ICampus Application for OWW/Official plain text version

QUESTIONS TO BE ANSWERED IN PRELIMINARY STUDENT PROPOSALS __________________________________________________

(1) Title for this proposal

OpenWetWare: A collaborative information tool for the biological research community __________________________________________________

(2) Name and email address of proposer

Jason Kelly (jasonk@mit.edu) __________________________________________________

(3) Project description

OpenWetWare (http://openwetware.org) is a collaborative environment designed to foster the sharing of expertise, information, and ideas among researchers in biological science and engineering. Inspired both by Wikipedia (http://www.wikipedia.org) and MIT OpenCourseWare (http://ocw.mit.edu/index.html), OpenWetWare is a wiki where content related to research laboratories can be generated and disseminated quickly and efficiently by any individual. We propose to expand the user community, develop tools to encourage contribution, and integrate content development with educational programs in the hope of creating a critical mass of users that will lead to a self-sustaining resource for the biological community. __________________________________________________

(4) Significance We designed OpenWetWare to address two problems that we, as students entering the field of biology, have had to struggle with:

1. Information resources are often incomplete, difficult to search, and out of date. This problem is exemplified by the absence of experimental details that are typically only communicated as "lore" passed between members in individual research labs.

2. Barriers to collaboration exist due to infrequent opportunities for communication, little knowledge about other researchers' ongoing work (prior to publication), and an absence of a common “intellectual space” to share ideas and hold informal discussions.

OpenWetWare allows all members to freely create, organize, and edit webpage contents, and is an attempt to alleviate the problems highlighted above. For example, by providing a means for researchers to contribute to a commons of biological information, "lore" can be disseminated to the community, evaluated, and stored electronically. In addition, opportunities for collaboration that currently take place on rare occasions will be dramatically increased by sharing an online space.

-- Improving information resources -- By serving as an information repository, OpenWetWare can improve educational and research experiences in a variety of ways. One example is information concerning biological protocols, such as the OpenWetWare entry on DNA ligation (http://openwetware.mit.edu/wiki/DNA_Ligation), which includes an explanation of the relevant biology, a general procedure, lab specific protocols, and notes with experimental nuances. A discussion section accompanying the entry enables researchers to pose questions and troubleshoot their approach. Additionally, by linking relevant educational material directly to the protocol, we expect the protocols themselves to become learning tools. Towards that goal, we will be working with Prof. Kuldell to integrate student contributions to the protocol collection into the biological engineering project lab (BE.109). We believe this will encourage students to gain a deeper understanding of the biology underlying each step in a protocol, as well as encourage a mindset of collaboration and contribution. However, protocols are just one example. Other information resources currently benefiting from collaborative development on OpenWetWare include: equipment, strains, vectors, safety, FAQs, and computing. Specifically, wiki pages for equipment have proven to be very useful technical resources housing maintenance logs, usage notes, and results from control experiments.

-- Reducing barriers to collaboration -- OpenWetWare has great potential to enhance collaboration between researchers. One example of how disparate groups can use OpenWetWare to improve information flow is that of the Synthetic Biology Working Group. This group comprises students from several labs at three schools (MIT, Harvard, UC Berkeley). Looking at their wiki page (http://openwetware.org/wiki/Synthetic_Biology), you can find:

1. Listing of news in the field (e.g., recent talks and lectures in the field) 2. Collaborative discussions (e.g., abstraction hierarchy and a synthetic biology ontology) 3. Listings of available resources (e.g., press articles, conferences, and online tools) 4. Collaborative initiatives (e.g., The BioBricks Foundation and the Synthetic Genomics Study) 5. Projects currently in progress (e.g., Biological Barcodes and Rebuilding T7) 6. Outreach programs (e.g., courses and competitions)

All of this information is updated continuously by community members. OpenWetWare allows members to communicate efficiently over a wide range of projects, and perhaps more importantly, gives others real-time information about what ideas and research the group is currently pursuing. __________________________________________________

