This course will introduce crop biologists to methods and approaches for analysing crop genomics data for genotyping. During the course participants will learn about genotyping experimental design, variant calling, comparative genomics using Ensembl, analyse variation data with Ensembl Variant Effect Predictor and explore concepts of genome wide association studies (GWAS).  The content will explain how to make use of existing public data, retrieve, submit and share your data with the community.

Trainers will cover the basics of diversity analysis using R, before analyzing various genomes to assess diversity, investigating gene-phenotype relationships and microsatellites. The course will be delivered through a combination of hands-on training sessions and lectures.

This course will be a virtual event. The content will be delivered over Zoom.  In order to make the most out of the course, you should make sure to have a stable internet connection throughout the week.

Computational practicals will be run on EMBL-EBI's virtual training infrastructure; this means there is no need to have a powerful computer to run exercises or a requirement to install complex software before the course.

Who is this course for?

This course is aimed at wet-lab researchers within Latin America (excluding Chile and Uruguay due to funding restrictions) who are working with and/or generating their own crop genomic data or who are working on genotyping technologies, including data analysis software development. 

Researchers who apply for CABANA courses should have projects in one or more of the CABANA challenge areas (sustainable crop production, communicable diseases, protection of biodiversity).

Please note this course will be taught in English, however some trainers are fluent in either Spanish/Portuguese, and can offer language support where feasible. Priority will also be given to those who have not attended a CABANA event yet.

Scientists from underrepresented ethnic and gender groups are especially encouraged to apply for this workshop, for example women and those with Black and/or Indigenous heritage.

Prerequisites: basic computational or previous bioinformatics experience is required for this workshop, such as basic commands in R. Undergraduate-level knowledge of plant biology would be an advantage.

Please note: The course will use genomic data from crop plant species throughout the week. It will not explore in detail methods for assembling genomes.

What will I learn?

Learning outcomes

After the course, participants should be able to:

• Describe how to design a crop genotyping experiment
• Conduct variant calling and search for a variety of crop genomic motifs such as SSRs and indels 
• Use Ensembl for comparative analysis to explore plant genomes
• Access plant variation data from public resources and use appropriate tools to analyse variation
• Input and study genomics data using R to evaluate genomic diversity
• Select the best method to investigate genomic diversity

Course content

During this course you will learn about:

• How to design sequence-based genotyping experiments and conduct variant calling
• Ensembl tools for browsing plant genomes and variant data
• Assess crop diversity
• Genome wide association studies (GWAS)

This training course is associated with a virtual Train the Trainer workshop you can register for. For any information about the workshop and the application process, please refer to the "How to apply" section on this webpage.

Trainers

Application for Plant bioinformatics course

Incomplete applications will NOT be considered. 

If you have any general queries about the workshop application/registration process please email Guilherme Oliveira and Piv Gopalasingam.

Please note that this course is free, but unexplained absence will result in blacklisting for future courses and opportunities.

There will be a maximum of 30 participants on this course and registration is dependent on selection after successful completion of the application process

Application/Registration will close on 1st November 2021 at 12:00 midday (GMT).

Please note, applicants for the Plant bioinformatics course can also apply for the Train the Trainer workshop.

Application for Train the Trainer workshop

The CABANA Plant bioinformatics workshop will be associated with a Train the Trainer (TtT) workshop. The TtT workshop is aimed at plant researchers from Latin America interested in developing their bioinformatics training skills with the intention of running their own courses in the future. For more information about CABANA TtT workshops please refer to the CABANA website.

The workshop will take place live across four half-day sessions between 7-10 December 2021 virtually using Zoom. Each session will take place around 09:00-13:00 Central Standard Time (UTC-6) with breaks.

The Train the Trainer component of the workshop will:

• provide guidance on general training techniques and appropriate use of methods based on learner needs, including some general 'DO's' and 'DO NOTs' for successful training
• provide a framework for successful curriculum design and further development, to enable trainers to build a course appropriate to their learners' needs
• provide opportunities to practice virtual training delivery.

Please note, applications for both of these workshops have now closed.

Participant flash talks

All participants of the plant bioinformatics course will be asked to give a short presentation about their research work as part of the course. These provide an opportunity to share their research with the other participants and provide a forum for discussion. Further details will be provided for selected applicants.