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cupSODA is a simulator of biological systems that exploits the remarkable memory bandwidth and computational capability of GPUs. cupSODA allows to efficiently execute in parallel large numbers of simulations, which are usually required to investigate the emergent dynamics of a given biological system under different conditions. cupSODA works by automatically deriving the system of ordinary differential equations from a reaction-based mechanistic model, defined according to the mass-action kinetics, and then exploiting the numerical integration algorithm, LSODA
Features
- Automatic conversion of reactions into ODEs
- Automatic Jacobian matrix calculation
- GPU acceleration
- Able to deal with stiff and non-stiff systems
- Integrated fitness evaluation
Categories
SimulationLicense
BSD LicenseFollow cupSODA
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