This course will take you through a selection of genomic tools and open resources to help you explore plant genomes and answer biological questions. Covering a range of omics data including genomic, proteomic, and imaging data, this course will show you where to find relevant data and how to use publicly available tools to connect across resources supporting plant genomic data-driven knowledge discovery. 

Throughout the course, you will address essential questions, such as: 

• How can genomic data inform crop breeding strategies? 

• Which genetic variations contribute to plant resilience in changing environments? 

• How can proteomics enhance agricultural productivity? 

The course instructors will guide you on how to navigate the different resources efficiently. You will be shown how to submit your sequence to a public archive, explore gene-related information and variants within specific genes. You will investigate functional conservation and expression patterns within gene families, explore protein functional information, as well as plant-derived metabolomics and lipidomics data, and analyse gene expression data.

Virtual course

Participants will learn via a mix of pre-recorded lectures, live presentations, and trainer Q&A sessions. Practical experience will be developed through trainer-led computational exercises. Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack.

Computational practicals will run using online tools, meaning participants will not require access to a powerful computer or install complex software on their own machines. In the week before the course, there will be a brief induction session.

Participants will need to be available between the hours of 09:00 – 17:00 GMT each day of the course. Trainers will be available to assist, answer questions, and provide further explanations during these times.

Who is this course for?

This course is aimed at plant scientists wishing to gain familiarity with open, online tools and resources hosting plant data, and how to query across those resources to answer biological questions. No programming experience is required. 

What will I learn?

Learning outcomes

After the course you should be able to: 

• Search for data across bioinformatics resources and explore the results
• Investigate plant samples and associated genomic and genetic variation data
• Explore conservation and expression of gene families
• Interpret functional genomics data including gene expression profiles, gene ontology annotations, and plant-derived metabolomics and lipidomics datasets
• Select tools to help you set up and manage plant experiments in the field
• Run image analyses on phenotypic images

Course content

During this course you will learn about: 

• Plant genomics resources including genomes from the Darwin Tree of Life project, sequences in the European Nucleotide Archive (ENA), variants in the European Variation Archive (EVA), and expression data in the Expression Atlas
• Navigating plant-related genomics knowledgebases including Ensembl Plants, Gramene, and MGnify (metagenomics)
• Protein resources including UniProt and links to AlphaFold DB’s 3D protein models
• Plant data stored in other resources such as Metabolights (for metabolomics data) and PRIDE (for proteomics) 
• Collecting plant phenotyping data and tools to support this such as Germinate and the BioImage Archive 

Trainers

Please read our support page before starting your application. In order to be considered for a place on this course, you must do the following:

• Complete the online application form.
• Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
  • pre-requisite skills and knowledge
  • current work and course expectations
• Upload one letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course.

Please submit all documents during the application process by 23:59 on Sunday 1 September 2024. Items marked * in the application are mandatory. Incomplete registrations will not be processed. 

All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by 16 September 2024. If you have any questions regarding the application process please contact your event organiser.

The registration fee of £225.00 includes a bespoke course handbook with links to all course materials

Flash talks
All participants 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. Successful applicants will be required to submit their talks upon registration.

Posters
All participants are expected to present a poster that will be shared via the course handbook and other virtual platforms used for the course. Successful applicants will be asked to submit their poster upon registration. 

All posters should:

• Be in PDF format
• Be in A2 - 420mm x 594 mm
• Have a maximum file size of 3 MB
• Not use a transparent background
• In portrait orientation
  • You can use PowerPoint, Canva, or another third-party application to design and save a 16:9 image.

We expect the posters to act as a talking point between you, other participants and the trainers on the course. The posters can be viewed before and during the course. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with other participants.

Financial assistance

Limited financial assistance is provided by EMBL-EBI Training in the form of registration fee waivers. 

Your place in the course is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Registration fee waiver

The fee waiver will cover the registration fee that you have paid to attend the course.

Application

You may apply for financial assistance when submitting your application. In your application you will be asked to provide justification for the financial assistance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your course application.

Selection

The scientific organisers will select the recipients of financial assistance during the course application selection process. Results will be communicated along with the course application outcome. Selection results do not impact your acceptance to the course. Selection for registration fee waivers is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career with priority given to applicants from low and middle-income countries.