We just finished two articles on modeling issues of genetic regulatory systems, with special emphasis on applications to synthetic biology. In a concrete example we discuss how to mathematically best describe an existing synthetic clock. The articles are based on the thesis by Ulrich Janus.
The Perl script described in Pre2010-1 can be downloaded here.
[Pre2010-1] Kirkilionis, M., Sbano, L., Janus, U.: Multi-Scale Genetic Dynamic Modelling I : An Algorithm to Compute Generators. Warwick Preprint 4/2010 [PDF]
[Pre2010-2] Kirkilionis, M., Sbano, L., Janus, U.: Multi-Scale Genetic Dynamic Modelling II: Application to Synthetic Biology. Warwick Preprint 5/2010 [PDF]