Open Door Workshop: Bangkok, Thailand (7th - 12th Feb 2016)

Open Door Workshop: 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 participants 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.

Applications now closed.

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Information

Course instructors
  • Jane Loveland (Wellcome Trust Sanger Institute)
  • Simon Gregory (Duke University)
  • 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.

Applications now closed

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@wellcomegenomecampus.org.

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.

Topics

Genome Browsing:
  • Ensembl
  • VEGA
  • UCSC
Comparative Sequence Analysis:
  • Homologous gene identification - Paralogues and Orthologues
  • Ensembl - orthologue prediction, MultiContigView
  • NCBI Gene - 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

Course Manuals

Timetable

Sunday pm:

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

18:00 - 19:00 Drinks
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