Washington, DC (26th and 27th June 2011)

The Bioinformatics of Mutant Mouse Resources

A two-day hands-on introduction

Omni Shoreham Hotel, Washington, DC

APPLICATIONS NOW CLOSED

Course Summary

In association with the Mouse Genetics 2011 conference and the Wellcome Trust Sanger Institute, we are pleased to announce a two day workshop "The Bioinformatics of Mutant Mouse Resources".

Each participant will be required to provide their own wireless enabled laptop for the duration of the course.

At the end of this training, participants will be able to find their favourite genes, understand their gene structures in detail, as well as the underlying experimental data supporting the annotation. They will gain basic understanding and usability of comparative genomics and be able to observe the synteny surrounding their regions of study. They will also be introduced to non-specialist data mining skills.

Participants will be able to find mutant mouse resources for their genes of interest using the IKMC (International Knockout Mouse Consortium) and similar resources. They will gain basic understanding of the different alleles available from various pipelines, identifying their strengths and weaknesses for different applications. They will be able to judge the quality of the KO strategies offered, draw their own vector maps and find key elements for the targeting strategy and genotyping.

Participants will be able to search IMPC (International Mouse Phenotype Consortium) phenotypic databases of IKMC mouse mutants such as EuroPhenome, gain an understanding of the high-throughput phenotype data generated and the statistical approaches required to analyse it. They will also be able to compare and interpret this data with other phenotype data sources and identify mouse models of relevance to their clinical domain of interest.

This course is limited to 40 participants and will be held in English.

The course manual will be made available as a PDF and will be sent out to participants one week prior to the course, and will also be available online during the workshop.

Please visit the registration page for on-line registration. For any queries please contact mouse-odw@sanger.ac.uk.

Alternatively visit the mouse genetics registration page. Ensure you select the 'Satellite workshop on Bioinformatics of mutant mouse resources' in the Optional Events section of the registration form.

There will be a course fee of $150 for all participants. Participants will be expected to arrange and fund their own travel and accommodation.

Programme overview

Day 1 (26th June 2011) Genome Browsing and datamining

  • Overview of Mouse gene datasets available. How these are derived, reliability, completeness and biotypes. (WTSI and MGI)
  • An introduction to Ensembl Genome browser. Examining comparative genomics, variation and whole genome alignments (including hands on excercises. (EBI)
  • Datamining using Biomart: From GWAS data to mouse protein sequences and domains (EBI)

Day 2 (27th June 2011) Mutant mouse resources

  • IKMC resource overview: Partners and pipelines. Knock out strategies available: traps, deletion and conditional alleles. Visualising knockouts in the genome browsers, downloading and drawing vector maps (WTSI)
  • Making the most of EUCOMM resources: Modular tools for targeting mouse genes (WTSI)
  • Mining phenotype databases, to identify mouse models of clinical relevance: interpretation and statistical analysis of high throughput phenotypic data. (MRC-Harwell)

Each session will include detailed "hands on" exercises requiring each participant to bring his/her laptop to the workshop.

Timetable

Day 1 (26th June 2011) Genome Browsing and Datamining

Introduction - Overview of Mouse Resources.
Mark Moore (Senior Consultant, NIH KOMP Project and Project Manager, IMPC)

  • 9am-10.30am Module 1
    MGI overview of resources, browsing genes sets at MGI and finding mouse resources in the International Mouse Strain Resource (IMSR). Including worked examples and exercises. (Carol Bult, MGI)
  • 11.00am-12.30pm Module 2
    Discussion on different mouse annotation datasets (CCDS) and how to use evidence to build gene models (otterlace and UCSC data) worked example and exercises (Jane Loveland, WTSI)
  • 1.30pm- 3pm Module 3
    Introduction to Ensembl browser and mouse genomic specific exercises (Jana Vandrovcova, EBI)
  • 3.30-4.30pm Module 3
    (Cont.) Biomart datamining and using Biomarts of different databases (Ensembl, MGI, EurExpress)
  • 5pm-6pm Users own examples and discussion with participants to go into more detail on subjects discussed on first day.

Day 2 (27th June 2011) Mutant mouse resources

  • 9am-10.30am Module 4
    IKMC resource overview. Knock out strategies, available traps, deletion and conditional alleles. Navigation of the IKMC web portal. Differences between IKMC targeting pipelines. Includes worked examples and exercises. (Barry Rosen, WTSI)
  • 11am-12.30pm Module 4
    (Cont.) Understanding knockout designs, making custom designs and visualizing designs on the genome browser. Making the most of EUCOMM resources: Modular tools for targeting mouse genes. Hands on exercises. (Mark Thomas, WTSI)
  • 1.30pm-3pm Module 5
    Introduction to International Mouse Phenotyping Consortium (IMPC). Mining phenotype databases to identify mouse models of clinical relevance: interpretation and statistical analysis of high throughput phenotypic data. (Michelle Simon / Ann-Marie Mallon, MRC-Harwell)
  • 3.30pm-5pm Module 6
    Nomenclature and Phenotypes, Alleles and Disease Models including hands on examples and time to work on own examples.(Janan Eppig, MGI)
* quick link - http://q.sanger.ac.uk/tqqdm68f