Bioinformatics Workshops

Date	Sunday, October 28
Time	9:00am - 12:00am
Place	Kyoto Terrsa, Meeting room
Registration	Registration Page * Registration will be closed when we have maximum participants for each workshop.

Three bioinformatics workshops will be offered. Each workshop will be a combination of lecture and hands-on exercises. Participants will need to bring their own laptop computers capable of connecting to a wireless network wired LAN cable.

The cost of the workshops is covered by main conference registration fee and includes workshop materials and refreshments. Because the workshops are concurrent, each participant can only attend one of the sessions. However, the course materials for all three workshops will be available on-line following the conference. A minimum of 8 participants will be required to run a particular workshop session. Each session is limited 15 participants.

Please direct questions about the bioinformatics workshops to Drs. Carol Bult (carol.bult@jax.org) or Deanna Church (church@ncbi.nlm.nih.gov).

• Workshop 1
• Workshop 2
• Workshop 3

Workshop 1: J/qtl: A graphical user interface for QTL analysis

Dr. Randy von Smith, The Jackson Laboratory

J/qtl is a graphical user interface for R/qtl which is an interactive environment for mapping quantitative trait loci (QTL). The R/qtl package is a command line library within the popular open source R software. J/qtl is a Java based graphical interface that enables data viewing and analysis via a user friendly menu and windowing system. J/qtl currently implements many of the functions available in R/qtl and enhances these with interactive Java versions of graphs and tables. Each J/qtl session generates a history of the R/qtl in the form of an executable script that can be used to document the analysis history.

During the workshop we will provide an overview of the software using real data examples and provide a hands-on tutorial for interested researchers. Details for downloading and installation of the software packages will also be covered.

Workshop 2: Gene Ontologies for Mouse Genetics and Genomics

Dr. Judy Blake, The Jackson Laboratory and the Gene Ontology Consortium

The major objective of this tutorial will be to inform biologists about the power and caveats of using functional and comparative annotations in their research program. Without a deep understanding of how functional annotations for genes and gene products are made and how this knowledge is structured, there is potential for data analysis to be misleading rather than informative. The Gene Ontology has become a widely-used research tool of particular utility to genome-scale data sets.

The workshop will provide the opportunity for new or casual users of the GO to learn more about this resource and how to use it. The workshop will also offer "power users" of GO the opportunity to discuss specific issues or concerns with one of the leaders of the Gene Ontology Consortium.

Workshop 3: Ranking candidate genes for positional-cloning studies

Dr. Tetsuro Toyoda, RIKEN Integrative Omics Research Team

Since whole genome sequences were first elucidated, knowledge-based ranking of candidate genes has become one of the most important bioinformatics tasks in the forward-genetics and positional-cloning approaches to identify phenotype-responsible gene mutations. PosMed suggests highly promising candidate genes in a given chromosomal interval(s) by connecting a user's phenotypic keyword and genes via text-mining of literature and omics data (Medline, OMIM, PPI, etc).

This tutorial explains how to use OmicBrowse and PosMed (Positional Medline) and gives you an understanding of how to narrow down likely candidate genes from hundreds of genes existing in the chromosomal intervals and design PCR primers, taking the mouse genome as an example.