Contrary to the semiconductor industry where investments in excess of $1 billion are needed to setup a fabrication plant, most synthetic biology projects rely on low-cost instruments and infrastructure commonly available to life scientists. What distinguishes a synthetic biology laboratory from a regular biological research laboratory is the application of engineering methods to develop DNA molecules meeting user-defined specifications. In particular, the life cycle of a synthetic biology project is generally broken down into three phases: design, fabrication, and testing. Unfortunately, only a very limited number of research groups and scientists have the breadth of expertise necessary to address the numerous scientific and technical challenges raised by each stage of a synthetic biology project. Some argue that progress in synthetic biology has been hampered by the lack of software tools allowing projects to move smoothly through the different stages of the design-build-test cycle. It is our opinion that synthetic biology is a very young engineering specialty still in search of its own paradigms. While there have been analogies made with microelectronics, software, and other mature engineering fields, no practical solutions exist to synthetic biology’s daunting scientific challenges today.

Several companies (Amyris, Intrexon) and government-funded labs (JBEI) have invested in the development of enterprise systems necessary to scale up their Research and Development (R&D) effort by building large teams composed of more specialized technical staff focused on a particular stage of the project. Unfortunately, the products of these multimillion dollar investments are proprietary infrastructures in which the underlying software is tightly coupled to specific manufacturing and test technologies. These facilities give their owners a competitive advantage but do little to promote the dissemination of engineering methods in the life sciences.

Rather than developing a one-of-a-kind facility, our vision is to catalyze a transformation of our national life science R&D infrastructure into a network of individual labs, core facilities, consortiums, small and larger biotech companies, and government laboratories. This can be achieved through the development of an integrated suite of software tools facilitating the design of synthetic DNA molecules (GenoCAD), their assembly through de novo synthesis and reuse of existing components (GenoCAM), the characterization of their dynamics in vivo (GenoSIGHT), while monitoring for the possible presence in the pipeline of sequences that may raise biosecurity or biosafety concerns (GenoGUARD). We call Genetic Design Automation (GDA) the integration of tools that span the entire design-build-test workflow; the tool chain resulting from the integration of GenoCAD, GenoCAM, GenoSIGHT, and GenoGUARD is called GenoGDA.

The GenoGDA applications are at different stages of development. Ultimately they will all have graphical user interfaces friendly to life scientists who do not have any engineering background. Their deployment will be facilitated by their client-server architecture and the use of web technologies that do not require the installation and support of stand-alone applications. They will be licensed open source and available from SourceForge allowing users to install them on their own servers. We acknowledge that the installation of all the software components may be challenging and expensive, possibly beyond the capabilities of some potential users. Thus, in order to reduce the cost of deployment while maximizing the computing performance, the software suite will also be made available preinstalled on High-Performance Computing (HPC) hardware designed to optimize the GDA computing workflows. We call the combination GDA software and custom hardware an HPC appliance.