Reference : COEL: A Cloud-based Reaction Network Simulator
Scientific journals : Article
Physical, chemical, mathematical & earth Sciences : Chemistry
Engineering, computing & technology : Computer science
Computational Sciences
http://hdl.handle.net/10993/26447
COEL: A Cloud-based Reaction Network Simulator
English
Banda, Peter mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Teuscher, Christof [> >]
2016
Frontiers in Robotics and AI
3
13
Yes
International
2296-9144
[en] COEL ; chemical reaction network ; chemical modeling tool ; web tool ; computational grid ; DNA-strand displacement
[en] 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, which 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.
http://hdl.handle.net/10993/26447
10.3389/frobt.2016.00013
http://journal.frontiersin.org/article/10.3389/frobt.2016.00013

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