Thursday Extra on 9/14

Thursday, September 14, 2017
4:15 p.m. in Science 3821
Refreshments at 4:00 p.m. in the Computer Science Commons (Science 3817).
Everyone is welcome to attend!

Cauldron: An IDE for modular development of chemical reaction networks will be presented by Prof. Klinge's summer research group: Jong Hoon Bae, Theo Kalfas, Nick Roberson, and Otabek Nazarov.

The chemical reaction network (CRN) model is a prominent molecular programming paradigm. In 2016, Klinge, Lathrop, and Lutz introduced three ways to modularly develop CRNs: I/O CRNs, extension operators, and closed sub-CRNs. I/O CRNs extend the CRN model to allow time-varying input concentrations. Extension operators are used to automatically add functionality to a CRN without affecting the original behavior. A closed sub-CRN encapsulates a behavior within an existing CRN that is self-contained. These new methods naturally support modular CRN design; however, existing tools do not support them. In this talk we introduce Cauldron, an integrated development environment (IDE) for modular CRN development. Cauldron supports I/O CRNs, extension operators, and closed sub-CRNs in addition to common features found in existing CRN tools. For example, users can divide a CRN into independent sub-CRNs, test them separately, and reuse them in other CRNs. Furthermore, users can mark species as inputs and specify them with common elementary functions, by drawing a function, or by connecting them to another CRN. Many commonly used CRNs and extension operators are also included as libraries in Cauldron. (This is joint work with James Lathrop at Iowa State University.)