Computational

Working with Parasite Database Resources

October 18th - 23rd 2015

Wellcome Genome Campus, Hinxton, UK

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.

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!!”

Programme

The programme will include lecture and practical computational sessions
covering the following topics:

  • 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).

Instructors and speakers

Instructors
The workshop 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).

Guest speakers
Kirk W. Deitsch Weill Cornell Medical College, USA
Mohamed-Ali Hakimi INSERM, France
Ross Waller University of Cambridge, UK

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 is subsidised by the Wellcome Genome Campus
Advanced Courses and Scientific Conferences Programme. This is a
residential
course and there is a fee of £525 towards board and lodging
for non-commercial applicants. Please contact us for the commercial fee.

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

Bursaries

Bursaries
UK: Advanced Courses are subsidised for non-commercial
applicants from anywhere in the world. Additional, limited bursaries are
available (up to 50% of the course fee) 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.

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