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

Developments in the tools and methodologies of synthetic biology.

Synthetic biology is principally concerned with the rational design and engineering of biologically based parts, devices, or systems. However, biological systems are generally complex and unpredictable, and are therefore, intrinsically difficult to engineer. In order to address these fundamental challenges, synthetic biology is aiming to unify a body of knowledge from several foundational scientific fields, within the context of a set of engineering principles. This shift in perspective is enabling synthetic biologists to address complexity, such that robust biological systems can be designed, assembled, and tested as part of a biological design cycle. The design cycle takes a forward-design approach in which a biological system is specified, modeled, analyzed, assembled, and its functionality tested. At each stage of the design cycle, an expanding repertoire of tools is being developed. In this review, we highlight several of these tools in terms of their applications and benefits to the synthetic biology community