Scripts and results from gene expression methods assessment paper:
D. Machado, M.J. Herrgard. Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism. PLoS Computational Biology, 10(4), 2014.
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003580
INSTRUCTIONS:
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Install cobra toolbox for matlab from: http://opencobra.sourceforge.net/
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Install MADE from: http://www.bme.virginia.edu/csbl/downloads-made.php
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Install a solver with support for LP, QP and MILP (recommended: Gurobi 5.5)
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Use main.m to run all tests from the paper.