  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.
