Integrated Biocad Toolchain Enables Search for Experimentally Validated Components

Biological computer-aided design (bioCAD) tools are gaining widespread adoption in commercial, academic, and government research settings. As more and more tools emerge, there is an increasingly urgent need to integrate them into a larger toolchain that aggregates functionality and data. We have recently integrated several of our bioCAD tools (DeviceEditor, DIVA, ICE, EDD Analytics, and EDD) to enable researchers designing biological systems to query for components (e.g., promoters) that have been experimentally validated to meet particular design criteria (e.g., high transcriptional levels in E. coli). In our bioCAD toolchain, the user first specifies the desired component’s properties in DeviceEditor, a visual bioCAD canvas. The user’s specifications form the basis of a query that, via the DIVA software platform, is sent from DeviceEditor to ICE. ICE replies to the query with the list of components that meet the user’s criteria. The user then selects from the list those desired components that should be added to the DeviceEditor design canvas. Importantly, EDD Analytics derived the specifications for the components in ICE from a combination of experiment data in the EDD (Experiment Data Depot) and context meta-data (e.g., microbial host) in ICE. As such, during the component selection process, the user has access to the primary experimental data in EDD supporting the design selection decision. Our initial demonstration of this integrated bioCAD toolchain consists of a researcher searching for low, medium, or high strength promoters with flow cytometry data supporting their strength classifications.