This is the Windows app named cupSODA whose latest release can be downloaded as cupSODAv1.1.0.zip. It can be run online in the free hosting provider OnWorks for workstations.
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- 7. Download Wine from your Linux distributions software repositories. Once installed, you can then double-click the app to run them with Wine. You can also try PlayOnLinux, a fancy interface over Wine that will help you install popular Windows programs and games.
Wine is a way to run Windows software on Linux, but with no Windows required. Wine is an open-source Windows compatibility layer that can run Windows programs directly on any Linux desktop. Essentially, Wine is trying to re-implement enough of Windows from scratch so that it can run all those Windows applications without actually needing Windows.
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
- Automatic conversion of reactions into ODEs
- Automatic Jacobian matrix calculation
- GPU acceleration
- Able to deal with stiff and non-stiff systems
- Integrated fitness evaluation
This is an application that can also be fetched from https://sourceforge.net/projects/cupsoda/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.