User:Ricardo Vidal/OWW internship

OWW Internship
The following information is regarding my 6 month internship that will take place at Endy Lab while working on OpenWetWare.

Topic

 * Applying semantic web technologies and collaborative tools to protocol development in experimental biological research

Overview
OpenWetWare (OWW) is an effort to facilitate the open communication of scientific information including methods, results, educational materials, discussions and publications. In research, the traditional mechanisms for sharing work are reference books, journal papers, personal communications via conferences and invited talks. OpenWetWare seeks to address limitations in these communication methods, by decentralizing and lowering the barriers to information exchange among all researchers, be they professors, students or research scientists.

Based on the same wiki software used by Wikipedia (MediaWiki), OpenWetWare is an attempt at providing the necessary infrastructure to capture and share biological knowledge as it is generated. The wiki allows for instantaneous distribution of information with few constraints on format or structure. Simple, quick and easy-to-use mechanisms for sharing information are essential if we expect scientists to share the many details underlying the research process.

To further promote the sharing and integration of research information, semantic web technologies should be implemented. The semantic web is an evolving extension of the World Wide Web in which web content can be expressed not only in natural language, but also in a format that can be read and used by software agents, thus permitting them to find, share and integrate information more easily.

Internship objectives

 * Work closely with OWW users so as to produce new or better tools to accomplish desired results.
 * This should be accomplished by changing the tools to accommodate the user and not the other way around, thus minimizing the learning curve.
 * Statistical analysis
 * of the effect that these new tools/procedures have on the OWW user community's productivity.
 * of visitors to OWW as a result of changes made to specific features of OWW (implementation of tags/categories, use of multimedia tutorials video/screencasts, etc)
 * Perform various case studies on the use of OWW and other web2.0 tools to demonstrate the usefulness and application of such technologies in everyday lab work/research.

Calendar (rough)
Legend:

Suggestions from random folks

 * Jason R. Kelly 10:04, 16 January 2008 (CST):Hey Ricardo, thanks for putting this together. One idea might be to take a certain "sub-group" of OWW users and follow up on what their needs are.  Since the way the site is used by say a student in a course is totally different then a researcher in a lab.  I've noticed that probably 10% of new user requests are looking to start a lab website.  I think this is something we really want to encourage, but are doing a bad job of at the moment.  You could imagine technical tools (e.g. easily invite the other members of your lab to join OWW, simple searching of just the labs' OWW pages) as well as non-technical stuff (better tutorials / templates for starting a lab website, a small volunteer group that serves as a "welcome wagon" for new labs, etc) that could address this.  Could run the stats on how new tools / policies effect the "conversion rate" of people requesting an account to start a lab website, and those that actually end up doing it.
 * Jason R. Kelly 20:12, 22 February 2008 (EST) we're trying to work out what the "point" of OWW blogs should be. As compared to a place like scienceblogs or Nature network blogs, etc.  Is there anything we can provide to our blogging community to help them do science better, or just to help new bloggers get "discovered" more easily.  just a random need, thought I would throw out there as I know you are pretty blog-savvy.
 * RVidal 23:29, 24 February 2008 (EST): I think that what is needed is focus. To make blogging different on OWW and make it also more science oriented, I think that the blogs should be sidekicks to the online notebooks. The blogs should be a sort of diary of what the researcher is doing and what they think about their results, expectations, etc. This would complement the Online notebook which would then be left for hard data and details. Aside from this, there should be further integration between the blogs and the wiki. I suggest some sort of a redesigning of the blog template to make it seem as if the blog was in the wiki and not outside of it. Internet users disperse themselves very quickly. So, everything should be a click away, everything. I'll get back to this.

Project topics

 * Identify classes of users (Use Google Analytics and following up with people)
 * Protocols - structuring the information
 * User pages
 * Since the user pages are automatically generated based on a form, I think that there is sufficient ground here to introduce some semantic content along with the user details. Or even just having some sort of wide range tagging. So, the forms could have mandatory fields that render information that is permanently on the user page and then the rest of the page could be editable at will.Ricardo Vidal 17:31, 29 February 2008 (EST)
 * Work-flows
 * Knowledge-management - where is the information on the wiki
 * Simile/Wibbit
 * This can help organize information visually and also reduce excessive scroll on pages with long lists of information (ex: E. coli genotypes) Ricardo Vidal 16:39, 27 February 2008 (EST)

Protocol Brainstorming

 * Annotation of protocols
 * This could be something that would allow to write between the text and then maybe have a toggle button to hide/show the annotations. A kind of inline commenting system?
 * Scoring protocols (vote for this protocol)
 * This can serve as a community driven pre-peer-review that could indicate readiness for publication (aka stamp of approval) - Interesting as publishing is regarded.
 * Seek out examples of protocol management/organization
 * There are companies that make protocol software but screenshots and demos are rarely available. (ex: Amphora Research Systems OpenELN)
 * Usability study on protocols
 * Pulling out the secondary comments about protocols (I used this protocol, needed to change X,Y,Z)
 * What links here is a start for this. A template of sorts could list the various pages that are linked, for inclusion on the original page. Tweaking would be needed as regards to what info links back.

Misc info

 * University of Algarve advisor: Emília Costa
 * MIT advisor: Drew Endy


 * Duration: 6 months
 * Start date: 25th February 2008
 * End date: 29th August 2008