Experimentally driven verification of synthetic biological circuits

Authors:
Boyan Yordanov;Evan Appleton;Rishi Ganguly;Ebru Aydin Gol;Swati Banerjee Carr;Swapnil Bhatia;Traci Haddock;Calin Belta;Douglas Densmore
Affiliations:
Microsoft Research, Cambridge, UK;Boston University, Boston, MA;Boston University, Boston, MA;Boston University, Boston, MA;Boston University, Boston, MA;Boston University, Boston, MA;Boston University, Boston, MA;Boston University, Boston, MA;Boston University, Boston, MA
Venue:
DATE '12 Proceedings of the Conference on Design, Automation and Test in Europe
Year:
2012

Citing 4
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DAC '87 Proceedings of the 24th ACM/IEEE Design Automation Conference
Model checking

Model checking
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Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli

Bioinformatics

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Abstract

We present a framework that allows us to construct and formally analyze the behavior of synthetic gene circuits from specifications in a high level language used in describing electronic circuits. Our back-end synthesis tool automatically generates genetic-regulatory network (GRN) topology realizing the specifications with assigned biological "parts" from a database. We describe experimental procedures to acquire characterization data for the assigned parts and construct mathematical models capturing all possible behaviors of the generated GRN. We delineate algorithms to create finite abstractions of these models, and novel analysis techniques inspired from model-checking to verify behavioral specifications using Linear Temporal Logic (LTL) formulae.