Introduction to Bioinformatics - COIN81
COIN 81 Week Twelve
BioPerl and XML are the final topics in our journey of bioinformatics, and they are both optional topics for the quarter. The BioPerl exercises are from a three course BioPerl series I attended at UCSC in fall of 2003. The exercises and answers to the problems are all listed from the links below. The XML component of the course derives from a CIS course in XML, as well as an XML course developed specifically for biologist and bioinformatics. If you have computational skills in programming,consider giving the BioPerl and XML tutorials a quick overview. if you don't have time to address them in this course, just come back and revisit them.
BioPerl - BioPerl exercises from UCSC. These examples come in three sections, starting with basic Perl, then Perl used for bioinformatics. You'll need a Perl interpreter, preferably a Perl editor, which makes editing and extending these programs much easier.
XML - XML tutorial from XML for Bioinformatics. You can use these tutorials to teach yourself the basics of XML, including well-formed documents, dtds, schema, and writing using elements and attributes. These tutorials also include an introduction to BioML and BSML, two early applications of XML to bioinformatics.
BioPerl.org - BioPerl.org wiki, your source of the latest BioPerl information.
BioML - link to BioML in XML Cover Pages, and BioML tutorials.
BSML - link to BSML in XML Cover Pages, and BSML tutorials.
CellML - CellML is an XML language for storing mathematical models of cellular processes. If you have a decent understanding of cellular processes, metabolic pathways, and enzymatic reactions, you'll really like CellML.