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.

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
• Please list other ideas here because the one above is lame
• Are we really trying to create something for the entire biological research community ie the equivalent of a Wikipedia for biology, or should it be kept more focused ? -- Alex
• I think it'd have better luck if it was less focused. A wikipedia for all labs or for all students or whatever, would have better chance of getting funding than something focusing on the biosciences and what already currently exists. We need to propose something that doesn't already semi-exist. --Austin 19:10, 9 Nov 2005 (EST)

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.

• I feel all the previous stuff either should go in motivations or is so overly general, we should fit it into the first paragraph. If people don't like this, see the discussion page for the old content. --Sri Kosuri 17:07, 12 Nov 2005 (EST)
• As for what I think this should say, Section 1 is a general introduction. Section 2 is how OWW helps individual labs organize and store information. Section 3 is how members can contribute to a shared area. Remember there is a whole significance section directly proceeding this section, which can be more substantial. This whole section, once again needs to be made better.
• OpenWetWare is a collaborative environment designed to promote 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. Member laboratories and individuals can post information concerning their research, protocols, tools, equipment, laboratory materials, biologicals, et. cetera onto their own areas and/or areas shared by various groups. 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, 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. Oftentimes 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.

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 -- ?
  
• 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)
  
• Reshma Shetty -- 4th year graduate student (will be a student in Fall 2006)
  
• Sean Clarke -- 1st-year graduate student (will be a student in Fall 2006)
  
• Alex Mallet -- 2nd-year graduate student (will be a student in Fall 2006)
  
• Ty Thomson -- 4th-year graduate student (will be a student in Fall 2006)
  
• Ilya Sytchev -- I'd like to participate but unofficially since "all key participants must be MIT students" which I'm not
  

Add your name here

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)?

1. Content Development
   • Dedicated wiki 'curators' who evaluate and implement different "templates" or other methods for organizing information on the wiki.
     • For instance, collecting and organizing 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
   • Better tools to make websites from wiki pages in order to encourage more groups to host their website through OpenWetWare. For an example, see here.
   • Improved import of other file types (excel,work,latex) in order to lower barriers to contribution.
   • Better integration with other MIT information sharing programs (OWW,Dspace).
3. Cultivating and Maintaining a large and vibrant 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 advertising 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