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.

Meeting

Friday, Nov 11, 12-1pm in 68-574.

Purpose of the meeting will be to have a discussion about the long term goals for OWW, as well as what specifically we would do with the grant money, etc.

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

The proposer must be a registered MIT student (graduate or undergraduate). You must supply a valid email address that we can use to communicate with you. List only one address only. This person will be the point of contact for all communications about the proposal. This person also must be the person who mails in the proposal, with the correct FROM email address.

• 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 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 which allows easy organization and editing of webpage content and linking between pages. It seeks to create a useful resource that relies on a community of users to keep the content accurate and up-to-date. We hope that OpenWetWare will foster enhanced collaboration among community members as well as provide a useful reference source for researchers around the world.

• didn't look at above when i wrote this, could combine them probably... please comment and edit heavily - JK

OpenWetWare is an effort to democratize contribution to a commons of information related to academic research in biological science and engineering. At its most ambitious, OpenWetWare seeks to bring all academic researchers under one roof. By cultivating an online space where ideas, approaches, and resources can be freely exchanged we hope to break down barriers to collaboration that currently exist between institutions and labs. Additionally, we hope to encourage the transition from static to dynamic documents for conveying information in academics.

While we have begun to implement our own ideas around which we hope researchers will self-organize (e.g. protocols), OpenWetWare is inherently non-hierarchical and our group is just a single node in the network. We fully expect (and look forward to!) being supplanted by (coexisting with?) other researchers with different ideas for organizing the community in the future. In particular, the flexible nature of the wiki software enables future community members to re-organize dynamically around new trends and areas of research. Finally, as researchers from disparate fields increasingly consider biological problems we expect the role of OpenWetWare in collecting, organizing, and disseminating information to be ever more essential.

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.

I'm thinking of this section as two paragraphs; the first one discussing the significance of the current OpenWetWare, and the second on the importance of the improvements that could be made with iCampus funding. -- tmt

PARAGRAPH 1 - Two versions (different focuses)

• In the biological sciences, the primary mechanisms for sharing information have traditionally been journal publications, reference books and personal communications. The success of a given experiment often depends on having access to the right expertise and equipment. Such a system can be contrasted with collaborative open source projects in computer science that use the World Wide Web as a means for soliciting and organizing contributions, and disseminating information. OpenWetWare has begun to fulfill that role for the biological sciences community. OpenWetWare (OWW) is based on WikiMedia software, which allows for all users to edit the content and organization of the site. Now including 17 laboratories at 7 universities, it has led to a series of important resources. One such resource is a collection scientific protocols which includes different variants of the same protocol, comments on their strengths and weaknesses, and descriptions of the protocol, and links to other related resources. OWW also contains information about the use and maintenance of laboratory equipment. An example of the usefulness of this is that a Google search for the Victor3 plate reader from Perkin Elmer returns OWW rather than the Perkin Elmer site as the top hit. Since all the pages on OWW are editable by all users, it also helps foster collaborations. By providing a common space for people to post information about their work, researchers can more easily keep apprised of work going on in other labs. Such a space increases the likelihood of collaboration and also provides a source for determining where certain expertise lies.
• In the biological sciences, the primary mechanisms for sharing information have traditionally been journal publications, reference books and personal communications. The success of a given experiment often depends on having access to the right expertise and equipment. Such a system can be contrasted with collaborative open source projects in computer science that use the World Wide Web as a means for soliciting and organizing contributions, and disseminating information. OpenWetWare has begun to fulfill that role for the biological sciences community. There are two main advantages of OWW, the knowledge base and the collaborative environment. There are many strengths of the knowledge base that can be accrued through OWW. By posting information about protocols, lab equipment, and research projects, labs can maintain a source of persistent information that is maintained through student and post-doc turnover. OWW also provides a single resource for the biological community for common and shared information, decreasing the amount of time spend across the biological sciences assembling lab-specific information. Since this information is dynamic (ie always editable), it allows for more rapid dissemination of new protocols and information about new technologies than traditional publication and scientific communication. The collaborative environment is almost a result of the knowledge base. As users participate in the OWW community by search for relevant information and edit data resources, they are increasing their likelihood of coming across researchers and labs with whom they share similar research interests. They may contact those researchers or labs directly, or through the OWW community make comments or begin a dialog on these research specific pages. In this manner, new collaborations can be formed.

PARAGRAPH 2 - ideas only

• Strength of OWW is the information content entered by the user base. Organizing information, enabling easier entry of information, and growing user base are most important goals towards increasing the power of OWW.

IDEAS IN ANOTHER FORM

In the biological sciences, the primary mechanisms for sharing information have traditionally been reference books, journal publications and personal communications. The success of a given experiment often depends on having access to the right expertise and equipment. Such a system contrasts with computer science which relies more heavily on more democratic means of dissemination like the world wide web. OpenWetWare is an initiative to promote greater interaction and communication among community members. It seeks to create a culture in which researchers openly share their experiences thereby reducing duplication of work. In addition to this overarching educational mission, OpenWetWare addresses several common problems facing researchers in biological sciences and engineering.

1. Persistent information: The amount of information and expertise that is accrued in labs is tremendous. Conveying this information and expertise to new lab members and to the greater scientific community currently relies on talking and interacting closely with the right people. One reason for this is that it is quite difficult to put these thoughts down in a systematic way. Tremendous amounts of individual expertise and information is lost when lab members leave (a key problem given the high turnover rate of academic labs). OpenWetWare provides a low-barrier of entry method for lab members to contribute their expertise to a database which will persist after they leave the lab.
2. Dynamic information: The methods and information generated in biological research is constantly changing. The dynamic nature of OpenWetWare allows the structure to form into the most useful way to convey information. The ease of linking between pages enables richer information sources than is possible with static documents. For instance, a user can link out to informative pages about particular words enabling someone reading the document who doesn't understand a concept to quickly locate a reliable, accurate definition. Moreover, since everyone can revise the information content of a wiki, mistakes are more quickly caught and corrected. Similarly, as new information is obtained, pages can be annotated accordingly.
3. Research collaborations: By providing a common space for people to post information about their work, researchers can more easily keep apprised of work going on in other labs. Such a space increases the likelihood of collaboration and also a provide a source for determining where certain expertise lies.
4. Shared materials information: There is much general information which is of use to a variety of labs like materials (chemical, vectors and strains), resources (online tools and references), protocols and equipment. OpenWetWare enables centralization of all of this information in one flexible location.
5. Student/Post-Doc/Faculty Recruiting: It is rare, on conventional websites, to find dynamic information about a lab which can convey the actual lab and research atmosphere and outlook to a potential new lab member. Since all lab members can contribute to the wiki content, the personality of the lab becomes more clear, and it is a lesser burden for the lab as a whole to keep its current research posted and accessible online.

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