COEL: A Web-based Chemistry Simulation Framework

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 http://coel-sim.org for selected research teams only. We plan to provide a part of COEL's functionality to the general public in the near future.Comment: 23 pages, 12 figures, 1 tabl

Updated version of final design and of the architecture of SEAMLESS-IF

Agricultural and Food Policy, Environmental Economics and Policy, Farm Management, Land Economics/Use, Livestock Production/Industries,

Migrating existing multimedia courseware to Moodle

Open source course management systems offer increased flexibility for instructors and instructional designers. Communities can influence the development of these systems and on an individual basis, the possibility to modify the system software exists. Migrating existing courseware to these systems can therefore be beneficial, sometimes even required. We report here about our experience in migrating an existing courseware system consisting of multimedia content and interactive, integrated infrastructure functionality to an open source course management system called Moodle. We will assess the difficulties that we have encountered during this process and, discuss the importance of standards in this context, and we aim to provide other instructors or instructional designers with guidelines and assessment support for other migration projects