AutoBioCAD: Full Biodesign Automation of Genetic Circuits

Synthetic regulatory networks with prescribed functions
are engineered
by assembling a reduced set of functional elements. We could also
assemble them computationally if the mathematical models of those
functional elements were predictive enough in different genetic contexts.
Only after achieving this will we have libraries of models of biological
parts able to provide predictive dynamical behaviors for most circuits
constructed with them. We thus need tools that can automatically explore
different genetic contexts, in addition to being able to use such
libraries to design novel circuits with targeted dynamics. We have
implemented a new tool, AutoBioCAD, aimed at the automated design
of gene regulatory circuits. AutoBioCAD loads a library of models
of genetic elements and implements evolutionary design strategies
to produce (i) nucleotide sequences encoding circuits with targeted
dynamics that can then be tested experimentally and (ii) circuit models
for testing regulation principles in natural systems, providing a
new tool for synthetic biology. AutoBioCAD can be used to model and
design genetic circuits with dynamic behavior, thanks to the incorporation
of stochastic effects, robustness, qualitative dynamics, multiobjective
optimization, or degenerate nucleotide sequences, all facilitating
the link with biological part/circuit engineering.