This introductory workshop will provide hands-on training on protein and structural bioinformatics resources in the context of molecular dynamics, biomolecular modelling, and simulations. The workshop is sponsored by the Collaborative Computational Project for Biomolecular Simulation (CCPBioSim).

Participants will gain knowledge and skills for searching, selecting, and assessing publicly available protein biodata for use in downstream methods relating to biomolecular modelling and molecular dynamics simulations. The workshop will begin with an introduction to basic concepts in genomics and associated resources, then to protein resources, their uses and limitations, and validation of both experimentally and predicted protein structures. 

Finally, the workshop will cover variant effect prediction and offer participants hands-on group projects to bring together the previous days’ training with highly-experienced mentors. During this time, participants will work with simulated datasets to answer small research questions, then present findings thereafter. Participants will also get the chance to network with one another, trainers, and workshop organisers.

Who is this course for?

This workshop is suitable for scientists in any sector performing or using biomolecular modelling, molecular dynamics and/or simulation in their work. 

You may be regularly using biodata from various databases but unsure about its quality, how to validate its quality, or know its limitations. 

You may have knowledge gaps in biological concepts such as alternative splicing and nuances of genomics, and how this could affect protein sequence, structure and other downstream biological and modelling processes.

You may be new to biomolecular modelling and/or simulation and wish to obtain knowledge and skills around the use of biodata in your work.

Your work can be bioinformatics, computational, wet-lab, or a mix. Experience in basic bioinformatics is not required but may be useful. 

Membership of the CCPBioSim community is desirable but not essential to participate. The intended audience for this workshop is broad and you are encouraged to read through the description, learning outcomes and course content to ensure you will benefit. Applications are welcome across the world and please note you do not have to fulfil all the criteria in order to apply for this workshop.

What will I learn?

Learning outcomes

After the workshop you should be able to: 

• Browse and search EMBL-EBI nucleotide, protein, and structure databases
• Validate experimentally determined and predicted protein structures
• Predict the effects of variants on protein structure and function
• Apply training to small research questions in groups and present findings

Course content

During this workshop you will learn about: 

• EMBL-EBI nucleotide resources such as: Ensembl, EVA, and ENA
• EMBL-EBI protein structure resources such as: UniProt, PDBe-KB, and the AlphaFold Database
• Variant effect prediction tools such as VEP

Trainers

Please read our support page before starting your application, noting that in this case, a letter of support is not required. In order to be considered for a place on this workshop, 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 workshop expectations
  • data availability

Please submit all documents during the application process by 09:00 BST on Monday 14 August 2023. 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 Friday 18 August 2023. If you have any questions regarding the application process please contact Jane Reynolds.

The registration fee of £50.00  includes:

• Catering as detailed on the workshop programme
• Daily shuttle service to and from Cambridge railway station and Wellcome Genome Campus
• Bespoke workshop handbook with links to all workshop materials
• Use of a computer in the EMBL-EBI training suite throughout the workshop

Catering

The workshop includes catering as detailed on the programme tab. Successful applicants will be asked for any dietary requirements and allergies upon registration. 

Posters

All participants are expected to present a poster that will be displayed during the workshop outside the training room. Successful applicants will be asked to submit their poster upon registration. We will print these for you and have them available when you arrive on site.

All posters should:

•         be A2 in size – 420mm x 594 mm
•         be in a portrait orientation
•         include your photograph and contact information

We expect the posters to act as a talking point between you, other participants and the trainers on the workshop. The posters will be displayed throughout the week so people can view them during breaks and lunch. 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 the gathered participants.