kinetic-modeling
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🚂 Python API for Emma's Markov Model Algorithms 🚂
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Sep 11, 2023 - Python
High-performance sensitivity analysis for large ordinary differential equation models
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Nov 5, 2025 - C++
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
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Jul 1, 2025 - Jupyter Notebook
ARC - Automatic Rate Calculator
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Nov 5, 2025 - Python
StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks
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Jun 20, 2025 - Python
Metabolic Engineering Workbench
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Jun 9, 2024 - Python
The official PySCeS project source code repository.
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Oct 19, 2025 - Python
Modeling molecular ensembles with scalable data structures and parallel computing
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Oct 29, 2025 - Python
Automatic-Differentiation-Enabled Plasma Transport in JAX
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Nov 4, 2025 - Python
A Python Framework for Modeling and Analysis of Signaling Systems
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Oct 13, 2025 - Python
Learning Kinetic Models from Time Series Proteomics and Metabolomics Data
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Jun 21, 2022 - Jupyter Notebook
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.
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Jun 2, 2021 - C++
Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations
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Mar 13, 2018 - Jupyter Notebook
Patient-Specific Modeling in Python
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Oct 13, 2025 - Python
EQ3/6, a Software Package for Geochemical Modeling
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Aug 16, 2022
GORILLA: Guiding-center ORbit Integration with Local Linearization Approach
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Jun 25, 2025 - Fortran
Rule-based modeling for whole-cell models.
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May 20, 2022 - Python
A package to build, run and optimise a kinetic multi-layer model for aerosol particles and films
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Jan 18, 2025 - Python
GEM-Standalone (GEMS3K) Solver of Chemical Equilibria for Coupled Simulation Codes
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Jun 30, 2025 - C++
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