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] - don't edit the linked page as it is a history of this page and will actually change this page. See here for more information.
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.
A description of OWW is -- could be a little clearer; need to explain what a wiki is.
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 by any individual member. Participating laboratories and individuals can post information concerning their research, protocols, tools, equipment, laboratory materials, biologicals, etc., onto both lab specific and community pages.
Where we expect it to go -- needs better wording... conceptually really unorganized right now
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.
Outline
Existing Problems
- Information resources (e.g., Protocols).
- static
- low information content
- no lore transfer/validation
- Barriers to Collaboration
- lack of information/understanding on what others are working on
- physical distance
- opportunities for informal communication
We assert that problems are all solved by removing bottlenecks to information contribution. Thus, we started OpenWetWare.
Specifics to get across:
Education & Information Repository
- protocols
- equipment
- Help/Q&A areas
- Strains/Vectors/Safety/Tutorials
- Class Information
Research: Development and Dissemination
- discussions
- initiatives
- lab websites
- Projects
Intro
As students entering the field of biology, we have noticed a couple of problems. First, existing information resources in biology, such as reference books, journal publications, and personal communications are often innadequate to naively begin a new line of research. For example, protocols in biology are often incomplete and unrepeatable. Second, often opportunities for synergistic collaborations are often missed for lack of information and/or understanding of what others are working on. This is sometimes due to physical distance which prevents interactions combined with many don't have updated information on what they work on. We feel both of these problems could be solved by removing bottlenecks to information dissemination by democratizing information contribution through the use of a wiki. OpenWetWare is a wiki (a service that allows users to freely create, organize, and edit web page contents) specifically built to address these two issues.
Knowledge base
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. OpenWetWare is serving as a repository for these types of information. For example, the OpenWetWare entry on DNA Ligation includes an explanation of the relevant biology, a general procedure, lab specific protocols, and notes with debugging tips. A discussion section accompanying the entry enables researchers to pose questions and troubleshoot their approach. This knowledge base will be a tremendous resource to practicing scientists as well as students. In particular, by enabling cross-linking between protocols and background information we expect the protocols themselves to be learning tools. This is especially apparent when contrasted with typical protocols that resemble recipes followed by journal references.
Replaced below with last couple sentences above, thought we should emphasize protocols as learning tools more directly (rather than just as a way to give a better picture of current practice). --JK
Previous text:"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."
Collaboration Space
OpenWetWare 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 OpenWetWare 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 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)
- 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)?
Software
In order to facilitate user interactions with OpenWetWare, we would like to employ several UROPs to work on tools to integrate OpenWetWare with other software platforms and to simplify data entry into the wiki. Tools that allow for direct import of Microsoft Excel, Microsoft Word, and Latex documents into the wiki format would substantially lower the barriers for information entry into OpenWetWare. Ideally, we hope to coordinate with the MediaWiki development team on such tools since they are likely to be of general use to the MediaWiki project. Tools for the auto-generation of static websites from wiki pages would encourage more groups to host their website through OpenWetWare since websites would benefit from having multiple contributors. For an example of such a site, see the openSUSE.org site. We would also like to pursue integration with other MIT initiatives, such as MIT DSPace and MIT OpenCourseWare. We would like to see mechanisms in place for uniting dynamic wiki pages with more permanent DSpace digital archives. Such an integration might take the form of user discussion and reviews of DSpace documents on the wiki. The number of UROPs required will depend on the quality and skills of the applicants.
Data management
We would like to hire UROPs to act as 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. Such organization should enhance the usability of OpenWetWare and highlight its advantages over traditional, static reference sources.
User base development
The success of OpenWetWare depends critically on cultivating and maintaining an active user base. We plan to dedicate funds to enable tutorials, conference visits, and other mechanisms for recruiting new users to OpenWetWare.
Advisor
Who is your project advisor?
Other
Any other comments or questions.
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.
- 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).
- OpenWetWare has reached a critical mass of undergraduates, graduate students, post-doctoral scientists and professors to expect its continuing development and future success. 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.
- 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.
- OpenWetWare is growing in parallel to the emerging field of synthetic biology. Many OpenWetWare users also work in synthetic biology. We expect that even if OpenWetWare fails to appeal to the mainstream biological science community, it will serve a central role in synthetic biology.
