Robustness analysis and tuning of synthetic gene networks.
BACKGROUND
The goal of synthetic biology is to design and construct biological systems that present a desired behavior. The construction of synthetic gene networks implementing simple functions has demonstrated the feasibility of this approach. However, the design of these networks is difficult, notably because existing techniques and tools are not adapted to deal with uncertainties on molecular concentrations and parameter values.


RESULTS
We propose an approach for the analysis of a class of uncertain piecewise-multiaffine differential equation models. This modeling framework is well adapted to the experimental data currently available. Moreover, these models present interesting mathematical properties that allow the development of efficient algorithms for solving robustness analyses and tuning problems. These algorithms are implemented in the tool RoVerGeNe, and their practical applicability and biological relevance are demonstrated on the analysis of the tuning of a synthetic transcriptional cascade built in Escherichia coli.


BACKGROUND
RoVerGeNe and the transcriptional cascade model are available at http://iasi.bu.edu/%7Ebatt/rovergene/rovergene.htm.
Centers for Information and Systems Engineering and for BioDynamics, Boston University, Boston, MA, USA. gregory.batt@imag.fr
Grégory
G
Batt
Boyan
B
Yordanov
Ron
R
Weiss
Calin
C
Belta
D000465:Algorithms; D003198:Computer Simulation; D004926:Escherichia coli / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D015870:Gene Expression / Q000502:physiology*; D020869:Gene Expression Profiling / Q000379:methods*; D008954:Models, Biological; D015398:Signal Transduction / Q000502:physiology*; D014158:Transcription, Genetic / Q000502:physiology
D029968:Escherichia coli Proteins