Deterministic and stochastic SIR and SIS models in Python covering vaccination, social distancing, Gillespie simulation and outbreak-size distributions.
Delay Gillespie Degrade and Fire with variable delay
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).
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.
Making signal restoration measurable: the same chemical reaction network run as deterministic mass-action ODEs and as an exact Gillespie SSA, and what the gap between them costs in free energy.
Gillespie stochastic-simulation model of BRCA1-mutant tumor clone dynamics, tracking wild-type, mutant, immune, and exhausted-immune populations under logistic crowding and immune interaction.
Exact stochastic simulation of a two-strain within-host viral model with an effector response, against its deterministic limit and branching-process theory
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.
Numba accelerated implementation of Gillespie's algorithm for simulating stochastic processes
Implementation of SIS epidemic model for large and heterogeneous networks
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
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