Monday, May 28, 2007

AMIA 2007 Spring Congress Synopsis

This year's AMIA Spring Congress involved researchers from many fields including Medical Communities, Nurses, Informatics, Basic Research (bench) and some industry representatives as well, all coming together with a common goal: translate biomedical knowledge into medical practice. The meeting included 5 tracks, spanning from nursing informatics to clinical decision support, personalized health records and translational research, so it was a good mix of several domains each with its own challenges and methodologies.
Adam Bosworth, vice-president of Google opened the meeting with a blast, his vision on how health related information will/should be handled in a not so distant future was mesmerizing, his insight on how google is prepared to adress this challenge an unexpected surprise. Here are his notes.
The translational research informatics track was one of the most interesting, it became clear how CTSA has had and is still having a key role in the development of a new science - Integrative Bioinformatics. Several CTSA awardees made their voices heard and lots of ideas flew around the room, from tools already being developed and evaluated to tools promising but still in the planning process, integration was the keyword and the main challenge.
caBIG was also given a chance to give their 2 cents, but the most enthusiastic seemed to rely mostly on in-house costumized tools. There were plenty of semantic web technologies aficionados, including users of Protege, but no Semantic or Sloppy Databases (exept ours :D).
Christopher Chute also made his presence felt, his insight in what regards the basic researchers vs clinical research "Chasm of Semantic Despair" was particularly insightfull.

Tuesday, May 15, 2007


Internal web-based resource for IBL people can be accessed here: IBLabook. If you have problems accessing it, think you should be given access, or have recommendations for changes to what is available there please bring it up at the weekly lab meeting, Tuesday's 9am at HMB 13.304.

Thursday, May 10, 2007

Integrative Bioinformatics 7

XML mediated interoperability between data structures. The basic idea is very simple: [environment/structure 1] --> XML --> [environment/structure 2]. A very powerful suite of tools, formal and computational, have been developed to deal with the mediation so we have plenty to keep you busy for a couple of hours.

For the Matlab centric exercises please note the xmlread, xmlwrite and xslt commends. Have a go at the W3C links listed in the help files of those commands. In today's class we are going to cheat and use tools that both rely on Matlab structures and/or can manipulate them using XPath. I'll also explain why this is a very popular and useful cheat in any language. Note also that the best libraries are often produced by people with the same problems as you. For example see these two: XML Toolbox and XML Parser. I also wrote a library to deal with XML mediation XML4MAT but one of you (no names please) told me it is ugly.

Thursday, May 03, 2007

Integrative Bioinformatics 6

Modelling Strings

Today we have a hands on tutorial on modelling strings and how you can use them to represent and/or retrieve structured information. This will be a class on menial Bioinformatics.

Modelling strings relies heavily on regular expressions. Spend some time getting familiar with the concepts of patterning, lazy and greedy quantifiers and tokens. Try the regexp function with all 5 output arguments to see what is there.