Networkx implementation of the SIS epidemic model for large and heterogeneous networks
A free, open-source tool for modeling chemical reaction networks in Python
Simulating and Optimising Dynamical Models in Python 3
Gillespie stochastic simulation algorithm (SSA / Direct Method) for jump Markov processes and chemical kinetics
Gillespie stochastic simulation algorithm (SSA / Direct Method) for jump Markov processes and chemical kinetics
Implementation of SIS epidemic model for large and heterogeneous networks
Numba accelerated implementation of Gillespie's algorithm for simulating stochastic processes
Bayesian inference of stochastic cellular processes with and without memory in Python.
Stochastic Simulator of Chemical Reactions
Working with Gillespie algorithm in order to exam Double step gene expression model.
Deterministic and stochastic SIR and SIS models in Python covering vaccination, social distancing, Gillespie simulation and outbreak-size distributions.
Python toolkit for the analysis and simulation of chemical reaction networks — the chemical master equation (finite state projection, tensor operators), stochastic simulation, moment closure, deterministic RRE analysis, and structural & ergodicity certificates (deficiency, ACR/RPA, Foster–Lyapunov, robust Lyapunov functions, BDC).
Delay Gillespie Degrade and Fire with variable delay
Deterministic and stochastic simulation of a synthetic repressilator and an mRNA-protein gene-expression model using ordinary differential equations and Gillespie SSA.
Gillespie simulation of SIR-type epidemic on contact networks, adapted to track two-type dynamics, support for weighted graphs, and infection-chain tracing
New implementation of a well-known stochastic model for carcinogenesis, augmented with competition dynamics and spatial structuring.
Physics-Informed Neural Inverse Control of Single-Cell Optogenetic Gene Expression
Computational epidemiology platform in Python: SIR/SEIR ODEs, Gillespie stochastic simulation, network and spatial epidemics, fitted to real outbreak data, with a Streamlit dashboard.
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