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14 materials found

Scientific topics: Simulation experiment 


Parameter Scanning and Sampling in COPASI

A video tutorial for the simulation software COPASI, showing how to create sequences of simulations that scan values of various parameters, or that sample those parameters at random.

COPASI logo

Scientific topics: Simulation experiment

Operations: Modelling and simulation, Analysis, Visualisation

Keywords: SystemsBiology, ComputationalBiology, Computational modelling, Kinetic modeling, COPASI

Resource type: Video

Metabolic Control Analysis in COPASI

A tutorial on Metabolic Control Analysis and how to apply it to kinetic models with the software COPASI.

COPASI logo

Scientific topics: Simulation experiment, Systems biology

Operations: Modelling and simulation, Analysis, Visualisation

Keywords: SystemsBiology, ComputationalBiology, Computational modelling, Kinetic modeling, COPASI

Resource type: Video

Steady State Analysis in COPASI

A short tutorial on how to carry out steady state simulations with the software COPASI.

COPASI logo

Scientific topics: Systems biology, Computational biology, Simulation experiment

Operations: Modelling and simulation, Visualisation

Resource type: Video

Time Course Simulation in COPASI

A short tutorial on how to carry out time course simulations based on ODEs with the software COPASI.

COPASI logo

Scientific topics: Simulation experiment

Operations: Modelling and simulation, Visualisation

Keywords: SystemsBiology, ComputationalBiology, Computational modelling, Kinetic modeling, COPASI

Resource type: Video

Model Creation using COPASI

A tutorial on how to create kinetic models with COPASI. Covers the basics of creating models, including definition of new rate laws, etc.

COPASI logo

Scientific topics: Simulation experiment

Operations: Modelling and simulation, Visualisation

Keywords: SystemsBiology, ComputationalBiology, Computational modelling, modeling, Biomodelling, Model, Kinetic modeling, COPASI

Resource type: Video

Biomedicine, supercomputers and simulations: in silico experiments and its applications in cancer research

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

Tutorials on COBREXA

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

Tutorial on CellNOpt

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

Introduction to qualitative modelling with MaBoSS

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

Analysis of huge metabolic models with COBREXA.jl

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

runBioSimulations tutorial and help

runBioSimulations is a web application for executing a broad range of modeling studies and visualizing their results. runBioSimulations uses BioSimulators to supports a broad range of modeling frameworks (e.g., logical, constraint-based, kinetic), simulation algorithms (e.g., CVODE, FBA, SSA),...

Scientific topics: Systems biology, Computational biology, Simulation experiment

Operations: Modelling and simulation

Keywords: biosimulators, COMBINE, OMEX, SED-ML, Modeling, dynamic simulations, SBML, BNGL

Resource type: Tutorial, Documentation

BioSimulators tutorial and help

BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms,...

Scientific topics: Systems biology, Computational biology, Simulation experiment

Operations: Modelling and simulation

Keywords: Modeling, biomodel, dynamic simulations, COMBINE, OMEX, SED-ML, SBML, BNGL

Resource type: Tutorial, Documentation

DE-Sim examples, tutorials, and documentation

DE-Sim is an open-source, Python-based object-oriented discrete-event simulation (DES) tool that makes it easy to use large, heterogeneous datasets and high-level data science tools such as NumPy, Scipy,...

Scientific topics: Simulation experiment, Computer science, Mathematics, Computational biology

Operations: Modelling and simulation, Visualisation

Keywords: data-driven modeling, Computational modelling, discrete-event simulation, DES, object-oriented programming, Python, data visualization, Data Science

Resource type: examples, Tutorial, Jupyter notebook, API reference

BioSimulations tutorial and help

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