The Bioinformatics of Mutant Mouse Resources (20th September 2011)
A one day hands-on introduction
EBI Training Room, EBI, Hinxton, Cambs, UK
APPLICATIONS NOW CLOSED
Course Summary
In association with Mouse Molecular Genetics 2011, Wellcome Trust Scientific Conferences, 20 -23rd September 2011, we are pleased to announce a one day workshop "The Bioinformatics of Mutant Mouse Resources". The focus of this one day workshop will be to develop a practical understanding of the basics of identifying and evaluating public resources which can be used to make mutant mice (focusing on EUCOMM/KOMP knockouts). Computer workstations will be available for all course participants.
Participants will learn to find mutant mouse/ES cell/targeting vector resources for their genes of interest using the IKMC website (International Knockout Mouse Consortium). They will gain a basic understanding of the different alleles available from various pipelines, identifying their strengths and weaknesses for different applications. Basic background skills in utilizing genomic browsers (ENSEMBL/UCSC) and elementary non-specialist data mining (Biomart) will also be covered as well as an introduction to various gene sets and an overview of the process gene annotation. Finally, informatic resources for obtaining mutant mice and browsing mouse phenotyping data will be presented.
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.
There will be a course fee of £50 for all participants. Participants will be expected to arrange and fund their own travel and accommodation. To arrange accommodation for the night of 19th September, please contact the Wellcome Trust Conference Centre reception at reception@wtconference.org.uk, tel +44 (0)1223 49 5000.
Mouse Resource Clinic - Wednesday 21st September:
- Tutors will be available to aid participants in identifying and understanding public resources related to their gene(s) of interest.
- This will take place during the poster session from 17:00-19:00.
Programme overview
- 08:30-10.00 - Module 1 MGI overview of resources, Ensembl and 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)
- 10:00-10:15 - Coffee
- 10:15-11:15 - Module 2 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)
- 11:15-12:30 - Module 3 Understanding knockout designs, making custom designs and visualizing designs on the genome browser. Using Biomart. Hands on exercises. (Mark Thomas, WTSI)
- 12:30-13:15 - Lunch
- 13:15-14:00 - Module 4 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)
- 14:00-14:30 - Discussion
