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)

Mar	Apr	May	Jun	Jul	Aug

Legend:

	Stage 1	Research (potential web tools and applications)
	Stage 2	Implementation and interaction with user base
	Stage 3	Continued development and interaction
	Stage 4	Statistical analysis of overall results and in depth analysis of case studies

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.

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

* This is a work in progress