Working with Protozoan Parasite Database Resources (Montevideo, Uruguay)

10–15 November 2019

Institute of Hygiene, Montevideo, Uruguay

Learn how to use online resources for genomic-scale data analysis of protozoan parasites


In collaboration with the Institute of Hygiene, Montevideo, Uruguay, we are pleased to announce the latest overseas course in Working with Protozoan Parasite Database Resources.

This week-long course aims to provide biomedical researchers and scientists working on protozoan parasites with hands-on experience in genomic-scale data analysis; including genome browsers and comparison tools, primary data analysis, 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 and resources focusing on protozoan parasites including Apicomplexa (i.e. Plasmodium, Toxoplasma & Cryptosporidium) and Kinetoplastida (ie. Trypanosoma & Leishmania). Applicants working on any organism included in these resources will benefit.

The intensive programme will combine hands-on exercises with lectures and discussions on genomics and bioinformatics techniques, along with seminars from distinguished regional guest speakers.

The course is free to attend and open to research scientists and clinicians/clinical scientists/healthcare professionals based Latin America and the Caribbean working with protozoan parasitic organisms. Additional limited bursaries are available to assist with travel and accommodation expenses.

Places are limited and the course will be taught in English, with language support from regional instructors.


The programme will include lectures, discussions 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 and J/GBrowse)
  • Formulating complex biological queries in computationally accessible form
  • Web-based resources including the and 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) using both command-line and web-based (Galaxy) methods
  • Introduction to community curation tools
  • Participants are encouraged to bring their own data, to use in consultation and/or in-workshop analysis

Learning Outcomes

After attending this course, participants should be able to:

  • Use state-of-the-art bioinformatics software including web-based resources as well as in a UNIX-like environment to explore parasite database resources.
  • Identify opportunities and limitations of the different methodologies in analysing parasite genomics data
  • Apply software and web-based resources to visualise and analyse next generation sequencing datasets for parasitology research.
  • Apply software and web-based services to browse genomes and to display genome comparisons.
  • Integrate and query large-scale genomic and functional genomic databases to answer biology-related research questions and develop testable hypotheses

Instructors and speakers

Course instructors

Ulrike Böhme
Wellcome Sanger Institute, UK

Kathryn Crouch
University of Glasgow, UK

Omar Harb
University of Pennsylvania, USA

Thomas Otto
University of Glasgow, UK

The course will also include distinguished regional instructors and speakers. Further details will be posted shortly.

How to apply

Applicants should be research scientists or clinicians/clinical scientists/healthcare professionals based Latin America and the Caribbean working with protozoan parasitic organisms.

Places are limited and the course will be taught in English, with language support from regional instructors.

How to Apply
Please click on the Apply button above to begin the online application process. Places are limited and will be awarded on merit. 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, line manager 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.


The course is subsidised by Wellcome Genome Campus Advanced Courses and Scientific Conferences and is free to attend for non-commercial applicants. Please contact us for the commercial fee.


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. If you would like to apply for a bursary, please complete the bursary section of the online application form.

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.

Please note that both the applicant and sponsor are required to provide a justification for the bursary as part of the application. Priority will be given to applicants from low- and middle-income countries.

Accommodation services phishing scam – please be vigilant. More information.


Feedback from the 2018 course (Malaysia):

“Thank you for holding such a useful course!”

“I wish to extend my gratitude to the screening committee for not only shortlisting me as participant but also providing me the bursary. I owe special thanks to Thomas and Omar for their exceptional guidance.”

“I really want to thank the instructors for making this course a memorable one and making us learn in an easy way.”

“All the instructors were very friendly and helpful all the way.”

“Overall the course is very informative covering most of the aspects of using big data. I liked the stay in Malaysia. Instructors were really great. Enjoyed learning from them. Above all it was a very good experience for me.”

“It was a very intensive course, but every topic was interesting and helpful.”

“The course was well organized”

“This course is very helpful for me to start the bioinformatic work especially on malaria parasite.”

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