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We developed the CoPE FBA and CoPE FBA 2.0 pipelines in Linux. The current version of our pipeline is implemented in Python. We make use of Polco and QSopt_EX.

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CoPE-FBA 2.0

Software

Download CoPE-FBA 2.0 pipeline (July 2015)

Models

Download Models

Manuscript data

We provide three examples (toy model, iTM686.light, and Ecoli_iAF1260_noox.glc) for which we programmed shell scripts that can be used directly to enumerate and analyze the optimal solution spaces of these models.

Download output generated after enumeration of the optimal solution space (P1-P7 of the pipeline).

E. coli (glc, aerobic restricted)

E. coli (glc, aerobic)

E. coli (glc, anaerobic)

Manuscript data analysis

Download Vertex enumeration analysis (P8-P9 of the pipeline)

E. coli (glc, aerobic restricted)

E. coli (glc, aerobic)

E. coli (glc, anaerobic)

CoPE-FBA

Download Software

CoPE-FBA pipeline (March 2012)

Download manuscript data

E. coli (iJR904): memesa output , model .

E. coli (iAF1260): memesa output, model.

M. Barkeri (iAF692): memesa output, model.

M. tuberculosis (iNJ661): memesa output, model.

core memesa: memesa output, model

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