Open Access Research article

Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model

Cihan Oguz1, Teeraphan Laomettachit2, Katherine C Chen1, Layne T Watson3, William T Baumann4 and John J Tyson1*

Author Affiliations

1 Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, USA

2 Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand

3 Departments of Computer Science and Mathematics, Virginia Tech, Blacksburg, Virginia 24061, USA

4 Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA

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BMC Systems Biology 2013, 7:53  doi:10.1186/1752-0509-7-53

Published: 28 June 2013

Additional files

Additional file 1:

Supplementary Tables. This pdf file includes the supplementary tables referred to in the main text.

Format: PDF Size: 195KB Download file

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Additional file 2:

viarray.txt, integrate.cpp, runOPTIMAL.m, runTL.m, integrate.mexw64, OPTIMAL.txt and TLset.txt. “viarray.txt” holds the viability array of the 119 strains (array values of 1 for viable strains and 2 for inviable strains), “integrate.cpp” is the C subroutine for the ODEs and, integrate.mexw64 is the mex file that allows Matlab to use the C subroutine for solving the ODEs. Altogether, these files reproduce the number of hits with the parameter values from the best performing DE run (OPTIMAL.txt from Additional file 2: Table S4, 111 hits) and the initial parameter values (“initial guess”) before the optimization (TLset.txt from Additional file 2: Table S4, with 72 hits). In order to reproduce these results, Matlab files “runOPTIMAL.m” and “runTL.m” need to be executed, respectively.

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Additional file 3:

Supplementary Text. This pdf file includes a detailed description of Latin Hypercube sampling.

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Additional file 4:

Supplementary Figures. This pdf file includes two additional figures.

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