coel: a cloud-based reaction network simulator
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ID: 207114
2016
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Abstract
Chemical Reaction Networks (CRNs) are a formalism to describe the macroscopic behavior of chemical systems. We introduce COEL, a web- and cloud-based CRN simulation framework that does not require a local installation, runs simulations on a large computational grid, provides reliable database storage, and offers a visually pleasing and intuitive user interface. We present an overview of the underlying software, the technologies, and the main architectural approaches employed. Some of COEL's key features include ODE-based simulations of CRNs and multicompartment reaction networks with rich interaction options, a built-in plotting engine, automatic DNA-strand displacement transformation and visualization, SBML/Octave/Matlab export, and a built-in genetic-algorithm-based optimization toolbox for rate constants.COEL is an open-source project hosted on GitHub (http://dx.doi.org/10.5281/zenodo.46544), which allows interested research groups to deploy it on their own sever. Regular users can simply use the web instance at no cost at http://coel-sim.org. The framework is ideally suited for a collaborative use in both research and education.
| Reference Key |
ebanda2016frontierscoel:
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|---|---|
| Authors | ;Peter eBanda;Christof eTeuscher |
| Journal | canadian journal of philosophy |
| Year | 2016 |
| DOI |
10.3389/frobt.2016.00013
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| URL | |
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