This course will provide participants with an introduction and hands-on training on modelling approaches, tools, and resources used in systems biology as well as touch on network analysis.
Computer models are increasingly used to understand the essential processes of biology. Researchers in academic institutions as well as the pharmaceutical industry use mathematical models to generate hypotheses on how complex biomolecular systems work. Modelling of biochemical pathways deregulated in disease conditions can offer mechanistic insights into the pathology, help to elucidate mechanisms behind drug action, and predict the dose required for treatment thus facilitating fundamental research and drug discovery. This course will provide a helpful brief introduction to key modelling concepts and hands on training to use popular tools and resources used in this scientific field.
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 group activities and trainer-led computational exercises. Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack.
Pre-recorded material may be provided before the course starts that participants will need to watch, read, or work through to gain the most out of the actual training event. In the week before the course, there will be a brief induction session. Computational practicals will run on EMBL-EBI's virtual training infrastructure, meaning participants will not require access to a powerful computer or install complex software on their own machines.
Participants will need to be available between the hours of 09:00 – 17:30 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 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.
What will I learn?
Learning outcomes
After the course you should be able to:
Identify the strength and weakness of systems qualitative and quantitative 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:
Network analysis and pathway enrichment
Qualitative (e.g. logic) modelling and quantitative (e.g. chemical kinetics, constraint based, statistical) modelling
Data resources for modelling, pathways, and molecular interaction: BioModels, Reactome, IntAct, ComplexPortal etc.
Model sharing: how to encode, annotate, and distribute models
Several tools will be used during the course, including accessing IntAct data from Cytoscape, COPASI, CompuCell3D, and CellCollective
Model curation through practical experience in a group challenge
Trainers
Oscar Dias, Universidade do Minho
Fabian Fröhlich, The Francis Crick Institute
Jordi Garcia-Ojalvo, Pompeu Fabra University
James Glazier, Indiana University
Tomáš Helikar, University of Nebraska-Lincoln
Kalpana Panneerselvam, EMBL-EBI
Miguel Rocha, Universidade do Minho
Rahuman Sheriff Malik Sheriff, EMBL-EBI
Blerta Shtylla, Pfizer Worldwide R&D
Krishna Kumar Tiwari, EMBL-EBI
Applications close: 26 November 2023
11 – 15 March 2024
Course fee: £225.00