Keywords: Biomodelling
A tutorial on how to create kinetic models with COPASI. Covers the basics of creating models, including definition of new rate laws, etc.
Scientific topics: Simulation experiment
Operations: Modelling and simulation, Visualisation
Keywords: SystemsBiology, ComputationalBiology, Computational modelling, modeling, Biomodelling, Model, Kinetic modeling, COPASI
Resource type: Video
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: Simulation experiment, Personalised medicine, Molecular interactions, pathways and networks
Operations: Modelling and simulation
Keywords: HPC, Biomodelling, cell simulations
Resource type: Webinar
COBREXA.jl provides tutorials and notebooks with the purpose of explaining the most important concepts and functions for metabolic modelling and model handling to users, and then practicing them.
The documentation contains basic tutorials (explaining the core package concepts and basic design...
Scientific topics: Personalised medicine, Simulation experiment
Operations: Modelling and simulation
Keywords: cell-level simulations, Biomodelling, HPC
Resource type: Tutorial
This tutorial aims to be an introduction to
i) the preparation of the Prior knowledge network (PKN) of signaling pathways and
ii) the training of the PKN against biochemical data to create cell-specific models.
Scientific topics: Personalised medicine, Simulation experiment, Molecular interactions, pathways and networks, Transcription factors and regulatory sites
Operations: Modelling and simulation
Keywords: HPC, Biomodelling, Signalling
Resource type: Tutorial
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: Simulation experiment, Personalised medicine, Molecular interactions, pathways and networks, Statistics and probability
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
BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and...
Scientific topics: Computational biology, Systems biology, Simulation experiment
Operations: Visualisation, Modelling and simulation
Keywords: SystemsBiology, ComputationalBiology, Computational modelling, Modeling, Biomodelling, Model, Kinetic modeling, SED-ML, COMBINE
Resource type: Documentation
A suite of >50 tutorials to enable beginners, as well as intermediate and advanced users to practice a wide variety of COBRA methods. Each tutorial is presented in a variety of formats, including as a MATLAB live script, which is an interactive document, or narrative...
Keywords: Biomodelling
Resource type: Tutorial