to disseminate information about every piece of data generated during the research process in more detail and much quicker than traditional communication methods. We seek to embed open sharing in the research process by making it easier for researchers to do the things they already do. OpenWetWare uses a wiki as the primary platform for capturing and sharing biological knowledge ''as it is generated''. To promote sharing and reuse of information, all content is freely reusable under a Creative Commons license. Our experience with the simple, collaborative, and online editing environment provided by wikis has been overwhelmingly positive. The flexibility of a wiki allows individuals and labs to use it however works best for them. A sampling of ways in which researchers are making use of OpenWetWare is discussed below and additional examples are listed in Table 1.
==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?
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 you to join the OpenWetWare community and help us establish a new ecosystem for sharing knowledge in biology.
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==
==Acknowledgments==
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'''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.
'''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=
===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 [http://igem2007.com]. 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 [http://openwetware.org/wiki/IGEM:IMPERIAL/2007]. 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 [http://openwetware.org/wiki/20.109%28F07%29].  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 [http://openwetware.org/wiki/OpenWetWare:PLoS_community_page]. Brainstorming ideas and discussions work especially well. For example, the top hit on google for "science 2.0" is a discussion page on OpenWetWare [http://openwetware.org/wiki/Science_2.0/Brainstorming].
===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 [http://reviews.openwetware.org].  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 [http://openwetware.org/wiki/Reviews:Directed_evolution/Library_construction]. We are also piloting the introduction of OpenWetWare blogs for those who prefer a more diary-like interface for expressing their work [http://blogs.openwetware.org/]. Finally, we are also working on developing curated consensus protocols [http://openwetware.org/wiki/DNA_Ligation].


__NOTOC__
__NOTOC__

Revision as of 09:05, 16 October 2007

See Jason and Sri's version

See Reshma and Austin's previous version

Article

OpenWetWare (http://openwetware.org) is an effort to facilitate the open communication of scientific information including methods, results, educational materials, discussions and publications. In research, the traditional mechanisms for sharing work are reference books, journal papers, personal communications via conferences and invited talks. OpenWetWare seeks to address limitations in these communication methods, by decentralizing and lowering the barriers to information exchange among all researchers, be they professors, students or research scientists. In addition, the goal is to foster a culture in which researchers openly share their experiences thereby reducing needless duplication of effort and increasing the pace of scientific discovery and technology development.

Problems with the current publication system

There currently exist huge inefficiencies in the process of dissemination of research. Here we describe a few of the problems with the current publication system that OpenWetWare seeks to address.

Journal articles fail to capture much of the information generated during the research process.

Journal articles are the most common way that researchers disseminate their work. Yet these articles are only written once a project is near completion and are, by necessity, limited in length. As a result, authors omit much of the information generated during research, such as alternative hypotheses, failed experiments, protocol details and raw data. Either these details are forgotten during the writing process or there is no space for them in the final article. Hence, much of the knowledge from a research project never finds its way into a formal publication medium and is easily lost forever. Instead, this work remains buried in lab notebooks or is passed on as collective wisdom between successive generations of students in a lab. Even within a lab, there exists the challenge of maintaining knowledge as people leave and enter the group. These gaps in published information creates barriers for other researchers to replicate a result.

Information sharing in research is slow and limited.

The lag time from final experimental result to appearance online of the finished publication can easily be months or years. Personal communications are faster at spreading results than publications. However, they are inefficient at disseminating information widely and fail to take advantage of the democratic and decentralized forms of communication made possible by the Internet. For many students and research scientists below the principal investigator level, there are scarce opportunities to discuss their work with a broad audience. Because of time constraints, a principal investigator necessarily cannot discuss the results of every lab member during talks and personal interactions. As a result, information is shared inefficiently and many potential opportunities for collaboration are lost.

OpenWetWare's solution

OpenWetWare provides efficient means for researchers to disseminate information about every piece of data generated during the research process in more detail and much quicker than traditional communication methods. We seek to embed open sharing in the research process by making it easier for researchers to do the things they already do. OpenWetWare uses a wiki as the primary platform for capturing and sharing biological knowledge as it is generated. To promote sharing and reuse of information, all content is freely reusable under a Creative Commons license. Our experience with the simple, collaborative, and online editing environment provided by wikis has been overwhelmingly positive. The flexibility of a wiki allows individuals and labs to use it however works best for them. A sampling of ways in which researchers are making use of OpenWetWare is discussed below and additional examples are listed in Table 1.

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

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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