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Open Access Highly Accessed Research article

Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production

Seth B Roberts13, Christopher M Gowen1, J Paul Brooks23 and Stephen S Fong13*

Author Affiliations

1 Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA, 23284, USA

2 Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, Richmond, VA 23284, USA

3 Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA

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BMC Systems Biology 2010, 4:31  doi:10.1186/1752-0509-4-31

Published: 22 March 2010

Additional files

Additional file 1:

Model details and results. This Excel workbook contains the final reaction list, metabolite definitions, biomass function, cellulosome reaction formulation, and gene-protein-reaction (GPR) relationships. In addition, it contains the complete list of results for the reciprocal best hits (RBH) of EC numbers missing from the current C. thermocellum annotations, and the complete results from the single gene- and reaction-deletion simulations and the model comparisons to growth on cellobiose and fructose.

Format: XLS Size: 786KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 2:

This model file includes tab delimited GPR relationships, reaction list, and sources and escapes for growth on minimal media.

Format: TXT Size: 87KB Download file

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Additional file 3:

This file contains the model in SBML format.

Format: XML Size: 541KB Download file

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Additional file 4:

Removed futile cycles. This results file shows reactions which were deleted from the original model build to remove futile cycles.

Format: TXT Size: 69KB Download file

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Additional file 5:

Calculations and additional methods. This file contains detailed methods and sample calculations for determining the biomass objective reaction and the fatty acid content reactions as well as details about simulations of alternative media formulations.

Format: DOC Size: 2.5MB Download file

This file can be viewed with: Microsoft Word Viewer

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