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This article is part of the supplement: Selected articles from the 4th International Conference on Computational Systems Biology (ISB 2010)

Open Access Report

An improved kinetic model for the acetone-butanol-ethanol pathway of Clostridium acetobutylicum and model-based perturbation analysis

Ru-Dong Li1, Yuan-Yuan Li12, Ling-Yi Lu1, Cong Ren3, Yi-Xue Li12 and Lei Liu12*

Author Affiliations

1 Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, China

2 Shanghai Center for Bioinformatics Technology (SCBIT), Shanghai, China

3 Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, China

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BMC Systems Biology 2011, 5(Suppl 1):S12  doi:10.1186/1752-0509-5-S1-S12

Published: 20 June 2011

Additional files

Additional file 1:

Results of single parameter perturbation tests with magnitude +5%. The data entries included are numerical results obtained by increasing the value of every kinetic parameter by 5%. All parameters are traversed. There are 50 entries and the dataset is organized as a table in the format of *.xls (Excel worksheet). The first column is the index of the parameter perturbed, the second column is the parameter perturbed, and the third column is the Rd value that is used to evaluate how much impact the perturbation causes to butanol production.

Format: XLS Size: 28KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Results of single parameter perturbation tests with magnitude -5%. The data entries included are numerical results obtained by decreasing the value of every kinetic parameter by 5%. All parameters are traversed. There are 50 entries and the dataset is organized as a table in the format of *.xls (Excel worksheet). The first column is the index, the second column is the parameter perturbed, and the third column is the Rd value that is used to evaluate how much impact the perturbation causes to butanol production.

Format: XLS Size: 28KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Results of double parameter perturbation tests with respective magnitudes +5% and +5%. The data entries included are numerical results obtained by increasing the values of every pair of kinetic parameters by 5% each. All 2-parameter combinations are traversed. There are 1225 entries and the dataset is organized as a table in the format of *.xls (Excel worksheet). The first column is the pair of indexes of the parameters perturbed, the second and third columns are the parameters perturbed, respectively, and the fourth column is the Rd value that is used to evaluate how much impact the perturbation causes to butanol production.

Format: XLS Size: 137KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Results of double parameter perturbation tests with respective magnitudes +5% and -5%. The data entries included are numerical results obtained by altering the values of every pair of kinetic parameters, increasing the first parameter by 5% and decreasing the other one by 5%. All 2-parameter combinations are traversed. There are 1225 entries and the dataset is organized as a table in the format of *.xls (Excel worksheet). The first column is the pair of indexes of the parameters perturbed, the second and third columns are the parameters perturbed, respectively, and the fourth column is the Rd value that is used to evaluate how much impact the perturbation causes to butanol production.

Format: XLS Size: 136KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Results of double parameter perturbation tests with respective magnitudes -5% and +5%. The data entries included are numerical results obtained by altering the values of every pair of kinetic parameters, decreasing the first parameter by 5% and increasing the other one by 5%. All 2-parameter combinations are traversed. There are 1225 entries and the dataset is organized as a table in the format of *.xls (Excel worksheet). The first column is the pair of indexes of the parameters perturbed, the second and third columns are the parameters perturbed, respectively, and the fourth column is the Rd value that is used to evaluate how much impact the perturbation causes to butanol production.

Format: XLS Size: 136KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

Results of double parameter perturbation tests with respective magnitudes -5% and -5%. The data entries included are numerical results obtained by decreasing the values of every pair of kinetic parameters by 5% each. All 2-parameter combinations are traversed. There are 1225 entries and the dataset is organized as a table in the format of *.xls (Excel worksheet). The first column is the pair of indexes of the parameters perturbed, the second and third columns are the parameters perturbed, respectively, and the fourth column is the Rd value that is used to evaluate how much impact the perturbation causes to butanol production.

Format: XLS Size: 136KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

The values of kinetic parameters There are 50 parameters in our kinetic model. The dataset is organized as a table in the format of *.xls (Excel worksheet). The first column contains the indexes of reactions, the second column contains the parameters involved in each reaction, and the third column contains the parameter values.

Format: XLS Size: 122KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 8:

Description of the modeling method This is the detailed description of the method of modeling, including the incorporation of BuP, the construction of time division pattern, the computation of EACs, parameter estimation procedure, and the computation of perturbation analysis. This file is in the format of * (Word document). This file contains 4 supplementary figures (Figure S1 - S4) and a supplementary table (Table S1).

Format: DOC Size: 446KB Download file

This file can be viewed with: Microsoft Word Viewer

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