AUTHOR=Banda Peter , Teuscher Christof 

TITLE=COEL: A Cloud-Based Reaction Network Simulator

JOURNAL=Frontiers in Robotics and AI

VOLUME=3

YEAR=2016

URL=https://www.frontiersin.org/journals/robotics-and-ai/articles/10.3389/frobt.2016.00013

DOI=10.3389/frobt.2016.00013

ISSN=2296-9144

ABSTRACT=<p><italic>Chemical Reaction Networks</italic> (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:<uri xlink:href="http://dx.doi.org/10.5281/zenodo.46544" xmlns:xlink="http://www.w3.org/1999/xlink">10.5281/zenodo.46544</uri>), which allows interested research groups to deploy it on their own sever. Regular users can simply use the web instance at no cost at <uri xlink:href="http://coel-sim.org" xmlns:xlink="http://www.w3.org/1999/xlink">coel-sim.org</uri>. The framework is ideally suited for a collaborative use in both research and education.</p><p><bold>Code available at:</bold><uri xlink:href="http://dx.doi.org/10.5281/zenodo.46544" xmlns:xlink="http://www.w3.org/1999/xlink">10.5281/zenodo.46544</uri></p>