Course at EMBL-EBI

EuroFAANG GENE-SWitCH workshop: utilisation of GENE-SWitCH data in Ensembl and beyond

This one and a half day workshop will provide detailed training on the utilisation of the wealth of data generated by the EuroFAANG GENE-SWitCH project that is delivering new underpinning knowledge for pig and chicken agriculture. The workshop will primarily focus on the comprehensive and integrated annotation of the chicken and pig genomes by the Ensembl Genome Browser. The course will also include a deeper dive from the Ensembl analysis teams into gene annotation and regulation, and demonstrations of the specific analyses and genomic prediction models generated by GENE-SWitCH researchers.

Additional information

The course fee is inclusive of one night of accommodation and catering, including dinner.

We plan to deliver this course in an in-person manner onsite at our training suite at EMBL-EBI, Hinxton.  Hybrid options are not currently available. Please be aware that we are continually evaluating the ongoing pandemic situation and, as such, may need to change the format of courses at short notice. Your safety is paramount to us; you can read our COVID guidance policy for more information. All information is correct at time of publishing.

Please also note that there are delays in the issuing of visas from the UK Government. We encourage you to check if you need a visa and apply in plenty of time before travelling. Current waiting times are more than six weeks. For more information please visit the UK Government website.

Who is this course for?

Industry stakeholders or academic researchers looking to utilise GENE-SWitCH data and analysis for translation into the pig and poultry sectors. Also researchers looking to utilise GENE-SWitCH data and Ensembl for furthering functional annotation research.

A number of spaces are reserved for EuroFAANG stakeholders and EU animal agriculture industry organisations.

What will I learn?

Learning outcomes

After the course you should be able to:

  • Utilise Ensembl to view genomic regions and manipulate the view to add features they are interested in
  • Employ Ensembl to view homologous genes and genomic regions, functional elements involved in gene regulation and their activity in different cell types and timepoints
  • Understand and explore the wealth of EuroFAANG data with Ensembl tools to utilise in research or industry settings.
  • Have a deeper understanding of the research being conducted, and genomic prediction models being generated, by GENE-SWitCH researchers
Course content

During this course you will learn about: 

  • Ensembl Genome Browser
  • Gene annotation and gene regulation analysis
  • The search loading and utilisation of Track Hubs into the Ensembl Genome Browser
  • FAANG analysis data standards
  • GENE-SWitCH results and genomic prediction models from GENE-SWitCH researchers

Trainers

Peter Harrison
EMBL-EBI
Garth Ilsley
EMBL-EBI
Benjamin Moore
EMBL-EBI
Alexey Sokolov
EMBL-EBI

Please read our page on application support 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

Please submit by 23:59 GMT on 27 November 2022. 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 5 December 2022. If you have any questions regarding the application process please contact Shereen Pethania.

The registration fee of £160.00 includes:

  • Catering as detailed on the course programme
  • Accommodation for one night (31 January) 
  • Bespoke course handbook with links to all course materials
  • Use of a computer in the EMBL-EBI training suite throughout the course
  • Shuttle bus on the final course day to Cambridge train station 

There are delays in the issuing of visas from the UK Government. We encourage you to check if you need a visa and apply in plenty of time before travelling. Current waiting times are 6+ weeks. For more information please visit the UK Gov website: https://www.gov.uk/guidance/visa-decision-waiting-times-applications-outside-the-uk#when-you-might-wait-longer

Accommodation 

Hotel rooms (including breakfast) will be provided onsite at Hinxton Hall Conference Centre. Please contact them directly if you wish to arrange to stay additional nights around the course dates.

Catering

The course includes catering. Successful applicants will be asked for any dietary requirements and allergies upon registration.

 

 

 

Applications close
27 November 2022

31 January - 01 February 2023
European Bioinformatics Institute United Kingdom
£160.00 (inclusive of one night of accommodation and catering, including dinner)
Contact
Shereen Pethania
Open application with selection
30 places

Organisers
  • Peter Harrison
    EMBL-EBI
  • Benjamin Moore
    EMBL-EBI

In association with:


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