Overview of the course program
- General Introduction
- Introduction to Database programming (SQL):
- What are databases?
- What are they good for?
- What is a relational database?
- Relational Model discussion
- Intro to MySQL;
- MySQL and databases in biology and bioinformatics;
- Database programming: setting up a relational database example: e.g. UniProt E.Coli proteome;
- Accessing local databases and local programs (e.g. blast) via a php interface;
- Web services. Accessing remote bioinformatics services trough the web:
- Introduction to web services: Biological Data/Services available over the web, SOAP and REST, Perl programming (LWP and SOAP::Lite);
- Biomart: Introduction, Web interface, Programatic access;
- Eb-Eye and Dbfetch;
- EBI Web services examples;
- Tools available; InterProScan (Perl example); Blast (PHP example);
- DAS distributed sequence annotation system;
- Taverna tutorial: for the construction and enactment of bioinformatics workflows:
- Practical session 1:Installing Taverna, Adding New Services, Finding and invoking services, Finding and running workflows, Building simple workflows
- Practical Session 2: Stringing services together, Displaying results, Saving results, Spotlight on BioMart, Spotlight on Biomoby, Iteration Control flow and fault tolerance, Shim services;
- The myGrid LogBook - recording your experiments;
- Introduction to myExperiment - sharing and reusing workflows;