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PyDAS
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public |
A Python wrapper to several differential algebraic system solvers
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2025-03-25 |
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cupsoda
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public |
cupSODA is a black-box deterministic simulator of biological systems for NVIDIA graphics cards (GPUs), using the CUDA framework.
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2025-03-25 |
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stochkit-lite
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public |
StochKit is an extensible stochastic simulation framework developed in C++ that aims to make stochastic simulation accessible to practicing biologists and chemists, while remaining open to extension via new stochastic and multiscale algorithms.
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2025-03-25 |
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atomizer
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public |
Project for the translation of SBML files into BNGL files
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2025-03-25 |
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stochkit
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public |
StochKit is an extensible stochastic simulation framework developed in C++ that aims to make stochastic simulation accessible to practicing biologists and chemists, while remaining open to extension via new stochastic and multiscale algorithms.
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2025-03-25 |
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kappa
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public |
Kappa is a rule-based language for modeling systems of interacting agents.
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2025-03-25 |
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graphviz
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public |
Graphviz is open source graph visualization software
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2025-03-25 |
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pygraphviz
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public |
PyGraphviz is a Python interface to the Graphviz graph layout and visualization package.
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2025-03-25 |
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pysb
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public |
PySB (pronounced "Pie Ess Bee") is a framework for building rule-based mathematical models of biochemical systems. It works nicely with scientific Python libraries such as NumPy, SciPy and SymPy for model simulation and analysis.
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2025-03-25 |
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nfsim
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public |
NFsim is a network-free stochastic simulator for biochemical reaction networks
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2025-03-25 |
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bionetgen
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public |
BioNetGen is software for the specification and simulation of rule-based models of biochemical systems
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2025-03-25 |