(5) Key participants Barry Canton -- 3rd year graduate student (will be a student in Fall 2006) Sean Clarke -- 1st year graduate student (will be a student in Fall 2006) Danielle France -- 4th year graduate student (will be a student in Fall 2006) Jeff Gritton -- 4th year graduate student (will be a student in Fall 2006) Jason Kelly -- 3rd year graduate student (will be a student in Fall 2006) Sriram Kosuri -- 5th year graduate student (will not be a student in Fall 2006) Alex Mallet -- 2nd year graduate student (will be a student in Fall 2006) Reshma Shetty -- 4th year graduate student (will be a student in Fall 2006) Ty Thomson -- 4th year graduate student (will be a student in Fall 2006)

Other Participants Ilya Sytchev -- 4th year graduate student at Northeastern University, bioinformatics intern at MIT __________________________________________________

(6) Goals for the spring

1. Double number of users - Hold 5 tutorial luncheons on MIT's campus - Actively recruit 10 laboratories 2. Improve on an existing tool to convert wiki pages to static webpages 3. Design and implement protocol templates __________________________________________________

(7) Goals for the one-year project

1. Integrate with 1-2 lab classes at MIT. - BE.109, 7.02 2. Implement software tools for conversion of other document formats into wiki markup language. 3. Integrate with DSpace via document discussion and review pages. 4. Develop institution-specific information hubs. __________________________________________________

(8) Funding

-- Software development -- In order to facilitate user interactions with OpenWetWare, we would like to establish UROP positions to work on a variety of software tools:

1. Tools to simplify data entry into the wiki (e.g., direct conversion of Excel/Word/Latex documents into wiki markup language) in order to increase usefulness to scientific community. 2. Tools to map wiki pages onto static websites in order to encourage labs to host websites on OpenWetWare. We have already begun to explore such possibilities (see http://syntheticbiology.org), and would be interested in making such tools easier to use and more widely available. 3. Tools to integrate permanent and evolving documents as a method for providing feedback on static documents. For example, what is the best interface between MIT's DSpace (http://dspace.mit.edu) and OpenWetWare? Ideally, we hope to coordinate with the MediaWiki open source community on tools that are likely to be of general use to the community (MediaWiki is the open source software that OpenWetWare is based on).

-- Cultivation of user base -- The success of OpenWetWare depends critically on cultivating and maintaining an active user base. We plan to dedicate funds to enable tutorials, conference visits, advertising, and other mechanisms for recruiting new users to OpenWetWare.

-- Data management -- In the long term, the success of OpenWetWare relies on the assumption that the number of users actively curating the information of OpenWetWare will scale with the amount of content generated. However, there has been little work to examine how collaborative tools can best be used to develop information resources, such as the OpenWetWare protocol collection. We believe the project would benefit dramatically from the active establishment of community standards for organizing content in OpenWetWare. We will establish a UROP position to evaluate and implement templates and other methods for organizing information in OpenWetWare. __________________________________________________

(9) Advisor(s) - Drew Endy, Assistent Professor of Biological Engineering - Natalie Kuldell, Instructor for BE.109 (BE Project Lab) __________________________________________________

(10) Other

OpenWetWare is far more than simply a wiki for scientists. It represents a conscious departure from standard operating procedure in biological science and engineering in that it enables the sharing of methods, ideas and work. OpenWetWare has a strong potential to make inroads into the highly competitive culture of biology for several reasons.

1. Despite only being six months old, OpenWetWare already has 265 users, 2725 pages and ~1000 visits per day (statistics current as of November 10, 2005). 2. OpenWetWare already has many undergraduates, graduate students, post-doctoral scientists and professors that contribute to content. Regular users include people from Biological Engineering, Biology, and the Computer Science and Artificial Intelligence Laboratory at MIT and the Department of Systems Biology at Harvard Medical School. Finally, based on the initial successes of OpenWetWare, the BioMicro Center at MIT recently has generously provided hardware and support to host the site. 3. OpenWetWare is attracting more and more attention from scientists outside MIT. We receive regular requests for accounts from users that happen across the site (often when searching for useful protocols) and want to participate.

Despite this initial success, if OpenWetWare is to reach its full potential, substantial investment of both time and money is needed. An MIT iCampus grant would be a significant step towards that goal.