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.

1 comment:

2017 said...

I think you will like to listen to this podcast from ASU, Mr. Sudhir Kumar. on comaprative sequence analysis in evolutionary genetics.