Working with Parasite Database Resources (Montevideo, Uruguay)

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 taught as a collaborative effort between the Parasite
Genomics Group (Wellcome Trust Sanger Institute, UK) and 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). 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 guest
speakers.

Please note: The course is open to scientists and
clinicins based in Latin American and Carribean institutes and there is
no fee to attend. Bursaries are available to cover travel and
accommodation expenses. There are 20 places available and the course will
be taught in English.

Feedback from the 2015 course

-The atmosphere encourages learning and I love that aspect so much.
Thank you for all of this.
-I would really like to thank all the instructors for this useful
workshop. The course structure was really well planned.
-Thank you very much for organizing this wonderful training.
-Thank you very much for running this course. It’s been absolutely
fantastic and I really have learned how to use a
huge repertoire of tools. It’s also been a fantastic thing to meet and
mingle with members of the parasitology
community and to experience different cultures and attitudes to
learning.

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.

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 (a multi-centre
collaborative
effort including the Universities of Georgia &
Pennsylvania in the
US and Liverpool in the UK).

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 guest speakers.

Guest speakers will be announced shortly.

Prerequisites
Applicants
should be scientists or clinicians based in institutes in
Latin America or the Carribean and should be
actively involved in, or
soon to commence, relevant research. Please note that
the course will be taught in English.

Cost
Overseas courses are free to attend for non-commercial applicants.
Additional bursaries are available for travel and accommodation expenses
(see “Bursaries” tab).

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: 17 June 2016

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.