OpenWetWare:PLoS community page

Overall thesis statement

OpenWetware facilitates the open communication of scientific information.

Intro

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.

Problems with the traditional publishing system

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.

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 mechanisms 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 growing. 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.

OpenWetWare

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

1. Lower the technical barriers to sharing and dissemination of knowledge in biological research.
   • 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 seen by the tremendous success of Wikipedia (the online encyclopedia that anyone can edit), the wiki's collaborative, online editing environment offers a great platform for capturing and sharing biological knowledge as it is generated. We are always seeking new tools and technologies that make this open sharing of research easier.
2. Foster a community of researchers in biology and biological engineering that values and celebrates the open sharing of information.
   • Peer review is a fundamental part of biological research. We use it to assess papers for publication, talks to be presented at conferences, grant proposals for funding and job hiring and promotion. Thus, an important step in promoting the open sharing of research is building a community that recognizes and values that sharing.
3. 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.

Although OpenWetWare is just over two years old, we've had a tremendous success to date. OpenWetWare has over 3000 registered contributors, 100 academic labs and approximately 200 protocols. For such common search terms as "beta galactosidase", "DNA ligation" and "TE buffer", OpenWetWare pages appear in the first page of Google's search results.

add something about latest site traffic

Using OpenWetWare

To get people to share information, you need to make it easier for them to do the things they already do. (This is where OWW differs from existing efforts which tend to seek ways of fundamentally changing the way people do the work.)

Also you need to embed digitization and sharing within the research process.

Delineate how OWW is different from open access and other efforts.

All content is creative commons licensed and daily dumps of the database is provided.

I am not sure we can include all of these. Would it be better to focus on a few?

Lab pages

common thing that most labs need but is annoying to do

Protocols

make it easier to share a protocol with labmates

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)

perhaps include something about authorship and usernames here? or should it be emphasized more strongly?

Courses

engage students in shaping and editing course materials.

your course materials have greater impact and are more easily reused.

Lab notebooks

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

Collaborative Writing

collaborative editing, get to see iterations of the scientific process, wiki reviews

Blogs

End this section with information on joining the site.

Future

1. Creating a publishing pipeline - embedding sharing and digitization into the research process from idea to paper
2. 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
3. user community: associate more data with all users, allow building more communities on top (nerdbook?)

Acknowledgments

• OpenWetWare community
• NSF grant