Mouse Genome Conference: Bioinformatics Workshop

Bioinformatics Workshop

Saturday 5th November 2005

Cost €60 per person for the full day. For more information visit http://www.ncbi.nlm.nih.gov/projects/Jax_GSA/IMGC_Workshop/announce.html

Deadline for registration - October 4, 2005

Bioinformatics tutorials are being organized again this year by Deanna Church (NCBI) and Carol Bult (The Jackson Laboratory). Three concurrent tutorials will be offered (see descriptions below). Each tutorial will be a combination of lecture and hands-on exercises. A minimum of 10 participants will be required to run a specific tutorial session. Due to time constraints each participant can attend only one of the tutorials. However, the course materials for all three workshops will be provided to all participants.

Tutorial 1: WebQTL

Learn how to use WebQTL, a unique internet resource for complex trait analysis in genetic reference populations. The system includes quantitative trait locus (QTL) mapping, gene expression analysis, genetic correlations with systems level phenotypes, candidate gene analysis and construction of trait covariance networks across biological scale.

Tutorial 2: Informatics Resources for Gene Expression Data (EMAGE and GXD)

This tutorial will cover both the GXD and EMAGE, databases that describe gene expression patterns during mouse embryogenesis (obtained from in situ hybridisations, immunohistochemistry, reporter knock-ins, RT-PCRs Northern blot and Western blot experiments as well as from cDNA source data). GXD focuses on standardized text annotation and EMAGE on graphical annotation (2D and 3D) of sites of gene expression. The tutorial will cover how to search each database and also how to use these resources to manage your own gene expression data in the lab.

Tutorial 3: Genome Sequence Analysis and Genome Browsers

This tutorial will cover the basics of commonly used programs such as BLAST and BLAT. In addition, we will cover how to use the three major genome browsers (Ensembl, NCBI's Map Viewer, and the UCSC Genome Browser) and a new sequence analysis workbench offered by NCBI called the Genome Workbench.