CAD/CAM Software for Synthetic Biology

Frank T. Bergmann1,2*, Deepak Chandran1, Herbert M. Sauro1
1. Department of Bioengineering, University of Washington, Seattle, USA
2. Computational & Systems Biology, Keck Graduate Institute, Claremont, USA
*email: fbergman@u.washington.edu

Abstract
This poster describes a novel software application that we are developing that will help
researchers in Synthetic Biology to design, simulate and fabricate biological systems.
The software system is designed from the ground up to be extensible. It features a rich
graphical platform, integration of a python script engine, an application plug-in
architecture and is compliant with the Systems Biology Workbench.
A new modular model definition language is under development that will provide the
default file format for this tool. The new format will be compatible with the de-facto
standard SBML. Thus many software tools will be able to consume models created by
our tool.
Introduction
The BioBricks parts registry is a repository of standardized, reliable biological parts
enabling synthetic biologists to design and build biological systems. The process of
designing, testing and fabricating new systems is still however arduous and error prone.
The software application that we are developing is designed to make the process of
design and construction simpler. We focus our attention on two areas: Standard formats
and an intuitive extensible software system based on standards.
Standard formats are especially important in this field. Looking back at the success of
digital and analog electronics, we find that this success is partly due to the
standardization of electrical components. This standardization allowed the creation of
computer aided design (CAD) tools that allowed engineers to focus on designing new
devices, rather than issues of compatibility between parts. With languages such as
VHDL, it became easy to characterize and fully test new devices using CAD tools, before
building them in hardware. BioBricks is a first step in this direction for synthetic biology.
Our software system will accompany synthetic biologists through all stages of design,
testing and fabrication using the following approach:
 First a generic model implementing the desired functionality is built and
simulated.
 Next constraints on the design are made, such as qualifying the host organism,
product outputs and input types.

 Based on those constraints on the generic model, the software will deliver a set of
concrete designs from a predefined library of parts.
 In a last step one of the concrete designs can then be built by the biologists, or sent
to a biological hardware fabrication company that will be contracted to build the
system.
Approach
The software system we developed is based on the .NET framework 2.0. Creating a
flexible plug-in architecture has been a primary focus during the design. Apart from
plug-in interfaces we also integrated the IronPython runtime, allowing expert users to
extend the capability of the software by Python scripts.
This plug-in system was used in the development process for all components except for
the core-graphics system, thus it is easy to exchange development modules by more
readily accessible components that we envision at a later stage of the project.
A growing library of parts, initially derived from BioBricks sequences and characterized
by initial parameters is included with the project. Biologists can make use of this
database, alter parts on their local copies, or submit parts for review.

Figure 1: Architecture of the Prototype
Results
We have created a working prototype of the application that allows a user to build
biological systems from parts and to combine them into more complex devices. Models
created, if kinetically characterized, can be simulated within the application. Models can
also be exported into the de-facto standard model definition language SBML, and thus be
analyzed by more than one hundred third-party software applications. We have also
integrated our prototype with the Systems Biology Workbench and thus all analysis