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==Overall thesis statement==
See [http://openwetware.org/index.php?title=OpenWetWare:PLoS_community_page&oldid=158761 Jason and Sri's version]
OpenWetware facilitates the open communication of scientific information.


==Intro==
See [http://openwetware.org/index.php?title=OpenWetWare:PLoS_community_page&oldid=155377 Reshma and Austin's previous version]


In the biological sciences, the primary mechanisms for sharing work have traditionally been reference books, journal papers and personal communications via conferences and invited talks.  These publication venues all have two critical problems.  First, each of these forms of publication comes at the end of a research project.  There are few means to share information during the course of the research.  As a result, much of the information generated during in research work is lost.  Second, these publication mechanisms have largely failed to take advantage of the democratic and decentralized forms of communication made possible by the Internet. OpenWetWare (http://openwetware.org) represents an initial effort to decentralize and lower the barriers to information exchange among all researchers, be they professors, students or research scientists. It seeks to help forge a culture in which researchers openly share their experiences thereby reducing needless duplication of effort and improving the quality of the work.
Either the use of the word 'we' should be made clear, or we should use the words 'OWW users' --SK


==Problems with the traditional publishing system==
=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.


The traditional publication process is slow and cumbersome.  The lag time from final experimental result to appearance online of the finished publication can easily be months or years.  Journal space limitations often mean that authors omit related but not directly relevant data and details on experimental methods.  As a result, much of the information generated during the course of a research project never finds its way into a formal publication medium.  Instead, this knowledge remains buried in lab notebooks or is passed on as collective wisdom between successive generations of students in a lab.  Consider all the information generated during a research project. Researchers formulate an initial hypothesis.  They then design a set of experiments to test the hypothesis.  While executing the experiments, they usually develop and optimize new protocols or materials.  Inevitably, they carry out many failed experiments before obtaining a good result.  Next, they analyze the resulting data and likely refine the initial hypothesis.  After several iterations through this process, the researchers may eventually publish a paper on their work.  Again, due to space limitations and the need to present a crisp message, much of the information generated during the work will never make it into the final publication.  With luck, these researchers may pass along some of what they learned to incoming members of the lab.  Yet almost all labs face the challenge of maintaining persistent knowledge across the flux of people leaving and entering the group.
===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).


That the current publication system only captures a small fraction of the knowledge generated in the research process is a significant problem in its own right. However, it also leads to a second and potentially even more serious issue.  The lack of available, detailed experimental information creates barriers to those entering biological research.  For new students, new labs or researchers from other fields, there is a steep learning curve to entering biology and biological engineering.  Often the key details needed to go from a failed experiment to a successful experiment are not available in the scientific literature.  They can only be found by talking to those actively working at the bench. For many students and research scientists below the principal investigator level, there are few opportunities to discuss their work on an ongoing basis with a broad audience.  Most conversations among researchers in the lab are restricted either to the local environment or to a handful of conferences each year.  With research in biology becoming both more interdisciplinary and more global, the need to lower the barriers to entry in biological research is intense.  Yet despite the huge inefficiencies in the research process, biology and biological engineering have largely failed to embrace the advantages offered by new publication mechanisms like wiki's, blogs and online digital archives.
===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.


==OpenWetWare==
'''[[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


OpenWetWare's mission is to support open research, education, discussion and publication in biological science and engineering.  Open science improves both the quality and pace of scientific discovery and technology development. We take three approaches to achieving this mission. 
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.


#Lower the technical barriers to sharing and dissemination of knowledge in biological research.
===Challenges moving forward===
#*Fast timescale publishing mediums that take full advantage of the web offer a great complement to slower, more traditional scientific publishing like journals and books.  OpenWetWare uses the free software wiki package MediaWiki as a platform for capturing and sharing biological knowledge ''as it is generated''.  As seen by the tremendous success of Wikipedia (the online encyclopedia that anyone can edit), wiki's offer a simple, collaborative, online editing environment.  We are always seeking new tools and technologies that make this open sharing of research easier.  More recently we have added blogs to OpenWetWare to provide another outlet for researchers to share their work.
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?
#Foster a community of researchers in biology and biological engineering that celebrates the open sharing of information.
#*Peer review is a fundamental part of biological research.  We use it to assess papers for publication, talks for conferences, grant proposals for funding and job hiring and promotion.  Thus, an important step in promoting the open sharing of research is building communities that recognize and value that sharing.  In just over two years since its inception and relying primarily on word of mouth advertising, OpenWetWare has over 3000 registered contributors and more than 100 academic labs from around the world. 
#Explore how open publication platforms like OpenWetWare can tie into existing reward structures in research.
#*Ultimately, for the open sharing and digitization of research to be standard practice in scientific research, it will need to be integrated into existing reward structures in science. 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.  As one step towards this goal, all new users on OpenWetWare are assigned a username based on their full, publication name.  Such a convention more closely aligns OpenWetWare with journals and conferences in which use of your full, real name is the norm. It also lays the foundation for contributions to OpenWetWare to be evaluated and recognized by existing academic reward structures.  As demonstration that contributions to OpenWetWare can garner a large audience, OpenWetWare's receives XXX hits per day with individual pages seeing as many as XXX views.


