Course at EMBL-EBI
Summer school in bioinformatics
This course provides an introduction to the use of bioinformatics in biological research, giving participants guidance for using bioinformatics in their work whilst also providing hands-on training in tools and resources appropriate to their research.
Participants will initially be introduced to bioinformatics theory and practice, including best practices for undertaking bioinformatics analysis, data management, and reproducibility. To enable specific exploration of resources in their particular field of interest, participants will then be divided into focused groups to work on a project.
Participants will be required to review some pre-recorded material prior to the start of the course.
Group projects
A major element of this course is a group project, where participants will be placed in small groups to work together on a challenge set by trainers from EMBL-EBI and external institutes. This allows people to explore the bioinformatics tools and resources available in their area of interest and apply them to a set problem, providing participants with hands-on experience relevant to their own research. The group work will culminate in a presentation session involving all participants on the final day of the course, giving an opportunity for wider discussion on the benefits and challenges of working with biological data.
Groups are mentored and supported by the trainers who set the initial challenge, but the groups will be responsible for driving their projects forward, with all members expected to take an active role. Groups are pre-organised before the course, and all group members will be sent some short “homework” in preparation for their project work prior to the start of the course.
Basic outlines of the projects on offer this year are given below. In your application, you must indicate your first and second choice of project, based on which you think would benefit your research most. Not all projects may be offered, and final decisions on which projects will be run during the course will be made based on the number of applicants per project.
Most of the projects cover mammalian data sets, however, in many cases, the methods and approaches taught are transferable to data from various species.
Group project one | Genome variation across human populations
Natural variation between individuals or between different human populations is a result of genome mutations throughout evolutionary history. Some mutations may become fixed because of their beneficial effect while most drift among individuals. During this project, you will investigate genomic variation between two separate human populations of European and Asian descent. Using sequence data from a number of individuals from each population, you will use a range of bioinformatics tools to discover variants that exist between them. In the second section of the project, you will attempt to analyse the functional consequences of the variants you have identified, attempting to find clinical association and linking them to phenotypes.
Project mentor: Baron Koylass | EMBL-EBI
Group project two | Interpreting functional information from large scale protein structure data
This project will introduce you to the wealth of publicly available data in the Protein Data Bank (PDB) and give you the opportunity to investigate how large subsets of structure data can be used to analyse protein features and determine function. In the project, you will learn how to: identify relevant protein structures, collate and interpret functional information, and implement this process programmatically.
Project mentor: Preeti Choudhary | EMBL-EBI; Marcus Bage | EMBL-EBI
Group project three | Modelling cell signalling pathways
Curating models of biological processes is an effective training in computational systems biology, where the curators gain an integrative knowledge of biological systems, modelling, and bioinformatics. You will learn to encode and simulate ordinary differential equation models of signalling pathways from a recent publication using user-friendly software such as COPASI even without extensive mathematical background. You will learn to perform in-silico experiments, new predictions, and develop hypotheses. Furthermore, you will learn how to annotate models and re-use pre-existing models from open repositories such as BioModels.
Project mentors: Rahuman Sheriff | EMBL-EBI; Krishna Tiwari | EMBL-EBI
Group project four | Networks and pathways
This project will cover typical bioinformatics analysis steps needed to put differentially expressed genes into a wider biological context. You will start with gene expression data (RNA-seq) to build an initial interaction network. Next, you will learn to combine public network datasets, identify key regulators of biological pathways, and explore biological function through network analysis. You will get first-hand experience in integration and co-visualising with additional data and functional enrichment analysis. All this helps to put the initial results into a previously known context and provide hypotheses for potential follow up experiments. We will use Cytoscape, Expression Atlas, g:Profiler, StringDb, among other tools. We also may give a few R packages a try.
Project mentor: Priit Adler | University of Tartu
Group project five | Reusing FAIR Bioimage data: an AI application
Biological imaging is a rapidly growing field with a vast potential of re-use for further scientific research and development. Re-use of bioimage data requires FAIR (Findable, Accessible, Interoperable, Reusable) data, by public repositories that support FAIR sharing, such as the BioImage Archive. This project aims to showcase one of many ways of reusing bioimage data, by applying artificial intelligence (AI) models on selected datasets in the BioImage Archive. In this project, you will learn to search and download the extensive variety of data that is held in this publicly available data resource. You will also use Jupyter Python notebooks to visualise image data in the archive and deploy AI models on selected datasets.
Project mentors: Aybuke Kupcu Yoldas | EMBL-EBI; Teresa Zulueta-Coarasa | EMBL-EBI
Additional information
Please note that we will operate this course face-to-face at EMBL-EBI in Hinxton. Hybrid options are not currently available. We reserve the right to change the format of this course or cancel it, due to the ongoing coronavirus pandemic.
Who is this course for?
Applicants are expected to be at an early stage of using bioinformatics in their research with the need to develop their knowledge and skills further. No previous knowledge of programming is required for this course; group projects may give you the opportunity to learn basic programming, but participants will be supported in this by their mentors. Depending on your chosen project, an introductory programming tutorial may be given as homework prior to attending the course.
Though programming skills are not a prerequisite for attending the course, we will ask participants to specify their current level of programming skills in the applications. This will allow the mentors to target the group projects better to the skills and needs of the final course participants.
What will I learn?
