ICampus Application for OWW

The MIT-Microsoft Alliance has provided funds for the development of tools to help research in technology education. This page will be used to collaboratively develop an application for funds to push OWW to be a more useful tool. Please put your input below. This is still in the early draft stages, so please put ideas down.

We've been doing a lot of editing--deleting comments etc--working towards a final draft. Find the old page here: [1]

Preliminary Student Proposal Questions

Title for this proposal

Give a short, descriptive title for this project

OpenWetWare: A collaborative information tool for the biological research community

Name and email address of proposer

• Jason Kelly: jasonk AT mit DOT edu

Project description

Please provide a brief (a few paragraphs at most) description of the proposed project.

OpenWetWare 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 and MIT OpenCourseWare, OpenWetWare is a wiki where content related to research laboratories can be generated and disseminated quickly and efficiently. Participating laboratories and individuals can post information concerning their research, protocols, tools, equipment, laboratory materials, biologicals, etc. onto both lab specific and community pages. We believe that the decentralized nature of editing provides more detailed, accurate, and up-to-date information than is otherwise possible with static websites where edits are usually funneled through one webmaster. Finally, we expect that these shared resources will encourage collaborative projects, increased communication, and renewed efforts towards repeatabilty, analysis, and standardization of biological experiments.

Significance

Describe, as succinctly and as compellingly as you can, why you think this project is significant - from an educational perspective, a technical perspective, or other.

In the biological sciences, the primary mechanisms for sharing information have traditionally been reference books, journal publications and personal communications. These sources of information are static (updated based on a publishing cycle) and fractured (access to information is dependent on one's location via access to costly publications and the expertise of peers in adjoining labs). Such a system contrasts with the open source movement in computer science which relies heavily on the World Wide Web as a means for disseminating information as well as soliciting and organizing contributions. OpenWetWare (OWW) is enabling similar collaboration for the biological science community. Even in its current early state, OWW has shown two significant contributions to scientific communication – a developing knowledge base and a collaborative research environment.

Learning a new technique in the biological sciences can be a daunting task, especially for interdisciplinary researchers entering biology for the first time. Oftentimes a single information source is not sufficient, and one must integrate basic biological facts, published protocols, and “lab folklore” from disparate sources in order to properly perform and debug an experiment. OWW is serving as a repository for these types of information. For example, the OWW entry on DNA Ligation includes a basic explanation of the relevant biology, a general procedure, lab specific protocols, and notes with debugging tips. This knowledge base will offer a tremendous productivity boost to practicing scientists. It will also be a great resource for students in biology related classes who will be able to learn how key experimental techniques are performed in practice and how the science they are learning feeds back to promote the development of new tools and techniques.

OWW offers users space where they can post information about their own research projects. Current users use this space to post research briefs, thesis proposals, posters, and even online lab notebooks. This openness will promote collaboration between scientists, since it will be easy for scientists with shared interests to find one another and combine their results and ideas into new research directions. We fully anticipate that this open spirit will grow along with OpenWetWare.

The strength of OWW is the information content entered by the user base. Consequently, organizing information, enabling easier entry of information, and growing the user base are the most important goals towards increasing the effetiveness of OWW.

Key participants

Who are the key participants in this project? What year are they at MIT? Will they all still be students through the fall semester 2006?

• Barry Canton -- 3rd year graduate student (will be a student in Fall 2006)
  
• Austin Che -- ?
  
• 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 (unsure if he will 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
  

Goals for the spring

List two or three specific milestones to be achieved in the project by May 2006.

• X number of labs on board
• X total pages
• X unique visitors to the site
• X other institutions
  • Any thoughts on target values here?

Goals for the one-year project

List two or three specific milestones to be achieved in the project by December 2006.

Funding

What kinds of things are you requesting funding for (e.g., what equipment, UROP positions, other)?

Hardware Due to the intial success and promise of the project, OpenWetWare is currently receiving web hosting support from the Computational and Systems Biology Initiative at MIT. Thus, iCampus funding is not needed for hardware.

Software

Data Management

1. Content development
   • Dedicated wiki 'curators' who evaluate and implement different "templates" or other methods for organizing information on the wiki. For instance, curators could collect and organize protocols posted on various labs' wiki pages into coherent protocol pages each of which might contain a 'meta-protocol','local protocols', and 'common questions/feedback' sections.
2. Tool development
   • There are several tools that will enhance the utility of OpenWetWare to its user base. We hope to finance the software development of such tools through either MIT UROP positions (preferred) or coordination with open source development teams. Below we describe three examples of tools that will enable OpenWetWare to better meet user needs.
   1. Auto-generation of static websites from wiki pages in order to encourage more groups to host their website through OpenWetWare. For an example, see the openSUSE.org site.
   2. Improved import of other file types (Excel,Word,Latex) into MediaWiki format to lower the barriers to contribution. Ideally, we hope to coordinate with the MediaWiki development team on such tools since they are likely of use to the MediaWiki project in general.
   3. Integration with other MIT information sharing programs like MIT DSPace and MIT OpenCourseWare. For instance, many OpenWetWare users contribute more static documents to MIT DSpace. Ideally, we would like to see mechanisms in place for uniting dynamic wiki pages with more permanent DSpace digital archives. Such an integration might involve encouraging users to discuss and review documents on the wiki.
3. Cultivating and maintaining an active user base
   • It is necessary to cultivare and maintain an active user base in order to ensure the sucess of OpenWetWare. We would like to dedicate funds to enable tutorials, conference visits, and other mechanisms for recruiting new users to OpenWetWare.

Advisor

Who is your project advisor?

• Drew Endy

Other

Any other comments or questions.

References

MIT iCampus Student Awards page

List of Past Student Projects

An initial proposal that recieved an award: DomeView