<font color=red>''add stats on latest site traffic''</font>
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.


===Using OpenWetWare===
===Acknowledgments===
Although the open sharing of research is a lofty goal, in practice it can be difficult to implement.  The Public Library of Science has had tremendous success in forwarding the goal of open access in publishing.  OpenWetWare's goals are aligned but somewhat different.  OpenWetWare is focused on open access to the information generated upstream of the publication process.  We seek to embed open sharing in the research process itself by making it easier for researchers to do the things they already do.  Only by integrating open sharing into the work flow can you ensure that more of knowledge is freely available.  In fact, it is important not only to share the information but also to digitize it.  Digitizing biological knowledge renders it searchable, browsable and accessible by others.  To further promote sharing and reuse of the information on OpenWetWare, all content is dual-licensed under the Creative Commons Attribution-ShareAlike 3.0 Unported license and the GNU Free Documentation License version 1.2.  Daily dumps of the entire site are also available for download.


In the following sections, we describe the different ways in which researchers are making use of OpenWetWare.
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.


====Lab webpages====
'''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].
A common task that most labs must do is host a lab webpage. Generally this task falls to one person in the lab and the webpage falls out of date over time.  OpenWetWare provides labs with an easy way of generating a "normal" non-wiki lab webpage from the OpenWetWare wiki. Although this is a simple feature having little to do with the research itself, it provides an initial incentive for labs to join OpenWetWare and start using the wiki.  It also permits all lab members to easily edit the lab webpage improving the chances that the webpage reflects the current work in the lab.


====Protocols====
=Box 1=
make it easier to share a protocol with labmates
<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]])'''


highlight popular protocols (Sean's protocols, perhaps get quote from him about how many people asked him about the protocol before he posted and how many after as rough indicator of whether people are actually using it)
===Lab webpages===


====Courses====
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?)
In 2001, MIT announced a new initiative to make all of its course materials freely available online.  Since then, MIT has published 1800 courses online encompassing virtually all of its classes.  Inspired by MIT OpenCourseWare's example, we have also encouraged professors to host their courses on OpenWetWare.  OpenWetWare offers several distinct features.  Most importantly, the collaborative editing interface of the wiki provides a new forum for students, teaching assistants and professors to interact and discuss course content.  For example, MIT's Department of Biological Engineering runs its introductory lab techniques course on OpenWetWare.  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.  Rather than passive consumers of the course materials, students are active contributors.  The built-in revision histories and the fact that every change to the wiki is attributable to an individual means that instructors can easily monitor changes to the course pages.  A somewhat unexpected benefit of hosting course content on OpenWetWare is the greater impact of the work.  Newcomers to biological research find the detailed class protocols intended for novice experimentalists very useful in their work. Also, educators at other institutions can easily draw upon the course content in their own classes (while giving proper attribution as required by the copyright license).


====Lab notebooks====
===Protocols===
coordinate group projects


save the minutiae of research in digital form for posterity, things that are usually not written down or are difficult to find later in traditional paper notebooks due to time and ease of use cost
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].


====Collaborative Writing====
===Lab notebooks===
collaborative editing, get to see iterations of the scientific process, wiki reviews


====Blogs====
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===


End this section with information on joining the site.
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.


==Future==
===Collaboration===
# Creating a publishing pipeline - embedding sharing and digitization into the research process from idea to paper
# Changing the current reward structure to promote sharing
#* if all edits are associated with a single real person and have a timestamp, you should be able to get credit for the edit/idea
# user community: associate more data with all users, allow building more communities on top (nerdbook?)


==Acknowledgments==
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.
*OpenWetWare community
 
*NSF grant
===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__

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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