Target audience: Any student, postdoc or RA ... or Anyone interested in simula...
This section provides a step-by-step by tutorial on how to develop Building Blocks using the permedcoe package and an application that uses them.
Scientific topics: Personalised medicine, Workflows, Bioinformatics
Keywords: HPC, building blocks
Resource type: Tutorial
At the lowest scale, PhysiCell uses BioFVM solver to simulate the chemical microenvironment using partial differential equations which model the diffusion, uptake and secretion of substrates and signalling molecules. At the cell scale, PhysiCell uses mechanical equations to model individual cell...
Scientific topics: Molecular interactions, pathways and networks, Personalised medicine, Simulation experiment
Operations: Modelling and simulation
Keywords: HPC, Biomodelling, cell simulations
Resource type: Webinar
Boolean modelling uses a simple representation of biological entities as either active or inactive, and describes their relations with logical formulas. MaBoSS extends Boolean modelling by adding a notion of continuous time, with the introduction of rates of (in)activation. This enable the...
Scientific topics: Statistics and probability, Molecular interactions, pathways and networks, Personalised medicine, Simulation experiment
Operations: Modelling and simulation
Keywords: HPC, Biomodelling, cell simulations, Boolean
Resource type: Webinar
COBREXA.jl is a new software package to enable the analysis and simulation of large metabolic models by taking advantages of modern HPC infrastructure. Mainly, it advanced the scalability of constraint-based method, using the Julia programing language and its mathematic ecosystem as a base...
Scientific topics: Simulation experiment
Keywords: cell-level simulations, HPC, Biomodelling
Resource type: Webinar
PerMedCoE is the HPC/Exascale Centre of Excellence for Personalised Medicine in Europe. The goal of PerMedCoE is to provide an efficient and sustainable entry point to the HPC/Exascale-upgraded methodology to translate omics analyses into actionable models of cellular functions of medical relevance.
Scientific topics: Personalised medicine
Keywords: HPC, Biomodelling, cell-level simulations
Resource type: Webinar