Bangkok, Thailand (7th - 12th Feb 2016)

Human and Vertebrate Genomics: Bioinformatics Tools and Resources.

Mahidol University, Bangkok, Thailand
Ref: ODW-Thailand

Course Summary

This 5-day Workshop provides an intensive introduction to bioinformatics tools freely available on the internet, focusing primarily on the Human Genome data. Students will be given hands-on training in the use of public databases and web-based sequence analysis tools. All course materials will be provided and also made available on the Web. The course has a strong emphasis on applied training, and practical exercises along with interaction and discussion between students and instructors are key features of the programme. Each student will have access to a desktop PC for the duration of the course.

This course is limited to 20 particpants from Asian and Australasian Institutes.

A number of bursaries are available for each overseas course. These are awarded by the selection committee according to merit. There is no course fee. The bursary will cover travel, accommodation and sustenance. The maximum award for travel (in economy/second class) will be £750.

Successful applicants will be notified as soon as possible.

Course instructors

  • Jane Loveland (Wellcome Trust Sanger Institute)
  • Matthew Clark (The Genome Analysis Centre)
  • Emily Perry (The European Bioinformatics Institute)
  • Rob Finn (The European Bioinformatics Institute)
  • Bert Overduin (Edinburgh Genomics, The University of Edinburgh)

How to apply

  • Pre-requisites - The workshop is open to research scientists based in institutes anywhere in Asia and Australasia (including laboratory and clinical staff as well as specialists in related fields). Applicants should have a minimum of a degree in a biological discipline.
  • Cost - There is no course fee for applicants from non-commercial institutes. Bursaries are available for travel and accommodation, these are subject to a selection process and are awarded by merit. Applicants may apply for a bursary during the online application process.
  • Applications - Applicants will be required to complete an online application form together with a 250-word outline of the relevance of the course to their work. Please note that documentation supporting the application will be required from the applicant's Supervisor/Head of Department.

Queries

Any queries should be sent to opendoor@hinxton.wellcome.ac.uk.

Deadlines

  • Closing date for application is 13th November. Applications will not be accepted after this date.
  • Notification of places will be as soon as possible ( TBC - but after the closing date ).
  • Full payment (if required) due on TBC.

Genome Browsing:

  • Ensembl
  • VEGA
  • UCSC

Comparative Sequence Analysis:

  • Homologous gene identification - Paralogues and Orthologues
  • Ensembl - orthologue prediction, MultiContigView
  • EntrezGene - BLink, Homologene
  • Comparative Genome Analysis - UCSC, ECR browser

Working with Encode Data:

  • Epigenetics
  • ENCODE project
  • ENCODE portal
  • Browsing ENCODE data with UCSC
  • Browsing ENCODE data with Ensembl
  • Ensembl Regulatory Build

Proteins, Complexes and Pathways:

  • UniProt
  • InterPro/Pfam protein
  • PDBe/PDBSum
  • IntAct
  • Reactome/Metacyc

ncRNA:

  • Rfam
  • MicroRNA/targets
  • lncRNA db and Vega
  • RNACentral

More Complex Genome Browsing:

  • Ensembl Biomart
  • UCSC Table Browser
  • Uploading your own data

Genomic Variation:

  • Ensembl SNP information, Geneview in dbSNP
  • Genotyping
  • Haplotypes and HapMap
  • Haploview

Variation, Function and Disease:

  • Polyphen, SIFT
  • Ensembl VEP
  • OMIM
  • COSMIC
  • DECIPHER
  • GEO
  • ONTOLOGIES

Module material

Coming soon.

Module presentations

Coming soon.

Sunday pm:

  • 15:30 - 16:00 Registration
  • 16:00 - 18:00 Introduction - Participant talks and Instructor talks
  • 19:00 Dinner

Monday Day 1:

  • 09:00 - 10:00 Introductory talk
  • 10:00 - 10:30 Coffee
  • 10:30 - 12:00 Module 1(Introduction to Ensembl)
  • 12:00 - 12:30 Own research / ask the instructors
  • 12:30 - 13:30 Lunch
  • 13:30 - 15:00 Module 2 (introduction to UCSC and other browsers)
  • 15:00 - 15:30 Coffee
  • 15:30 - 17:00 Own research / ask the instructors

Tuesday Day 2:

  • 09:00 - 10:30 Module 3 (Comparative Sequence Analysis)
  • 10:30 - 11:00 Coffee
  • 11:00 - 12:30 Own research / ask the instructors
  • 12:30 - 13:30 Lunch
  • 13:30 - 15:00 Module 4 (Working with Encode data)
  • 15:00 - 15:30 Coffee
  • 15:30 - 17:00 Own research / ask the instructors

Wednesday Day 3:

  • 09:00 - 10:30 Module 5 (Proteins, Complexes and Pathways)
  • 10:30 - 11:00 Coffee
  • 11:00 - 12:30 Module 5 cont.
  • 12:30 - 13:30 Lunch
  • 13:30 - 15:00 Module 6 (ncRNA)
  • 15:00 - 15:30 Coffee
  • 15:30 - 16:30 Own research / ask the instructors
  • 16:30 - 17:00 Module 7 Talk (Metagenomics)

Thursday Day 4:

  • 09:00 - 10:30 Module 8 (More complex genome browsing)
  • 10:30 - 11:00 Coffee
  • 11:00 - 11:30 Module 8 continued
  • 11:30 - 12:30 Own research / ask the instructors
  • 12:30 - 13:30 Lunch
  • 13:30 - 15:00 Module 9 (Genomic Variation)
  • 15:00 - 15:30 Coffee
  • 15:30 - 16:00 Module 9 cont.
  • 16:00 - 17:00 Own research / ask the instructors
  • 19:00 Course Dinner

Friday Day 5:

  • 09:00 - 10:30 Module 10 (Variation, Expression and Disease)
  • 10:30 - 11:00 Coffee
  • 11:00 - 12:00 Own research / ask the instructors
  • 12:00 - 12:30 Module 11 Talk (Next Gen Sequencing)
  • 12:30 - 13:30 Lunch
  • End of Workshop
* quick link - http://q.sanger.ac.uk/e37s1wo9