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 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.

OpenWetWare

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.

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 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.
2. 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.
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. 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.

add stats on latest site traffic

Using OpenWetWare

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.

Lab webpages

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

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)

Courses

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

In biological research, the lab notebook is the most detailed record of what a researcher does and what they learn in their work. Therefore, any effort to capture more knowledge from the research process must foster sharing of the lab notebook. Rather than allowing information to languish in paper lab notebooks, OpenWetWare encourages users to document their work digitally online so that the work is searchable and browsable. OpenWetWare-based lab notebooks have gained the most traction with teams of undergraduate students participating in the international Genetically Engineered Machines (iGEM) competition. iGEM teams spend a summer specifying, building and testing a synthetic biological system of their own des Many teams in the competition opt to document their entire projects on OpenWetWare. For example, the 2007 Imperial College, London iGEM team includes their brainstorming session, describes their chosen team projects, keeps their daily lab notebooks, lists their DNA constructs, documents their protocols and more. It is a complete, digital, online record of their research project.

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