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Open Access Highly Accessed Research article

Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms

Pablo Carbonell, Davide Fichera, Shashi B Pandit and Jean-Loup Faulon*

Author Affiliations

iSSB, Institute of Systems and Synthetic Biology, University of Evry, Genopole Campus 1, Genavenir 6, 5 rue Henri Desbruères, 91030 EVRY Cedex, France

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BMC Systems Biology 2012, 6:10  doi:10.1186/1752-0509-6-10

Published: 6 February 2012

Additional files

Additional file 1:

Figure S1. Distribution of graph hierarchies (Butts, C J Stat Soft, 24:1-50, 2008) in heterologous metabolic networks (0.169 ± 0.11) in comparison with the graph hierarchy of central (0.032), nucleotide (0.027), lipid (0.051), and amino acid (0.030) metabolic networks in E. coli.

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Additional file 2:

Figure S2. Performance comparisons for FindPath, ExPA and efmtools for run time per output and memory use in function of size of input and size of output.

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Additional file 3:

An example of pathway enumeration with bootstraps. An example of pathways enumeration with Findpath using bootstraps.

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Additional file 4:

Availability and requirements. Description of the available MetaHype web server for running the algorithms for KEGG compounds.

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Additional file 5:

Figure S8. Minimal constrained hyperpath problem reduction of a 3-SAT formula.

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Additional file 6:

Figure S9. Instance of minimal constrained hyperpath problem.

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