MPCC Solution of Genetic Regulatory Circuit Design Problems

Demonstration of a novel MPCC-based technique for solving gene circuit design problems.

Description

This submission provides a demonstation of a MPCC (mathematical program with complementarity constraints) based solution of a genetic regulatory circuit design problem. It corresponds to the method introduced in the following publication:

Tinghao Guo, James T. Allison. 'On the Use of MPCCs in Combined Topological and Parametric Design of Genetic Regulatory Circuits.' In the Proceedings of the 10th World Congress on Structural and Multidisciplinary Optimization. May 19–May 24 2013.

which can be obtained from:

http://systemdesign.illinois.edu/publications/Guo13a.pdf

It solves a mixed discrete/continuous design problem. Complementarity constraints are used to model gene circuit topology, and circuit parameters are modeled as continuous optimization variables. This method provides a means for scaling up to somewhat larger problems than can be designed using existing methods.

This method involves direct transcription for managing the optimization of nonlinear dynamic systems.

Please see the readme file for usage details.

• Required Products: Optimization Toolbox; MATLAB
• MATLAB release: MATLAB 8.0 (R2012b)
• Other requirements: TOMLAB