Open Access Highly Accessed Research article

Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

Caroline B Milne12, James A Eddy23, Ravali Raju7, Soroush Ardekani1, Pan-Jun Kim2, Ryan S Senger5, Yong-Su Jin26, Hans P Blaschek246 and Nathan D Price1238*

Author Affiliations

1 Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, IL, USA

2 Institute for Genomic Biology, University of Illinois, Urbana, IL, USA

3 Department of Bioengineering, University of Illinois, Urbana, IL, USA

4 Center for Advanced BioEnergy Research, University of Illinois, Urbana, IL, USA

5 Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA

6 Department of Food Science and Human Nutrition, University of Illinois, Urbana, IL, USA

7 Department of Chemical Engineering and Material Science, University of Minnesota, MN, USA

8 Institute for Systems Biology, 401 Terry Avenue N, Seattle, WA 98109, USA

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BMC Systems Biology 2011, 5:130  doi:10.1186/1752-0509-5-130

Published: 16 August 2011

Additional files

Additional file 1:

Model Details. This Excel file contains detailed information about the following aspects of the iCM925 model: • reaction information (reactionData). • metabolite information (metaboliteData). • reaction additions from BiGG based on GapFill suggestions and BLAST scores (GapFill additions from BiGG). • biomass equation and details about its construction (Biomass Composition). • fatty acid and phospholipid molecular formulas (Phospholipid Formulas).

Format: XLS Size: 584KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Additional Figures and Analyses. This PDF contains information about the following supporting results, figures, analyses: A. Annotation Database Gene-Protein-Reaction (GPR) Agreement. B. Annotation Database Pathway Contribution. C. Experimental Data. D. Substrate Uptake Rates & Product Formation Rates. F. Flux Variability Analysis.

Format: PDF Size: 1.2MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Model SBML File. This file contains the model in the Systems Biology Markup Language format. This file can be read into MATLAB using the COBRA Toolbox.

Format: XML Size: 1.2MB Download file

Open Data