The Infobiotics Workbench: Computer-Aided Design for Synthetic Biology

Synthetic Biology aspires to design and compose biological systems that implement specified behaviour in engineered biological system. Although more and more complex designs have been reported in the literature over the recent years, progress appears relatively slow compared to other engineering disciplines. This is because Synthetic Biology designs are necessarily based on parts that are themselves not engineered and often cause unforseen and unwanted interactions that thwart scalable designs. Currently, laborious trial-and-error wet lab experiments is therefore the most prominent mode of operation in Synthetic Biology systems design. Here, we present the Infobiotics Workbench (IBW2) as a tool to provide a computer-assisted design process to Synthetic Biology. IBW2 supports an integrated workflow for modelling, simulation, verification, and biomatter compilation of biological systems prior to their laboratory implementation and within a single software environment.

The talk will introduce the Infobiotics Language that has been devised as a domain specific declarative language for computational biologists to ease the definition of biological parts, interactions, and modular, scalable designs. We will also present the implementation of IBW2 as an Eclipse Rich Client Platform application, and demonstrate how this software infrastructure allows to interface IBL with cutting edge stochastic simulators, model checkers, and biomatter compilers, as well as standard development tools from traditional software engineering. The first public release of IBW2 is scheduled for November 2014.