Open Door Workshop: Montevideo, Uruguay (11th - 16th Sept 2016)

Open Door Workshop: Montevideo, Uruguay (11th - 16th Sept 2016)

Human and Vertebrate Genomics: Bioinformatics Tools and Resources.

Institute of Hygiene, Montevideo, Uruguay.
Ref: ODW-Uruguay

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 Latin America and the Caribbean. Please note: The course will be taught in English.

Learning Outcomes:

By the end of this workshop the participants will be able to:

  • Browse and query genomes, and be able to interpret how genes and other features are displayed. Download data with BioMart and Table browser, upload their own data and interpret different biotypes.
  • Identify paralogous and orthologous genes, compare genomes and identify evolutionary conserved sequences.
  • Explore and interpret ENCODE data.
  • Query protein and domain databases, interpret protein structures, perform basic homology modelling and investigate pathway databases.
  • Access non-coding RNA databases, microRNA resources and view and interpret them.
  • Query genomic variation resources, integrate variation information and view this in the context of the genome and interpret genotypes and haplotypes.
  • Explore variation and the relationship between genotype, phenotype and disease using a variety of tools and databases.
  • Evaluate Next Generation Sequencing methods and their applications.

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.

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Information

Course instructors
  • Jane Loveland (Wellcome Trust Sanger Institute)
  • Simon Gregory (Duke University)
  • Ben Moore (The European Bioinformatics Institute)
  • Matt Clark (The Genome Analysis Centre)
  • Pablo Rabinowicz (Independent Consultant)
  • 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 Latin America and the Caribbean (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 - 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.

Applications are now open via the Wellcome Trust Advanced Courses portal:

https://wtac.hinxton.wellcome.ac.uk/portal/desktopdefault.aspx

Queries

Any queries should be sent to opendoor@wellcomegenomecampus.org.

Deadlines

Closing date for application is 27th May 2016. 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

Timetable

Likely timetable (TBC)
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 - 14:00 Lunch
14:00 - 15:30 Module 2 (introduction to UCSC and other browsers)
15:30 - 16:00 Coffee
16:00 - 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 - 14:00 Lunch
14:00 - 15:30 Module 4 (Working with Encode data)
15:30 - 16:00 Coffee
16:00 - 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 - 14:00 Lunch
14:00 - 15:30 Module 6 (ncRNA)
15:30 - 16:00 Coffee
16:00 - 17:00 Own research / ask the instructors

Thursday Day 4:

09:00 - 10:30 Module 7 (More complex genome browsing)
10:30 - 11:00 Coffee
11:00 - 11:30 Module 7 continued
11:30 - 12:30 Own research / ask the instructors
12:30 - 14:00 Lunch
14:00 - 15:30 Module 8 (Genomic Variation)
15:30 - 16:00 Coffee
16:00 - 16:30 Module 8 cont.

19:00 Course Dinner

Friday Day 5:

09:00 - 10:30 Module 9 (Variation, Expression and Disease)
10:30 - 11:00 Coffee
11:00 - 12:00 Own research / ask the instructors
12:00 - 12:30 Module 10 Talk (Next Gen Sequencing)
12:30 - 14:00 Lunch
End of Workshop