reaction-network
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Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
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Oct 27, 2025 - Julia
Reaction Network is a Python package for predicting likely inorganic chemical reaction pathways using graph theoretical methods. Project led by@mattmcdermott (formerly at Berkeley Lab).
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Feb 4, 2025 - Python
A Julia package that implements a category of reaction (transportation) network-type dynamical systems.
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Aug 18, 2025 - Julia
Gillespie Stochastic Simulation Algorithm
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Jun 29, 2013 - MATLAB
An interface between the Materials Project software suite and the Schrodinger Python API, designed to allow for high-throughput execution of Jaguar and AutoTS calculations for molecular thermodynamics and kinetics.
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Apr 8, 2024 - Python
The precomplex generator is a tool for obtaining suitable input structures for automated transition-state (TS) searches (precomplexes) based on single-ended reaction path optimization algorithms.
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Oct 9, 2024 - Python
A python implementation of open-source packages to explore the chemical reaction space associated with elementary prebiotic chemistry.
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Jun 3, 2024 - Jupyter Notebook
Open Markov Proceses as TensorFlow objects, Petri Nets and Chemical Rxn Nets in Haskell
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May 7, 2022 - Jupyter Notebook
Automated chemical reaction networking with long-timescale kinetic simulations in Julia
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Aug 2, 2025 - Julia
Various ODEs
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Oct 14, 2018 - Jupyter Notebook
A Python package for representing reaction networks and simulating their behaviors
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Jul 11, 2018 - Python
Modeling signaling networks in cancer
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Jul 20, 2020 - Python
A package for researchers working with biological oscillations
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Aug 6, 2024 - Julia
MASSpy mathematical simulation program via BioSimulators-compliant command-line interface and Docker container
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Oct 31, 2024 - Python
The biological network mining workflow identifies frequent structural patterns in biochemical reaction networks encoded in the Systems Biology Markup Language (SBML)
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Jan 6, 2018 - Shell
Cleaning Astrochemical Reaction network via Thermodynamics principles
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Dec 24, 2023 - Jupyter Notebook
Code used in arXiv:1808.08630
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Jun 1, 2021 - Mathematica
Dynamic Boltzmann Machine for Lattice Chemical Kinetics
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Jun 1, 2021 - C++
This repository contains the source code of the paper "State and parameter estimation from exact partial state observation in stochastic reaction networks" by Muruhan Rahinam and Mingkai Yu.
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Feb 11, 2021 - MATLAB
Code used in paper "Deep Learning Moment Closure Approximations using Dynamic Boltzmann Distributions" arXiv 1905.12122
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Jun 1, 2021 - Mathematica
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