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 ability for users from any location to edit any page will result in more detailed, accurate, and up-to-date information than is otherwise available from traditional publishing sources and web sites. Finally, we expect that by sharing expertise, researchers will be more likely to engage in collaborative projects and increased communication with other OpenWetWare users.
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.
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
We designed OpenWetWare to address problems that we, as students entering the field of biology, have had to struggle with:
- Information resources are inaccessible, not easily searchable, and frequently out of date. This problem is often magnified by the absence of experimental details that are typically only communicated as "lore" passed between members in individual research labs.
- Barriers to collaboration exist due to infrequent opportunities for communication, little knowledge about other researcher’s ongoing work (prior to publication), and a lack 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 these problems. For example, by providing a means for researchers to contribute to a commons of biological information, "lore" could 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, both educational and technical. One example is 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 enabling cross-linking between protocols and background information we expect the protocols themselves to become learning tools. Towards that goal, we will be working to integrate student contribution to the protocol database into the biological engineering project lab. We feel this will encourage students to gain a deeper understanding of the biology underlying each step in a protocol, as well as to encourage a mindset of collaboration and contribution.
Alleviating barriers to collaboration
OpenWetWare has great potential to enhance collaborative experience between researchers. One example of how disparate groups can use OpenWetWare to enhance collaboration and information flow is by looking at the Synthetic Biology Working Group. This group compromises students from several labs and individuals at three schools. Looking at their wiki page ( http://openwetware.org/wiki/Synthetic_Biology ), you can find:
- Listing of news in the field (e.g., recent talks and lectures in the field)
- Collaborative discussions (e.g., Abstraction hierarchy and a synthetic biology ontology)
- Listings of resources available (e.g., Press articles, conferences, and online tools)
- Collaborative initiatives (e.g., The BioBricks Foundation and the Synthetic Genomics Study)
- Projects currently in progress (e.g., Biological Barcodes and Rebuilding T7)
- Outreach Programs (e.g., courses and competitions)
All of this information is updated continuously by all members of the community. OpenWetWare allows members to communicate efficiently over a vast range of projects, and perhaps more importantly, gives others real-time information about what ideas and research the group is currently pursuing.
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.
UROPS will be hired to develop software and currate OWW, as detailed below. By May 2006 it is expected that what is specific and reasonable? 1) UROPS will create an organized space for protocols (not specific) 2) ?
In order to develop the user base for OWW, a series of tutorial luncheons will be orgainzed on MIT's campus. At least four such recruitment sessions will be held by May 2006 (about once per month.)
Previous text: (Do we care about these values?~ cmc 23:30, 14 Nov 2005 (EST))
- 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 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). 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 [2]. 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 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?
- Drew Endy
- Natalie Kuldell -- pending
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 catch on in the mainstream biological science community, it will serve a central role in synthetic biology.
