3d engine implementation in DNA code!

General purpose tools for high-throughput catalysis

Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations

SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit

Automated creation and manipulation of Chemical Reaction Networks (CRNs) in heterogeneous catalysis, allowing the evaluation of species and reaction properties with data-driven ML models and the network simulation with microkinetic modelling.

BioSCRAPE (Bio-circuit Stochastic Single-cell Reaction Analysis and Parameter Estimation)

The Meta-Species Oriented Biosystem Syntax in Python (MobsPy) was invented to facilitate the design of complex Chemical Reaction Networks

Finite State Projection algorithms for chemical reaction networks

DelaySSAToolkit.jl: a tool in Julia for stochastic simulation with delays

This repo contains the code for the paper "Data-driven discovery of multiscale chemical reactions governed by the law of mass action"

Network analysis from a list of molecules

An application for simulating Chemical Reaction Networks

genCRN: Fast enumeration of non-isomorphic chemical reaction networks

Benchmarking Surrogates for coupled ODE systems.

Reaction Pathway Database

Matlab implementation of automated model reduction of biochemical reaction networks

a SageMath package to work with sign vector conditions for chemical reaction networks

Simulates Chemical Reaction System of Partial-Log-Linear Model

This repository contains codes developed in 2022 to simulate the bacterial biofilm formation with the proposed stochastic biofilm disruption model based on quorum sensing mimickers and chemical reactions.

Reaction Network Structure and Simulation Library for Resilience