Building Bioinformatics Web Applications

   IMPORTANT DATES for this Course
   Deadline for applications: June 25th 2011
   Course date: July 4th to July 7th 2011


David Leader obtained his D.Phil. in biological sciences in the University of Oxford, and, after a post-doc at the University of Chicago, took up a position as lecturer at Glasgow University. Initially he worked on molecular biological problems in the area of ribosomes, protein kinases and viral genomes, where he had acquired experience of bioinformatics tools. He then took an MSc in Information Technology, and moved his research and teaching into the area of Bioinformatics. He has written a standalone genome browser (BugView) and has produced a web application for querying a database of protein structural motifs (Motivated Proteins). Most recently he has set up a web server (Pathos) for processing mass spectrometry data for metabolomics and visualizing the results on maps of metabolic pathways.

Affiliation: College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK

Richard Cooper was a lecturer in the Department of Computing Science at the University of Glasgow and now holds the position of Honorary Research Fellow. He has been a technical leader with ESPRIT projects and has also initiated a series of International Workshops on Interfaces to Database Systems. He has worked and taught extensively in the area of usability of database systems, concerning himself with both data modeling and user interface issues. The latter increasingly involved internet applications, has been applied to a variety of different subject areas.

Affiliation: School of Computing Science, University of Glasgow, Glasgow, UK

Course description

The course will involve constructing a web application in which a user may send a request from a web page to a Unix server which queries a biological database and returns results to the user.
Participants will download files containing COG (Clusters of Orthologous Groups) data from NCBI and use them to construct a simple relational database in MySQL, which they will learn to query. After instruction in the basics of HTTP (the Hypertext Transfer Protocol) they will learn how to construct a simple server application which can return a web page in response to a form-based query, using a choice of Perl, PHP or Java. They will then extend this server application so that it is able to query their MySQL database, returning a web page to the user with results in either textual or graphical form. Finally they will learn how to use Ajax to provide an improved user interface for their web application.
It is expected that participants acquire sufficent skills to be able to autonomouly deliver a data resource or an application on a website.

Target Audience

Students and researchers with some (minimal) programming skills (Perl, PHP, Java) that have produced or planned a data resource or a bioinformatics tool that may be useful to communities (internally or worldwide) but lack the skills to quickly deploy such a resource on the Web.

Course Pre-requisites

It is envisaged that attendees should be familiar with one scripting or programming language so as to be able to benefit from a crash course in Perl which assumes familiarity with standard programming concepts such as variables, conditional structures, repetition, arrays and subroutines. Familiarity with SQL, while an advantage, is not a requirement, as the course will include lectures on relational databases and SQL.

Detailed Program

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

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Last updated:  June 29th 2011