OpenWetWare:PLoS community page
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| Pre-publication | → | Preprint | → | Publication | → | Post-publication | |
|---|---|---|---|---|---|---|---|
| Discussions | Science 2.0/Brainstorming | → | → | Science 2.0 | → | ||
| Lab notebooks | IGEM:IMPERIAL/2006 | → | → | "Engineering a molecular predation oscillator" in IET Synthetic Biology | → | ||
| Labs & people | Kafatos:Research Fotis C. Kafatos |
→ | → | kafatos.openwetware.org | → | ||
| Protocols | DNA ligation | → | DSpace | → | "Directional Cloning into Plasmid Vectors" in Molecular Cloning (subscription only) |
→ | Talk:DNA ligation, Protocol Online Bioforum |
| Databases | BioNumbers, Yeast Pheromone Model wiki |
→ | DSpace | → | NCBI, RCSB Protein Data Bank |
→ | E. coli genotypes, WikiProteins |
| Courses | 20.109: Laboratory Fundamentals of Biological Engineering | → | → | "20.109" on MIT OpenCourseWare | → | ||
| Articles | OpenWetWare:PLoS community page | → | (insert dspace/nature link to PLoS preprint), arXiv, DSpace Nature Precedings |
→ | (insert link to PLoS Biology article) in PLoS Biology, PLoS ONE |
→ | OpenWetWare_talk:PLoS community page, reviews.openwetware.org, Postgenomic, PLoS ONE commentary |
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).
Intro
OpenWetWare (http://openwetware.org) is an effort to facilitate the open communication of scientific information, including research, educational materials, discussions, and publications. In the sciences, the traditional mechanisms for sharing work are reference books, journal papers, and 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.
Because traditional publications come at the end of a research project, there is often a long and unnecessary lag of months to years between obtaining results and publication. Journal space limitations often lead to the omission of much of the information generated during research, such as alternative hypotheses, failed experiments, protocol details, and raw data. As a result, much of the information generated during the course of a research project never finds its way into a formal publication medium and is easily lost forever. Instead, this knowledge 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 single lab, there is the challenge of maintaining knowledge as people leave and enter the group.
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 communicated inefficiently.
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 the traditional communication methods. OpenWetWare uses a wiki as a platform for capturing and sharing biological knowledge as it is generated. As seen by the tremendous success of Wikipedia, wikis offer a simple,collaborative, and online editing environment. 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 are always seeking new tools and technologies to make open sharing of research easier. More recently, we have added blogs to OpenWetWare to provide another outlet for researchers to share their work.
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 final publication. 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
The experimental protocol is one of the most critical types of information there is in biological research. Yet in the face of journal space limitations, materials and methods sections are often the first to get shortened. This trend makes it difficult for others to reproduce published results: a cornerstone of the community research process. Although journals dedicated to methods papers exist, most researchers don't publish their protocols either because the protocol development doesn't warrant a separate publication or because the effort needed is too great. By providing a low transaction cost means of posting protocols, OpenWetWare is again capturing knowledge that would otherwise never be shared or digitized. In fact, many OpenWetWare users post protocols not because they wish to share their protocols with the world but because they want to share their protocols with people down the hall. Rather than digging out old lab notebooks and photocopying pages, they can just point their labmates to the site. For example, when Sean Moore, a member of Bob Sauer's lab at MIT posted his protocol for β-galactosidase assays, his labmate Kathleen McGinness then annotated the protocol with sample results she obtained while using it [1]. Thus, archiving protocols on OpenWetWare allows for feedback by others on how well the protocol worked. Over time, this process should give rise to a reliable, widely-used protocol set on the site.
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 the teams of undergraduate students participating in the international Genetically Engineered Machines (iGEM) competition (http://igem2007.com). Each year, iGEM teams spend a summer specifying, building and testing a synthetic biological system of their own design. 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 cloned DNA constructs, summarizes modeling results and more [2]. The easy-to-use and collaborative nature of the OpenWetWare wiki allows all the students and their advisors to stay apprised of how the work is progressing. In short, the Imperial College London iGEM team's notebook is a complete, digital, online record of their research project complete with timestamps and author attribution. It is the model for how embedding of sharing and digitization of biological knowledge in the research process should work.
Wiki reviews
Wiki's have clearly demonstrated their usefulness as a collaborative writing platform in the astounding success of Wikipedia, the online encyclopedia that anyone can edit. Wiki's can make a similar contribution to streamlining the scientific writing process. In particular, 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. Rather that periodical review articles that survey the recent literature, researchers can collaboratively update wiki reviews on an ongoing basis. For an ongoing wiki review, please see Cameron Neylon's review on directed evolution and library construction [3].
ask Cameron Neylon if article can mention his review
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 [4]. 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).
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.
Experiences to date
Our experience with OpenWetWare has been overwhelmingly positive. The flexible nature of the OpenWetWare wiki allows individuals and labs to use it as works best for them as seen by the examples above. However, we have also encountered researchers with reservations regarding the site. Most commonly, people are concerned about negative editing or vandalism of their postings. However, when they learn that every user account is attributed to an individual and that more recently, all account names are the person's full, publication name, these concerns are allayed. Moreover, OpenWetWare offers several mechanisms to easily track any changes that are made to your pages of interest. A second issue is the resistance to posting research progress and topics prior to their publication due to fear of being 'scooped'. This concern derives more from academic community norms, rather than a limitation of the technology. In fact, all posts to the site are automatically timestamped and attributed to the user potentially decreasing the likelihood that someone can really be 'scooped'. Moreover, we hope to start to change these norms by demonstrating that sharing information about research in progress is far more likely to lead to collaboration than to competition. Finally, some researchers value the barriers of the traditional publication process as a convenient means to limit the flow of extraneous and potentially unreliable information available. However, we feel that search technology will improve as the digitally available commons of biological knowledge grows. 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. Ultimately, the most useful biological information sources on the web will win out over time.
Future
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 and rewarded 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. In principles, many of the key mechanisms are in place for this to happen on 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. In addition, every update to the wiki has a timestamp and is attributable to an individual under their full publication name. Thus, in the future, it should be possible to give credit to researchers for contributions beyond papers and conferences. What we lack is a means to go from documented research project on the site to a peer-reviewed journal publication. Constructing this complete pipeline is a key step in promoting the open sharing of research.
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.
