Gillespie Stochastic Simulation Algorithm
-
Updated
Jun 29, 2013 - MATLAB
Gillespie Stochastic Simulation Algorithm
The biological network mining workflow identifies frequent structural patterns in biochemical reaction networks encoded in the Systems Biology Markup Language (SBML)
A Python package for representing reaction networks and simulating their behaviors
Various ODEs
Modeling signaling networks in cancer
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.
Dynamic Boltzmann Machine for Lattice Chemical Kinetics
Code used in arXiv:1808.08630
Code used in paper "Deep Learning Moment Closure Approximations using Dynamic Boltzmann Distributions" arXiv 1905.12122
MASSpy mathematical simulation program via BioSimulators-compliant command-line interface and Docker container
Open Markov Proceses as TensorFlow objects, Petri Nets and Chemical Rxn Nets in Haskell
This is a program to query and extract all the species info, inside KIDA database.
Cleaning Astrochemical Reaction network via Thermodynamics principles
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.
A Julia package that implements a category of reaction (transportation) network-type dynamical systems.
Reaction Network is a Python package for predicting likely inorganic chemical reaction pathways using graph theoretical methods. Project led by @mattmcdermott (Lawrence Berkeley National Lab).
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.
A package for researchers working with biological oscillations
Automated chemical reaction networking with long-timescale kinetic simulations in Julia
Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
Add a description, image, and links to the reaction-network topic page so that developers can more easily learn about it.
To associate your repository with the reaction-network topic, visit your repo's landing page and select "manage topics."