Learning outcomes
After this course you should be able to:
- Discuss applications of bioinformatics in biological research
- Browse, search, and retrieve biological data from public repositories
- Use appropriate bioinformatics tools to explore biological data
- Describe ways that biological data can be stored, organised and integrated
Course content
During this course you will learn about:
- Bioinformatics as a science
- Designing bioinformatics studies
- Data management and reproducibility
- Basic tools and resources for bioinformatics
The exact range of resources and tools covered will vary depending on the group project undertaken; there will be no opportunity for you to analyse your own data during this course.
Trainers
Priit Adler
University of Tartu Dayane Rodrigues Araujo
EMBL-EBI Marcus Bage
EMBL-EBI Alex Bateman
EMBL-EBI Preeti Choudhary
EMBL-EBI Baron Koylass
EMBL-EBI Loïc Lannelongue
University of Cambridge Lee Larcombe
Apexomic Hedi Peterson
University of Tartu Amanda M. Saravia-Butler
NASA Ames Research Center Anna Swan
EMBL-EBI Rahuman Sheriff Malik Sheriff
EMBL-EBI Krishna Kumar Tiwari
EMBL-EBI Aybuke Kupcu Yoldas
EMBL-EBI Teresa Zulueta-Coarasa
EMBL-EBI
University of Tartu
EMBL-EBI
EMBL-EBI
EMBL-EBI
EMBL-EBI
EMBL-EBI
University of Cambridge
Apexomic
University of Tartu
NASA Ames Research Center
EMBL-EBI
EMBL-EBI
EMBL-EBI
EMBL-EBI
EMBL-EBI
Programme
Time | Topic | Trainer |
Day one – Monday 12 June 2023 | ||
10:00 – 10:30 | Registration and coffee | |
10:30 – 11:30 | Welcome and introduction | Dayane Araújo and Anna Swan |
11:30 – 12:30 | An introduction to EMBL-EBI data resources | Anna Swan |
12:30 – 14:00 | Lunch and poster session | |
14:00 – 15:00 | The science of bioinformatics | Alex Bateman |
15:00 – 15:30 | Coffee break | |
15:30 – 17:00 | Good data management: making your data FAIR | Dayane Araújo |
17:00 – 18:00 | Accommodation check-in at Hinxton Hall Conference Centre | |
18:00 – 19:30 | Pre-dinner talk with Jenny Cook, networking, and drinks | |
19:30 | Evening meal | |
Day two – Tuesday 13 June 2023 | ||
09:00 – 09:30 | Day introduction and mini-challenge | Dayane Araújo and Anna Swan |
09:30 – 11:00 | Introductory computational and data visualisation skills | Priit Adler |
11:00 – 11:30 | Coffee break | |
11:30 – 13:00 | Introductory computational and data visualisation skills | Priit Adler |
13:00 – 14:00 | Lunch featuring EMBL-EBI biocurators and poster session | |
14:00 – 15:00 | Tips, tricks, and guidance for bioinformatics | Hedi Peterson |
15:00 – 17:30 | Introduction to group projects and meet your mentors | All mentors |
17:30 | End of day two | |
19:00 | Evening meal | |
Day three – Wednesday 14 June 2023 | ||
09:00 – 09:15 | Day introduction and project update | Dayane Araújo and Anna Swan |
09:15 – 10:30 | Group work | All |
10:30 – 11:00 | Coffee break | |
11:00 – 12:30 | Group work | All |
12:30 – 13:30 | Lunch | |
13:30 – 14:30 | Keynote | Loïc Lannelongue |
14:30 – 15:30 | Group work | All |
15:30 – 16:00 | Coffee break | |
16:00 – 17:30 | Group work | All |
17:30 | End of day three | |
19:00 | Evening meal | |
Day four – Thursday 15 June 2023 | ||
09:00 – 09:30 | Day introduction and project two-minute updates | Dayane Araújo and Anna Swan |
09:30 – 10:30 | Group work | All |
10:30 – 11:00 | Coffee break | |
11:00 – 13:00 | Group work | All |
13:00 – 14:00 | Lunch | |
14:00 – 15:00 | Keynote | Amanda M. Saravia-Butler |
15:00 – 15:30 | Coffee break | |
15:30 – 18:00 | Group work | All |
18:00 – 18:30 | Walk to dinner | |
18:30 | Dinner at The Red Lion, Hinxton | |
Day five – Friday 16 June 2023 | ||
09:00 – 09:15 | Day introduction | Dayane Araújo and Anna Swan |
09:15 – 10:30 | Preparation of group projects | All |
10:30 – 11:00 | Coffee break | |
11:00 – 12:00 | Group presentations | All |
12:00 – 13:00 | Lunch | |
13:00 – 14:00 | Group presentations and award ceremony | All |
14:00 – 14:30 | Course feedback and wrap up | All |
15:00 | Coach to Cambridge Train Station |
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
- data availability
- Select your first and second choices for the group project options. Please note you must choose two separate projects.
- 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 BST on 12 March 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 20 March 2023. If you have any questions regarding the application process please contact Sophie Spencer.
The registration fee of £825.00 includes:
- Catering as detailed on the course programme
- Accommodation for four nights (12, 13, 14, and 15 June)
- 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
Accommodation
Hotel rooms 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 as detailed on the programme tab. Successful applicants will be asked for any dietary requirements and allergies upon registration.
Course materials
The course materials from the 2022 edition of the course are now live and available for you to use. They provide a mixture of pre-recorded lectures, presentations, and practicals from the course, and will give you a snapshot of what to expect in the 2023 edition.
Posters
All participants are expected to present a poster that will be displayed during the course 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 course. 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.