Knowledge Managment with Drupal for Genomics Research:

SESSION OVERVIEW: Knowledge Managment with Drupal for Genomics Research: creating data mashups from multiple external databases and web services for biomedical research.

My background: I am a trained academic scientist (Ph.D. in Biophysics, from U.C. Berkeley): I study the genes that control nervous system development, using a variety of techniques: genetics; genomics; gene transcription analysis; neuronal differentiation analysis.

I am using Drupal as a web interface / portal / knowledge managment hub for me to access the massive amounts of previously stored biological information and knowledge that is available online. I also use Drupal to analyse this information: to create knew knowledge by discovering previously unknown relationships in the data; and to publish that knowledge online for others to see and use.

TRACK: Site building / interface design for data access and presentation.

AGENDA:

Web Portals: Every scientist needs a web portal, to interface with the various large online databases for their area of research.
* Using Drupal as a web interface / portal giving access to multiple online biology databases:
* genetics: Flybase; Wormbase; Mouse Genetic Database.
* genomics: DNA sequence for entire genomes from humans and dozens of other species.
* medical: human disease databases such as OMIM.
* biochemical: protein structure databases, metabolic pathway databases.

Data Access: multiple technologies used for different types of data sources:
* SQL queries of MySQL and PostgreSQL relational databases
* Queries of XML databases..
* RSS feeds: virtually every scientific journal has one or more RSS feeds.
* PubMed / HubMed
* Web services: the future .

Data Mashups: the biological questions you can ask and answer depend on what data and knowledge you have access to, and how you can combine that information - mashups - in new an creative ways.

GOALS: I would like to share my experience with using Drupal as a web framework / CMS / Knowledge Managment system for me to publish my own work online. I also would like to learn from others their experiences in using Drupal as a CMS and web framework for complex information analysis, including integration of web services.

RESOURCES: No background knowledge or resources are needed. I will provide the information necessary to undstand this lecture / seminar style presentation.