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Working with Parasite Database Resources

18-23 October 2015

Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

Now closed for applications

Course summary

This residential workshop aims to provide experimental biologists working on protozoan parasites with hands-on experience in genomic-scale data analysis, including genome browsers and comparison tools, methods for data integration, and resources for sophisticated data mining. Examples and exercises will be drawn primarily from the EuPathDB.org and GeneDB.org resources and will include a variety of eukaryotic parasitic organisms including Apicomplexa (ie. Plasmodium and Toxoplasma) and kinetoplastida (ie. Trypanosoma and Leishmania). Applicants working on any protozoan parasite from these resources will benefit.

This course is taught as a collaborative effort between the Parasite Genomics Group (Wellcome Trust Sanger Institute, UK) and the Eukaryotic Pathogen Bioinformatics Resource Center (University of Georgia & University of Pennsylvania, US). The majority of this intensive programme will be based on hands-on exercises with lectures on genomics and bioinformatics techniques, in addition to daily keynote presentations by world-renowned parasitologists.

Course programme

  • Visualisation of sequence features and next generation sequencing data using the Artemis genome browser and annotation tool
  • Genome browsing and comparative genomics (ACT, J/GBrowse, SynView)
  • Formulating complex biological queries in computationally accessible form
  • Web-based resources including the GeneDB.org and EuPathDB.org family of databases
  • Integrating functional genomics data (RNA-seq, ChIP-seq, ChIP-chip, microarrays, proteomics, etc) with genome sequence data
  • Theoretical aspects of genome re-sequencing
  • Querying genetic diversity on a genome-wide scale
  • Metabolic pathways and pathway analysis, and compounds
  • Working with next-generation sequence data (mapping, variant calling, etc)
  • An introduction to community curation tools
  • Special topics of particular interest to workshop participants* (*participants will be polled on material they would like to see discussed).

Guest speakers

  • Professor Kirk W. Deitsch (Weill Cornell Medical College, USA)
  • Professor Mohamed-Ali Hakimi (INSERM, France)

Feedback from the 2014 workshop

“Thank you for this wonderful course!”

“The workshop was really amazing! It gave to me the opportunity to investigate in deep some aspects of my research in a very simple way. The instructors were all very competent and friendly.”

“It was a great experience!! I learnt a lot, discovered stuff hands-on and am taking an amazing experience back with me, to my work and life!!”

How to apply

Applicants should have a minimum of a degree in a biological discipline and be actively involved or soon to commence relevant research.

The course tuition fees are subsidised by The Wellcome Trust for researchers based in non-commercial institutions anywhere in the world. This is a residential course and there is a fee of £525 towards board and lodging for non-commercial applicants. The fee for commercial applicants is £1575.

Limited bursaries are available for non-commercial applicants (up to 50 per cent of fee) and are subject to open competition. If you would like to apply for a bursary, please complete the bursary section of the online application form (see below for application process).

Now closed for applications

Wellcome Trust, Gibbs Building, 215 Euston Road, London NW1 2BE, UK T:+44 (0)20 7611 8888