Working with Parasite Database Resources (Blantyre, Malawi)

October 15th - 20th 2017

Blantyre, Malawi

Summary

This week-long course aims to provide experimental biologists working on
eukaryotic pathogens 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 (including
the EuPathDB
search strategy system).

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). One important aspect is for the participants
to understand the origin of the underlying data in the databases and how
to analyse it. Applicants working on any organism included in these
resources will benefit.

This course is a collaborative effort between the Parasite Genomics Group
(Wellcome Trust Sanger Institute, UK), the Eukaryotic Pathogen
Bioinformatics Resource Center (a multi-centre collaborative effort
including the Universities of Georgia & Pennsylvania in the US and
Liverpool in the UK), and the University of Malawi College of Medicine in
Blantyre,

The majority of this intensive course will be based on hands-on exercises
with lectures on genomics and bioinformatics techniques, in addition to
keynote presentations by distinguished regional guest speakers.

Please note: The course is open to scientists and
clinicins/healthcare professionals based in African institutes and there
is no fee to attend. Bursaries are available to assist with travel and
accommodation expenses. Places are limited and the course will be taught
in English.

Learning outcomes
After attending this course, participants should be able to:

  • Comfortably work with state-of-the-art bioinformatics software both using online resources as well as in a UNIX-like environment
  • Have
    a good understanding of the application, opportunities, visualization
    and analysis of next generation sequencing datasets for parasitology
    research
  • Integrate and
    query large-scale genomic and functional genomic databases to answer
    biology-related research questions and develop testable hypotheses
  • Use software and web-based services to browse genomes, visualise next generation data and display genome comparisons

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 and GO enrichment analysis
  • Working with next-generation sequence data (mapping, variant calling, RNA-Seq etc)
  • An introduction to community curation tools
  • Participants are encouraged to bring own data, to use in consultation and/or in-workshop analysis.

Learning outcomes
After attending this course, participants should be able to:

  • Comfortably work with state-of-the-art bioinformatics software both using online resources as well as in a UNIX-like environment
  • Have a good understanding of the application, opportunities, visualization and analysis of next generation sequencing datasets for parasitology research
  • Integrate and query large-scale genomic and functional genomic databases to answer biology-related research questions and develop testable hypotheses
  • Use software and web-based services to browse genomes, visualise next generation data and display genome comparisons

Instructors and speakers

This course is a collaborative effort between the
Parasite Genomics
Group (Wellcome Trust Sanger Institute, UK), the
Eukaryotic Pathogen
Bioinformatics Resource Center (a multi-centre
collaborative effort
including the Universities of Georgia &
Pennsylvania in the US and
Liverpool in the UK), and the University of
Malawi College of Medicine
in Blantyre,

The programme will also feature keynote presentations by distinguished
regional guest speakers.

How to apply

Prerequisites
Applicants
should be scientists or clinicians/healthcare professionals
based in institutes in African and should be
actively involved in, or
soon to commence, relevant research/clinical work. Please
note
that the course will be taught in English.

Cost
Overseas courses are free to attend for
non-commercial applicants. Please contact us for the commercial fee.

Limited bursaries are also available to assist with travel,
accommodationa nd sustenance expenses. Please see the “Cost/Bursaries”
tab above for more information.

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 and bursaries

Cost
Overseas courses are free to attend for non-commercial applicants. Please
contact us for the commercial fee.

Bursaries
Limited bursaries to assist with 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.

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