🚂 Python API for Emma's Markov Model Algorithms 🚂

Advanced Multilanguage Interface to CVODES and IDAS

ARC - Automatic Rate Calculator

The goal of this toolbox is to provide open-source research-level and prototyping software tools for hyperpolarized MRI experiments. It is currently based on MATLAB/Octave code, and includes code for designing radiofrequency (RF) pulses, imaging gradients, data reconstruction, and data analysis. doi: 10.5281/zenodo.1198915

StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks

Metabolic Engineering Workbench

The official PySCeS project source code repository.

Modeling molecular ensembles with scalable data structures and parallel computing

Learning Kinetic Models from Time Series Proteomics and Metabolomics Data

A Python Framework for Modeling and Analysis of Signaling Systems

Automatic-Differentiation-Enabled Plasma Transport in JAX

Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations

XOOPIC is a two-dimensional 3-velocity particle-in-cell simulator. It can handle electrostatic and electromagnetic models, has a large variety of boundary conditions, supports multiple gasses and gas chemistry, and is easily reconfigurable via an input file.

Patient-Specific Modeling in Python

EQ3/6, a Software Package for Geochemical Modeling

GORILLA: Guiding-center ORbit Integration with Local Linearization Approach

Rule-based modeling for whole-cell models.

This repository contains a MATLAB implementation of the 1D Finite Difference Time Domain (FDTD) method for simulating the propagation of plane electromagnetic waves in a plasma medium.

A package to build, run and optimise a kinetic multi-layer model for aerosol particles and films