Join us for our upcoming SAFARI Live Seminar:
Speaker:
Arnau Montagud, Institute for Integrative Systems Biology (I2SysBio), CSIC-UV and Barcelona Supercomputing Center
Date: Tuesday, Nov 12, 11:00 Zurich time (CET)
Where: CAB G59 & Livestream on YouTube (Link)
Title: Multiscale modelling for personalised medicine
Abstract:
Multiscale modelling has proven its usefulness in several biomedical projects by explaining and uncovering mechanisms in diseases (1). However, current models often fall short, offering limited scope, lacking cell-specific characterisation, dynamic interactions, and a comprehensive environment description. PhysiBoSS stands at the intersection of signalling and regulatory networks simulated using Boolean modelling and multicellular systems studied using agent-based modelling (2,3). This positioning allows PhysiBoSS to bridge the gap between protein activities, communication across signalling pathways, and the cellular and environmental heterogeneities of cell populations. The result is a more holistic, integrated approach to biomedical research. One of the standout features of PhysiBoSS is its ability to personalise Boolean models using patients’ data. By integrating spatial omics, PhysiBoSS can create a comprehensive and accurate representation of biological systems. This level of personalisation brings us one step closer to truly patient-specific treatment strategies (4,5). Moreover, PhysiBoSS harnesses the power of High-Performance Computing (HPC) to scale-up to real-sized organs. This critical capability is a significant stride towards the realization of Digital Twins, enabling the exploration of biological phenomena at an unprecedented scale and providing invaluable insights into disease progression. In conclusion, PhysiBoSS is paving the way for scalable, real-sized simulations of biological systems. By enabling complex setups that mirror real-world biomedical scenarios, PhysiBoSS is not just advancing the field of multiscale modelling, but also bringing us closer to a future with Digital Twins.
Speaker Bio:
Arnau Montagud is a Tenured Researcher at the Institute for Integrative Systems Biology (I2SysBio), CSIC-UV, in Valencia and visiting researcher at Barcelona Supercomputing Center (BSC). He focuses on understanding the mechanisms behind diseases by using personalised models in biomedical and biotechnological projects. He earned a B.Sc. in Biology and M.Sc. in Cellular Biology by the Universitat de València and a PhD in Applied Mathematics by the Universitat Politècnica de València. Then, he became a postdoc researcher at Institut Curie, France and at the Barcelona Supercomputing Center, Spain. He has published research papers on metabolic modelling, signalling pathways modelling, Boolean modelling and agent-based modelling. Lately he has been working on optimising models to run efficiently in high-performance computers, scaling-up the simulation to have real-sized digital human twins.
References:
1. Montagud, A., Ponce-de-Leon, M. & Valencia, A. Systems biology at the giga-scale: Large multiscale models of complex, heterogeneous multicellular systems. Current Opinion in Systems Biology 28, 100385 (2021).
2. Letort, G. et al. PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling. Bioinformatics bty766 (2019) doi:10.1093/bioinformatics/bty766.
3. Ponce-de-Leon, M. et al. PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks. npj Syst Biol Appl 9, 1–12 (2023).
4. Béal, J., Montagud, A., Traynard, P., Barillot, E. & Calzone, L. Personalization of logical models with multi-omics data allows clinical stratification of patients. Front. Physiol. 9, 1965 (2019).
5. Montagud, A. et al. Patient-specific Boolean models of signalling networks guide personalised treatments. eLife 11, e72626 (2022).