COEL: A cloud-based reaction network simulator

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, 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 (doi: 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 coel-sim.org. The framework is ideally suited for a collaborative use in both research and education.