Document Type

Pre-Print

Publication Date

7-16-2014

Subjects

Chemical reactions -- Computer simulation, Chemical reactions -- Mathematical models, Chemistry -- Simulation methods, Computational grids (Computer systems)

Abstract

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.

Description

This is the pre print version of a paper presented at the 7th workshop on Complex Systems Modelling and Simulation (CoSMoS 2014).

Persistent Identifier

http://archives.pdx.edu/ds/psu/12297

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