Advanced Programming for Biologists 2007



Course objectives

The course is aimed at biomedical graduate students and research scientists with experience in Unix and script programming (see below) who would like to expand their programming knowledge for practical biological applications.

During the first two days of the course, the participants will learn how to set up a simple relational database (e.g. MySQL) containing for instance the UniProt proteome of a prokaryotic organism. The third day of the course will be devoted to learning how to access local databases and bioinformatics software by command line and to write a simple web interface, e.g. to run SQL queries on databases and to run certain analysis on the data. The fourth day of the course will be dedicated to web services: how to access external bioinformatics resources via web protocols, e.g. EBI bioinformatics web services and DAS annotation of genomes/proteomes. On day 5 of the course there will be a tutorial on Taverna workflows, to give students another angle how to automate and link different bioinformatics programs together.

The practical component of the course is substantial and it will take at least ½ of each day of the course.


Audience

Biologists and research scientists with experience in programming (UNIX & PERL). Comparable skills and knowledge of the content of our past EMBnet courses, “Unix & Perl for life science”, especially day 1 to 3 & day 5: For more details see:
http://www.ch.embnet.org/CoursEMBnet/Basel06_II/Schedule.html
and
http://www.ch.embnet.org/CoursEMBnet/Basel06_II/Material.html

Registration and Fee


The registration fee for academics is 100 CHF.
The registration fee for industry participant is 150 CHF.

Fees include attendance of the course, course material, coffee breaks, and a social dinner during the week. Extras will have to be paid by participants.

We might offer partial reimbursement of travel expenses to students from the Swiss Universities or other Swiss academic institutions. We have no grants to support accomodation costs for the participants of the course.

Registration deadline: until the maximum number of participants (20) will be reached.

Schedule

The final schedule is available [here].

Location, housing and transportation


See Organisation page.