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=Figure=
See [http://openwetware.org/index.php?title=OpenWetWare:PLoS_community_page&oldid=158761 Jason and Sri's version]
{{:OpenWetWare:Scientific Pipeline}}


Caption: OpenWetWare fills current communication gaps in the scientific pipeline. Existing communication outlets focus on publication whereas OpenWetWare fills both the pre-publication and post-publication needs of scientists. Specific example pages from OpenWetWare are given (normal font, pages can be found at http://openwetware.org/wiki/XXX). For a complete listing of links, please see XXX page on OpenWetWare.
See [http://openwetware.org/index.php?title=OpenWetWare:PLoS_community_page&oldid=155377 Reshma and Austin's previous version]
 
Either the use of the word 'we' should be made clear, or we should use the words 'OWW users' --SK


=Article=
=Article=
In the face of expensive printing and distribution costs, scientists and publishers established the current publication system to exchange the most critical information among researchers; namely research results.  The publishers built the infrastructure to print and publicize scientific results important to the scientific community.  In conjunction, the scientific community developed a set of norms around using the peer review system to assess the validity, novelty and importance of scientific findings and merit.  While success of the current system is reflected in the health of the scientific community today, new technologies allow us to reevaluate the process of sharing scientific information.  One flaw of the current peer-review publication system is that much of the information that is required and/or generated in the research process, such as protocols, failed experiments, and informational sources, is not currently communicated in a broad or timely manner. Not sharing such information slows the pace of science, creates barriers of entry to researchers coming from different fields, reduces collaboration, and inhibits the replication of results.  OpenWetWare is an experiment to establish a new venue for sharing information throughout the research process in biology and biological engineering.  We are focused both on developing new software tools to facilitate sharing and fostering research communities that value dissemination of work from project conception to final publication.


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.
===Infrastructure===
Based on the same wiki software used by Wikipedia, OpenWetWare (http://openwetware.org) 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).


==Problems with the current publication system==
===Community===
The current publication system is not based on infrastructure 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 communities on OpenWetWare 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 other lab members.  Yet 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 only a 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.


There currently exist huge inefficiencies in the process of dissemination of research.  Here we descrbe a few of the problems with the current publication system that OpenWetWare seeks to address.
'''[[Sri Kosuri]] ([[User talk:Skosuri|talk]])''': Something that needs to be added to the above paragraph is talk about why the work here doesn't necessarily have to be peer-reviewed to succeed (i.e., reproducibility and user trust may be more important) & and in relieving that requirement, you get different types of information


===Journal articles fail to capture much of the information generated during the research process.===
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, resources like instructions on operating common laboratory equipment [http://openwetware.org/wiki/Endy:Victor3_plate_reader], lists of ''Escherichia coli'' strain genotype information [http://openwetware.org/wiki/E._coli_genotypes] and a how-to on searching the literature [http://openwetware.org/wiki/Searching_the_literature] are rarely disseminated widely online. Second, the depth of content on OpenWetWare is also unlike that found elsewhere.  For example, there are several examples of detailed laboratory notebooks. In particular, several teams of undergraduates participating in the international Genetically Engineered Machines competition (http://igem.org) used OpenWetWare daily to document and coordinate their research project.  By embedding digital information capture in the research process itself, much information that would normally be lost like alternative hypotheses, failed experiments, protocol details and raw data was preserved in way that is amenable to distribution and reuse.


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. These gaps in published information creates barriers for other researchers to replicate a result. Even within a lab, there exists the challenge of maintaining knowledge as people leave and enter the group.
===Challenges moving forward===
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?


===Information sharing in research is slow and limited.===
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.


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.
===Acknowledgments===


==OpenWetWare's solution==
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. 


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 a platform for capturing and sharing biological knowledge ''as it is generated''. As seen by the success of Wikipedia, wikis offer a simple, collaborative, and online editing environment. We are always seeking new tools and technologies to make open sharing of research easier. To further promote sharing and reuse of the information on OpenWetWare, all content is freely reusable (as long as it is properly referenced) under a Creative Commons license.
'''Funding.''' Funding for OpenWetWare has come awards from the U.S. National Science Foundation Biological Databases and Informatics program award 0640709, the NIH award (get number) to DE/PS, and a MIT/Microsoft iCampus grant awarded to JK.  Also would to specifically thank those users who commented on the wiki version of this document[ref].


Our experience with OpenWetWare 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.
=Box 1=
<font color=green>Needs to be shortened!</font>. I dropped direct misgivings of the current system.  I also think information sources should be added to this list, and I'm not exactly sure if courses fits here as a whole section (as we don't talk about it anywhere else). '''[[Sri Kosuri]] ([[User talk:Skosuri|talk]])'''


===Lab webpages===
===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.
Current information about laboratory members and their research directions provides colleagues increased opportunity for synergy and collaboraiton. OpenWetWare provides labs with an easy, decentralized way of generating a non-wiki laboratory webpages from the wiki. (links?)


===Protocols===
===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, 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.  
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. OpenWetWare provides an easy way to post not only finished protocols but also protocols in development and discussions on protocols [http://openwetware.org/wiki/DNA_ligation].


===Lab notebooks===
===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.
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.  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://igem.org). 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 team's notebook is a complete, digital, online record of their research project complete with timestamps and author attribution.


===Courses===
===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.
MIT has published virtually all of its course materials online via OpenCourseWare [http://ocw.mit.edu]. Inspired by OpenCourseWare's example, we have also encouraged professors to host their courses on OpenWetWare. 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.  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===
===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].
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. One early and best described example are the activities of the Synthetic Biology community on OpenWetWare. Describe.


===Initiatives in development===
===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].
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].
 
==Challenges for the future==
 
We have encountered researchers with reservations regarding the site. Here we outline some of the most common concerns. 
 
