Human and Vertebrate Genomics: Bioinformatics Tools and Resources (Montevideo, Uruguay)

September 12th - 16th 2016

Montevideo, Uruguay

Summary

This 5-day course 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 course, 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.

Programme

The programme will include lectures and practical, computer-based
sessions covering the following topics:
(View
the full list of resource URLs here
  |  View
the draft timetable here
)

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

non-coding RNA:

  • 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

Instructors and speakers

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

Prerequisites
The course 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
Overseas courses are free to attend for non-commercial applicants.

Applications
Applications for this course can be completed online. If you have any
problems with the online application process, please contact us.

Please note: Applications
must be supported by a
recommendation from a scientific or clinical sponsor (e.g. supervisor or
head of department). A request for a supporting
statement will be sent
to your nominated sponsor automatically during
the application process.
Applicants must ensure that their sponsor
provides this supporting
statement by the application deadline. Applications without a supporting
statement cannot be considered.

Deadlines
Deadline for Applications: Closed

 

Cost

Bursaries
Overseas courses are free to attend for non-commercial
applicants. Limited bursaries to cover travel, accommodation and
sustenance costs are available and are awarded on merit. If you would
like to apply for a
bursary, please complete the bursary section of the
online application
form.

Please note that both the applicant
and sponsor are required to provide
a justification for the
bursary as part of the application

Bursary terms and conditions

UK Courses (held at the Wellcome Genome Campus, Hinxton,
Cambridge)
A
limited number of bursaries are available for each course. These are
awarded by the selection committee according to merit. The bursary
covers a maximum of 50% of the course fee, though in exceptional
circumstances an application for the total course fee may be considered.
Where there are many bursary applications, the selection committee may
issue smaller amounts. We cannot assist with travel costs to attend UK
courses.

Overseas Courses (held outside of the UK)
A
limited number of bursaries are available for each course. These are
awarded on merit to cover travel, accommodation and sustenance. The
maximum award for travel (economy class) will be £750.

Bursaries can be applied for as part of the course application form.
Applicants
will be notified of a bursary award along with their place on
the
course, usually within one month of the application deadline. The
decision of the selection committee is
final.

Back to top Back to top