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Advances in computational modelling of cellular processes and high-performance computing


Friday, 4th September


17:00 - 20:00 (CEST)


  • Anna Niarakis | University Evry, University of Paris-Saclay, France
  • Arnau Montagud | Barcelona Supercomputing Center, Spain
  • Miguel Ponce de León | Barcelona Supercomputing Center, Spain


  • Paul Macklin | Indiana University. Bloomington, United States
  • Jonathan Karr | Icahn School of Medicine, Mount Sinai, New York, United States
  • Rosa Maria Badia | Barcelona Supercomputing Center, Spain
  • Maria Rodriguez Martinez | IBM Zurich, Switzerland
  • Joerg Stelling | ETH Zurich, Switzerland
  • Denis Thieffry | IBENS Paris, France
  • Marta Cascante| Universitat de Barcelona, Spain


A cellular phenotype can be viewed as the endpoint of multiple cellular processes that define the morphology and function of the cell. Understanding how complex interactions between different biological entities give rise to a variety of cellular phenotypes is a primary challenge in Systems Biology. Computational modelling has been employed to study processes on a molecular level such as gene regulation, signal transduction and metabolism. Such models, together with analytical and statistical approaches, can help to disentangle the complex mechanisms that govern cellular fate. 

The aim of the workshop is to bring together researchers working in the field of computational systems biology who use various formalisms to model different biological functions in cells. The focus will be on presenting the state of the art in the field and how computational modelling can benefit from high-performance computing (HPC) advances. The highlight talk of the workshop will be dedicated to the community driven effort to create a prototype of SARS-CoV2 multiscale model.

Target audience

The target audience is students, early and advanced researchers and professionals from the fields of Systems Biology, Computational Biology, Computer Science and Bioinformatics who apply or are interested in applying computational modelling techniques and machine learning approaches for studying cellular functions.


Time (CEST)
17:00 - 17:10 Welcome and introduction to the workshop
SESSION 1 - Chair: Arnau Montagud
17:10 - 17:30 HPC and parallelization - Rosa Maria Badia

Dislib: parallelizing machine learning and its application to scientific applications

17:30 - 17:50 Whole cell models - Jonathan Karr

Novel technologies for whole-cell modeling

SESSION 2 - Chair: Anna Niarakis
17:50 - 18:10 Discrete mechanistic models - Denis Thieffry

Logical modelling of cell fate specification – Application to T cell commitment.

18:10 - 18:30 Deep learning models - Maria Rodriguez Martinez

DEPICTION: extracting insight from deep learning models in computational biology

18:30 - 19:10 Multiscale model of SARS-CoV-2 - Highlight talk by Paul Macklin
SESSION 3 - Chair: Miguel Ponce de León
19:10 - 19:30 Constraint-based models - Marta Cascante

A Systems biology approach to unveil metabolic phenotypes and vulnerabilities in cancer metastasis and drug resistance.

19:30 - 19:50 Constraint-based models - Joerg Stelling

Data integration via metabolic network models.

19:30 - 19:50 Closing remarks