Simulating and Optimising Dynamical Models in Python 3
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Updated
Jun 20, 2024 - Python
Simulating and Optimising Dynamical Models in Python 3
Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
A new implementation of a well-known stochastic model for carcinogenesis, augmented with competition dynamics and spatial structuring.
Simplest simulation to use non-Exponential transitions
SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit
Stochastic simulation of CRISPR nucleases cleaving a pool of DNA or RNA
Finite State Projection algorithms for chemical reaction networks
Julia Catalyst.jl importers for various reaction network file formats like BioNetGen and stoichiometry matrices
DelaySSAToolkit.jl: a tool in Julia for stochastic simulation with delays
Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations
A free, open-source tool for modeling chemical reaction networks in Python
Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology
Bayesian inference of stochastic cellular processes with and without memory in Python.
Stochastic chemical kinetics using Gillespie algorithm and chemical master equation, application to enzyme kinetics
A collection of some handy utilities
Networkx implementation of the SIS epidemic model for large and heterogeneous networks
Implementation of SIS epidemic model for large and heterogeneous networks
Implementation of SIS epidemic model for large and heterogeneous networks using Fortran.
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