Computer models are increasingly used by researchers as well as the pharmaceutical industry to investigate disease initiation, progression and therapy. Modelling of biochemical pathways deregulated in disease condition offers mechanistic insights into the pathology; helps to elucidate mechanisms behind drug action and predict dose required for treatment and thereby greatly facilitates fundamental research and drug discovery. Such modelling requires a background in both molecular biology and mathematics. 

The four days virtual workshop will train researchers from life science and mathematics to communicate and work together to learn to build and analyse computer models using user-friendly open-source software. The workshop will be jointly organised by the BioModels team from EMBL-EBI along with the Centre for Integrative Biology and Systems Medicine (IBSE) and the Robert Bosch Centre for Data Sciences and Artificial Intelligence (RBC-DSAI) from Indian Institute of Technology Madras (IITM). Various modelling approaches and tools will be introduced to the participants. They will explore a few of the disease-specific computer models from a recent publication, freely available in BioModels repository.

Other EMBL-EBI resources including Reactome, IntAct, OmicsDI, PRIDE, ExpressionAtlas will be introduced to the participants. The BioModels team will lead the training on kinetic modelling of signalling pathways, curation and annotation of mathematical models as well as standards in modelling (SBML, SED-ML, etc). The IITM/IBSE team will partner in the training on kinetic modelling approaches, and also introduce other paradigms such as constraint-based modelling (e.g. Flux Balance Analysis (FBA)) for the analysis of metabolic pathways.   

An essential agenda in the meeting will be group projects where participants from both experimental and theoretical background would work together to curate mathematical models and submit them to the BioModels repository. This workshop will allow EMBL-EBI to partner with IITM to share expertise on kinetic modelling and gain expertise on the curation of non-kinetic models (specifically, constraint-based models, using the newly developed FBC curation packages) in BioModels repository. Furthermore, this joint workshop would be used as an opportunity for long term partnership with IITM to establish training for EMBL-EBI resources in India, explore the possibility of joint data curation engagement and scientific collaboration.

Who is this course for?

This course is aimed at experimental biologists, bioinformaticians and mathematicians who have just started in systems biology, are familiar with the basic terminology in this field and who are now keen on gaining a better knowledge of systems biology modelling approaches to understand biological and biomedical problems.

An experience of using a programming language (e.g Python, R, Matlab) would be a benefit but is not mandatory.

An undergraduate knowledge of molecular and cellular biology or some background in mathematics is highly beneficial.

Priority will be given to applicants from low and middle income countries - however applications are open to candidates from all over the world.

What will I learn?

Learning outcomes

After the course, participants should be able to:

• Identify the strength and weakness of systems biology modelling approaches
• Access, query and retrieve data/ models from public repositories for systems biology modelling
• Use modelling software to develop reproducible systems biology models
• Discuss the real-life application of models in fundamental and industrial research

Course content

During this course you will learn about: 

• Introduction to kinetic modelling
• Model curation and annotation with COPASI
• Data resources for modelling
• Constraint-based modelling
• Reproducibility in Systems Biology Modelling

Trainers

In order to be considered for a place on the course applicants must complete the application form.