ssandrews / Smoldyn
Smoldyn is a particle-based biochemical simulator for modeling molecular diffusion, surface interactions, and chemical reactions
☆24Updated last week
Related projects ⓘ
Alternatives and complementary repositories for Smoldyn
- Encoding Dynamic Flux Balance Analysis in SBML☆11Updated 4 years ago
- Modeling toolkit for biochemical simulation☆72Updated last month
- Rule-based modeling framework☆59Updated last month
- BioSCRAPE (Bio-circuit Stochastic Single-cell Reaction Analysis and Parameter Estimation)☆20Updated 3 months ago
- Python package for stochastic simulations☆16Updated this week
- Simulation platform of animal embryogenesis☆20Updated 2 years ago
- PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology☆60Updated 3 months ago
- StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks☆40Updated last year
- Python / C++ based particle reaction-diffusion simulator☆52Updated 2 years ago
- ☆32Updated 2 years ago
- GPU-accelerated multicellular modelling framework☆57Updated 7 months ago
- A general-purpose, stochastic, biochemical reaction simulator for large reaction networks☆17Updated 5 months ago
- Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML☆27Updated last year
- Advanced Multilanguage Interface to CVODES and IDAS☆108Updated this week
- Python utilities for SBML☆37Updated last week
- Introduction to Biophysics, requires one semester of calculus-based Physics.☆25Updated last year
- CompuCell3D public source code repository☆63Updated last week
- Whole Cell Model of E. coli☆18Updated this week
- Utilities for Caltech course BE 150☆21Updated 11 months ago
- Virtual Cell Framework☆66Updated this week
- Tool to convert an ODE model specified in the YAML format to SBML.☆12Updated last year
- A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results☆39Updated this week
- An application for parameterization of biological models available in SBML and BNGL formats. Features include parallelization, metaheuris…☆22Updated 10 months ago
- COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.☆92Updated this week
- 2022 PhysiCell Hackathon and Workshop☆12Updated 2 years ago
- NonEquilibrium Reaction-Diffusion Self-assembly Simulator☆13Updated last week
- The SBML Test Suite is a conformance testing system. It allows developers and users to test the degree and correctness of the SBML suppor…☆23Updated 8 months ago
- Coral, a library and framework for specifying synthetic biology design processes.☆33Updated last year
- framed: a metabolic modeling package for python☆25Updated 5 years ago
- localCIDER - sequence analysis tool for disordered protein sequences☆22Updated last year