🚂 Python API for Emma's Markov Model Algorithms 🚂
High-performance sensitivity analysis for large ordinary differential equation models
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
ARC - Automatic Rate Calculator
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
Automatic-Differentiation-Enabled Plasma Transport in JAX
A Python Framework for Modeling and Analysis of Signaling Systems
Learning Kinetic Models from Time Series Proteomics and Metabolomics Data
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.
Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations
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.
A package to build, run and optimise a kinetic multi-layer model for aerosol particles and films
GEM-Standalone (GEMS3K) Solver of Chemical Equilibria for Coupled Simulation Codes
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