Reference : COEL: A Web-based Chemistry Simulation Framework
Scientific congresses, symposiums and conference proceedings : Paper published in a book
Physical, chemical, mathematical & earth Sciences : Chemistry
Engineering, computing & technology : Computer science
Computational Sciences
COEL: A Web-based Chemistry Simulation Framework
Banda, Peter mailto [Portland State University > Department of Computer Science]
Blount, Drew [> >]
Teuscher, Christof [> >]
CoSMoS 2014: Proceedings of the 7th Workshop on Complex Systems Modelling and Simulation
Stepney, Susan
Andrews, Paul
Luniver Press
CoSMoS 2014: 7th Complex Systems Modelling and Simulation Workshop
[en] COEL ; chemical reaction network ; chemical modelling tool ; web tool ; computational grid ; DNA-strand displacement transformation
[en] The chemical reaction network (CRN) is a widely used formalism to describe macroscopic behavior of chemical systems. Available tools for CRN modelling and simulation require local access, installation, and often involve local file storage, which is susceptible to loss, lacks searchable structure, and does not support concurrency. Furthermore, simulations are often single-threaded, and user interfaces are non-trivial to use. Therefore there are significant hurdles to conducting efficient and collaborative chemical research. In this paper, we introduce a new enterprise chemistry simulation framework, COEL, which addresses these issues. COEL is the first web-based framework of its kind. A visually pleasing and intuitive user interface, simulations that run on a large computational grid, reliable database storage, and transactional services make COEL ideal for collaborative research and education. COEL's most prominent features include ODE-based simulations of chemical reaction networks and multicompartment reaction networks, with rich options for user interactions with those networks. COEL provides DNA-strand displacement transformations and visualization (and is to our knowledge the first CRN framework to do so), GA optimization of rate constants, expression validation, an application-wide plotting engine, and SBML/Octave/Matlab export. We also present an overview of the underlying software and technologies employed and describe the main architectural decisions driving our development. COEL is available at this http URL for selected research teams only. We plan to provide a part of COEL's functionality to the general public in the near future.

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1407.4027v1.pdfarXiv versionAuthor preprint1.19 MBView/Open

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