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
• ACID
• SQL
• RDBMSs
• 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;