Working with Protozoan Parasite Database Resources (Virtual)

Due to the ongoing situation with Covid-19, this course will be delivered in a virtual format.

This week-long course aims to provide experimental biologists 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 VEuPathDB search strategy system).

Examples and exercises will be drawn primarily from the VEuPathDB.org and GeneDB.org resources focusing on protozoan parasites including Apicomplexa (ie. 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 guest speakers.

For this virtual course, we plan to use a combination of video conferencing, streaming, and online and virtual machine (VM) teaching resources to deliver the different elements of the course as interactively as possible.

The course will run approximately 10:00-17:00 (GMT+1) daily. Some teaching materials may be pre-recorded but participants must be available to attend live, interactive sessions between these times.

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 and JBrowse/GBrowse)
• Formulating complex biological queries in computationally accessible form
• Web-based resources including the GeneDB.org and VEuPathDB.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) using both command-line and web-based (Galaxy) methods
• Introduction to community curation tools

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

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 include instructor talks and guest speaker seminars.

Prerequisites
Applicants should be research scientists or clinicians/clinical scientists/healthcare professionals working on protozoan parasitic organisms.

Please note that due to the virtual format for this course, participants will require minimum computer specifications and internet access to fully benefit.
A guide to these requirements can be found here (PDF).

How to Apply
Please click 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 fee is subsidised by Wellcome Genome Campus Advanced Courses and Scientific Conferences and applies to non-commercial applicants. Please contact us for the commercial fee.

Bursaries
Limited bursaries are available (up to 50% reduction on 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.

Where there are many bursary applications, the selection committee may issue smaller amounts.

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.

Additional funding opportunities
Visit our support page for additional financial support currently available.

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Feedback from the 2019 course (Uruguay):

The manual was very clear and complete, the lectures were dynamic and the tutors fulfil all the doubts we had; we had time and opportunities to talk and make networks between us and to know different works from Uruguay and Brazil during the seminars. Also was really important that the schedule was accomplished perfectly.

It was a great course, in all aspects. Thank you for the opportunity to participate.

I would like to thank you for the excellent opportunity, the knowledge learned will be extremely important for my phd as well as for my life. I would also like to thank all those involved in the organization.

This was one of the best course I have ever done! I mention this in terms of commitment and organisation of the company. Besides, we had a team that was available all the time to help us. Serious professionals, polite and, above all, charismatic. As for the content, I am completely satisfied! Everyone is to be congratulated. And thank you very much.

I would like to thanks again for the amazing work that you do, and the great opportunity. We had a good time learning a lot!.

Thank you so much, this was an incredible opportunity that I would never forget. And thanks to the instructors for sharing their knowledge with us.