Some tools for performing Monte Carlo simulations of chemical reaction networks in my research

Dedicated command-line compiler for Systems Biology

Detect reactions from atomic simulation trajectory

The source for the ReactSearch project's website.

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.

Performed molecular programming research at Grinnell College and Iowa State University in collaboration with 3 professors. Developed translation from CRNs to FRP, Reactamole language. Published.

Reaction Network Structure and Simulation Library for Resilience

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

Reaction Pathway Database

Simulates Chemical Reaction System of Partial-Log-Linear Model

Matlab implementation of automated model reduction of biochemical reaction networks

Benchmarking Surrogates for coupled ODE systems.

genCRN: Fast enumeration of non-isomorphic chemical reaction networks

An application for simulating Chemical Reaction Networks

Network analysis from a list of molecules

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

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

Finite State Projection algorithms for chemical reaction networks

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