Athena: Modular CAM/CAD Software for Synthetic Biology

TL;DR

Athena is a modular software platform designed for synthetic biology, enabling construction, simulation, and editing of biological models with interchangeable parts and extensible tools.

Contribution

It introduces a modular, plugin-compatible software environment for synthetic biology modeling and design, supporting biological engineering principles like encapsulation and interchangeable modules.

Findings

Supports modular biological model construction

Includes tools for simulation and DNA sequence editing

Extensible via plugins and scripting languages

Abstract

Synthetic biology is the engineering of cellular networks. It combines principles of engineering and the knowledge of biological networks to program the behavior of cells. Computational modeling techniques in conjunction with molecular biology techniques have been successful in constructing biological devices such as switches, oscillators, and gates. The ambition of synthetic biology is to construct complex systems from such fundamental devices, much in the same way electronic circuits are built from basic parts. As this ambition becomes a reality, engineering concepts such as interchangeable parts and encapsulation will find their way into biology. We realize that there is a need for computational tools that would support such engineering concepts in biology. As a solution, we have developed the software Athena that allows biological models to be constructed as modules. Modules can be connected to one another without altering the modules themselves. In addition, Athena houses various tools useful for designing synthetic networks including tools to perform simulations, automatically derive transcription rate expressions, and view and edit synthetic DNA sequences. New tools can be incorporated into Athena without modifying existing program via a plugin interface, IronPython scripts, Systems Biology Workbench interfacing and the R statistical language. The program is currently for Windows operating systems, and the source code for Athena is made freely available through CodePlex, www.codeplex.com/athena.