ICampus Application for OWW: Difference between revisions

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''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.''
''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. -- [[Ty Thomson|tmt]]
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 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 environment.
:- I prefer option 2 and have edited it a bit--[[User:Bcanton|BC]] 13:10, 14 Nov 2005 (EST)
:- I like option 2 better as well, and have moved option 1 to the discussion page--[[User:Bcanton|BC]] 13:10, 14 Nov 2005 (EST)


In the biological sciences, the primary mechanisms for sharing information are journal publications, reference books and personal communications.  Research can often be hindered by a lack of access to expertise and equipment. This 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 (OWW) is enabling similar collaboration for the biological science community.  OWW in its current, early state has already shown two significant advantages over traditional scientifc communication - the knowledge base and the collaborative environment.  By posting information about protocols, equipment, and projects, labs are creating a knowledge base of persistent information that is maintained despite the high turnover of lab personnel. Because of the open nature of OWW, that knowledge base is shared among all participating groups so the community can benefit from the different expertize of each group. Since this shared information is not only persistent but also dynamic (i.e. always editable), the dissemination of new methods and technologies is much more rapid than via traditional scientific communication.  Through Mediawiki technology, it is easy for researchers to post information, comment on the information of others researchers and contact them directly.  In this shared online environment, scientists are brought closer together, increasing the likelihood of fostering collaborations to achieve common scientific goals.
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 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.


====Ideas in rough form====
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.
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. 
 
#'''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.
#'''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.
#'''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.
#'''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.
#'''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===
===Key participants===

Revision as of 12:22, 14 November 2005

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

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. The success of a given experiment often depends on having access to the right expertise and equipment. 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 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 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?

Other

Any other comments or questions.

References

MIT iCampus Student Awards page

List of Past Student Projects

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