Section: Software

ISee

Participants : Annick Chamontin, Philippe Genoud [ Correspondent ] , François Rechenmann, Danielle Ziébelin.

The aim of ISee (In Silico biology e-learning environnement ) is to explain the principles of the main bioinformatics algorithms through interactive graphical user interfaces and to illustrate the application of the algorithms to real genomic data. Written in Java, ISee defines a generic framework for combining algorithms with courses. More precisely, the environment implements the metaphor of a lab notebook: the left pages present and explain the experiments to be carried out by the student, whereas the right pages display the progress of these experiments, i.e. the execution of the associated algorithms. In its present state, the environment offers different algorithmic modules structured into three main chapters: sequence comparison, statistical analysis of DNA sequences for the identification of coding regions, and basic pattern-matching algorithms including the use of regular expressions. These and other algorithms have been integrated in two original practical courses. The first one is an introduction to the statistical analysis of genetic sequences and leads the student to the identification of the origin of replication within bacterial genomes. The second one shows the student how to identify coding regions in bacterial genomes and to characterize their products. The latter course is developed in collaboration with the CCSTI (``Centre de Culture Scientifique Technique et Industrielle'') in Grenoble, which uses ISee for its ``École de l'ADN''. For more information, see: http://www-helix.inrialpes.fr/article124.html .