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Working with Parasite Database Resources

19-24 October 2014

Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

Deadline for applications: 20 June 2014

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 Boris Striepen (University of Georgia, USA)
  • Professor Julius Lukeš (Biology Centre, ASCR, Czech Republic)

Feedback from previous courses

“Can't wait to get back to the lab to put into practice what I've learned...”

“Congratulations for this very well organised and scientifically very rich course!”

“This course was an excellent opportunity for me to visualise the parasite databases and the extreme progress made in the field of parasitology.”

How to apply

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

Cost
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, without exception, and there is a fee of £500 towards board and lodging for non-commercial applicants. The fee for commercial applicants is £1500

Bursaries
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).

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

Please note: Applications must be supported by a recommendation from a scientific sponsor. This can be your 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.

Deadlines
Deadline for applications: 20 June 2014

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