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 fast estimation of the network energy profile with GAME-Net-UQ, an uncertainty quantification-based DFT-trained graph neural network.

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

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

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"

genCRN: Fast enumeration of non-isomorphic chemical reaction networks

Network analysis from a list of molecules

An application for simulating Chemical Reaction Networks

Benchmarking Surrogates for coupled ODE systems.

Reaction Pathway Database

Matlab implementation of automated model reduction of biochemical reaction networks

Simulates Chemical Reaction System of Partial-Log-Linear Model

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

Reaction Network Structure and Simulation Library for Resilience

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.