OpenWetWare:PLoS community page: Difference between revisions
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See [http://openwetware.org/index.php?title=OpenWetWare:PLoS_community_page&oldid=155377 Reshma and Austin's previous version] | 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 | 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=== | ===Infrastructure=== | ||
OpenWetWare (http://openwetware.org) | 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 | 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]] ([[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 | |||
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. | |||
===Challenges | ===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? | 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? | ||
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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'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.''' 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= | =Box 1= | ||
<font color=green>Needs to be shortened!</font> | <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=== | ||
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. | 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. | 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. | 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. | 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=== | ||
Latest revision as of 08:53, 19 October 2007
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].
