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DTSTAMP:20260925T214319Z
UID:d0ace370-132e-4633-ac9a-6996e5f3d594
DTSTART:20211214T090000Z
DTEND:20211214T170000Z
DESCRIPTION:Computational simulations of cellular processes (e.g. metabolis
 m\, gene expression\, signal transduction) are critical tools to formulate
  mechanistic explanations that facilitate the interpretation of experiment
 al results. However\, complex biological processes such as tumour evolutio
 n span across different time-space scales. For instance\, a population-lev
 el description is needed to account for genetic heterogeneity and phenotyp
 ic variability due to environmental noise\, whereas intracellular models\,
  such as cell signalling networks need to address the effect of mutated ge
 nes. In this context\, multi-scale models are ideal tools to address syste
 ms biology questions as they can consider several time-space scales by com
 bining different approaches into a hybrid simulation.\n\nPhysiCell is an o
 pen-source\, agent-based extensible multi-scale modelling framework that a
 llows simulating complex multicellular systems such as healthy tissues and
  tumours. At the lowest scale\, PhysiCell uses BioFVM solver to simulate t
 he chemical microenvironment using partial differential equations which mo
 del the diffusion\, uptake and secretion of substrates and signalling mole
 cules. At the cell scale\, PhysiCell uses mechanical equations to model in
 dividual cell movement\, cell-cell interactions\, as well as interactions 
 between cells and the microenvironment’s physical components\, e.g. as e
 xtracellular matrix. Additionally\, different cells types and heterogeneou
 s populations can be defined by using different submodels for cell growth\
 , death as well as user-defined custom behaviours.\n\nFurthermore\, PhysiC
 ell can be extended to provide cell agents with more complex intracellular
  networks\, such as signalling and metabolism. For instance\, PhysiBoSS is
  an addon-based extension that provides cell agents with individual Boolea
 n models of regulatory networks which are simulated using the [MaBoSS](htt
 ps://embl-org.zoom.us/webinar/register/WN_iyxJqczgTJGv7C_pTG_mGg) algorit
 hm. The Boolean model inputs can be connected to different cell variables 
 and their outputs can be used to trigger changes in the cell behaviour. Al
 together\, PhysiBoSS bridges intracellular dynamics to the population leve
 l. Because of its flexibility\, the PhysiCell Framework can be applied to 
 a broad range of biological problems related to cancer\, immunology\, infe
 ctious diseases\, and microbial ecology\, among others. In this webinar\, 
 we will introduce the basic concepts of the PhysiCell/PhysiBoSS modelling 
 framework and its HPC-based implementation using different biological exam
 ples focusing on applications to treatment optimisation in models of tumou
 r growth.\n\n### About the speaker\n\nMiguel Ponce de León is a recognize
 d postdoctoral researcher at the Computational Biology Group at the Life S
 cience Department of the Barcelona Supercomputing Center (BSC). His area o
 f expertise is in the field of systems biology and scientific computation 
 where most of his research has been on reconstruction and simulation of bi
 ological networks. His line of research at BSC is the development of syste
 ms biology approaches to personalized medicine\, with a particular focus o
 n cancer. He uses different modelling approaches to integrate heterogeneou
 s sources of information with two main objectives: 1) developing tools to 
 assist in the decision-making process of choosing the most adequate therap
 y for specific patients given their unique genetic/background\; and 2) imp
 roving the knowledge of basic cancer biology.
LOCATION:\, 
SUMMARY:Biomedicine\, supercomputers and simulations: in silico experiments
  and its applications in cancer research
URL;VALUE=URI:https://www.ebi.ac.uk/training/events/biomedicine-supercomput
 ers-and-simulations-silico-experiments-and-its-applications-cancer-researc
 h
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