#Some are concerned about vandalism of their postings. To address this issue, every edit on OpenWetWare is attributable to an individual with their full publication name. Moreover, OpenWetWare offers several mechanisms to easily track changes made to pages of interest.
#Some researchers value the barriers of the traditional publication process as a convenient means to limit the flow of extraneous and potentially unreliable information. However, we feel that search technology will improve as the digitally available commons of biological knowledge grows. The first step is to make sure scientific information is digitized rather than be lost forever. Just as researchers develop new tools to mine information from the wealth of genomic data, researchers are developing tools to mine information from the web.
#Some scientists have a resistance to posting research progress and topics prior to their publication due to fear of being 'scooped'. This concern derives from academic community norms in which researchers only receive credit upon publication of the final research article. We hope to change these norms by demonstrating that sharing information about research in progress is far more likely to lead to collaboration than to competition.
 
Although OpenWetWare has been very successful to date, there is still much to be done to advance the open sharing of research in biological science and engineering.  In particular, until the open sharing of research is recognized in the traditional reward structure in science, initiatives like OpenWetWare will remain on the fringes of most fields.  We need to construct a publishing pipeline in which sharing and digitization is integral to the process of research: from project conception to final publication.  Researchers need to "receive credit" when they make their protocols, datasets, model files etc. freely available to others.  We consider this to be a critical but long-term goal of OpenWetWare.  There needs to be a means to go from documented research project on OpenWetWare to a peer-reviewed journal publication. Constructing this complete pipeline is a key step in promoting the open sharing of research.
 
In just over two years since OpenWetWare's inception and relying primarily on word of mouth advertising, the site has over 3200 registered contributors and more than 100 academic labs from around the world. We invite all researchers in biology and biological engineering to join the OpenWetWare community.  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.


__NOTOC__
__NOTOC__

Latest revision as of 08:53, 19 October 2007

See Jason and Sri's version

See Reshma and Austin's previous version

Either the use of the word 'we' should be made clear, or we should use the words 'OWW users' --SK

Article

In the face of expensive printing and distribution costs, scientists and publishers established the current publication system to exchange the most critical information among researchers; namely research results. The publishers built the infrastructure to print and publicize scientific results important to the scientific community. In conjunction, the scientific community developed a set of norms around using the peer review system to assess the validity, novelty and importance of scientific findings and merit. While success of the current system is reflected in the health of the scientific community today, new technologies allow us to reevaluate the process of sharing scientific information. One flaw of the current peer-review publication system is that much of the information that is required and/or generated in the research process, such as protocols, failed experiments, and informational sources, is not currently communicated in a broad or timely manner. Not sharing such information slows the pace of science, creates barriers of entry to researchers coming from different fields, reduces collaboration, and inhibits the replication of results. OpenWetWare is an experiment to establish a new venue for sharing information throughout the research process in biology and biological engineering. We are focused both on developing new software tools to facilitate sharing and fostering research communities that value dissemination of work from project conception to final publication.

Infrastructure

Based on the same wiki software used by Wikipedia, OpenWetWare (http://openwetware.org) 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).

Community

The current publication system is not based on infrastructure 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 communities on OpenWetWare 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 other lab members. Yet 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 only a 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.

Sri Kosuri (talk): Something that needs to be added to the above paragraph is talk about why the work here doesn't necessarily have to be peer-reviewed to succeed (i.e., reproducibility and user trust may be more important) & and in relieving that requirement, you get different types of 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, resources like instructions on operating common laboratory equipment [1], lists of Escherichia coli strain genotype information [2] and a how-to on searching the literature [3] are rarely disseminated widely online. Second, the depth of content on OpenWetWare is also unlike that found elsewhere. For example, there are several examples of detailed laboratory notebooks. In particular, several teams of undergraduates participating in the international Genetically Engineered Machines competition (http://igem.org) used OpenWetWare daily to document and coordinate their research project. By embedding digital information capture in the research process itself, much information that would normally be lost like alternative hypotheses, failed experiments, protocol details and raw data was preserved in way that is amenable to distribution and reuse.

Challenges moving forward

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. Funding for OpenWetWare has come awards from the U.S. National Science Foundation Biological Databases and Informatics program award 0640709, the NIH award (get number) to DE/PS, and a MIT/Microsoft iCampus grant awarded to JK. Also would to specifically thank those users who commented on the wiki version of this document[ref].

Box 1

Needs to be shortened!. I dropped direct misgivings of the current system. I also think information sources should be added to this list, and I'm not exactly sure if courses fits here as a whole section (as we don't talk about it anywhere else). Sri Kosuri (talk)

Lab webpages

Current information about laboratory members and their research directions provides colleagues increased opportunity for synergy and collaboraiton. OpenWetWare provides labs with an easy, decentralized way of generating a non-wiki laboratory webpages from the wiki. (links?)

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. OpenWetWare provides an easy way to post not only finished protocols but also protocols in development and discussions on protocols [4].

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. 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://igem.org). 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 [5]. The team's notebook is a complete, digital, online record of their research project complete with timestamps and author attribution.

Courses

MIT has published virtually all of its course materials online via OpenCourseWare [6]. Inspired by OpenCourseWare's example, we have also encouraged professors to host their courses on OpenWetWare. For example, MIT's Department of Biological Engineering runs its introductory lab techniques course on OpenWetWare [7]. All background material, protocols and homework assignments are posted. 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. One early and best described example are the activities of the Synthetic Biology community on OpenWetWare. Describe.

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 [8]. 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 [9]. We are also piloting the introduction of OpenWetWare blogs for those who prefer a more diary-like interface for expressing their work [10]. Finally, we are also working on developing curated consensus protocols [11].


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