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General Information
| Manuscript title | A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture. |
| PubMed ID | 21247470 |
| Journal | BMC Systems Biology |
| Year | 2011 |
| Authors | Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer |
| Affiliations | University of Rostock, Institute of Computer Science, Department of Systems Biology & Bioinformatics |
| Keywords | Clostridium acetobutylicum, continuous culture, effect of pH, solvent production |
| Full text article |
Haus_2011.pdf
|
| Project name | not specified |
| Data used for | Model building |
Model Information
| Model name | second forward shift | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Organism | Clostridium acetobutylicum | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Model type | ordinary differential equations | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Category | Metabolism | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Number of reactions | 13 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Number of species | 12 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Number of regulators | not specified | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Number of parameters | 26 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Number of compartments | 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Dilution rate (h-1) | 0.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Model file(s) and history |
LATEST KIMOMODELID20.xml
(2014-04-11 17:26:19 UTC
by Administrator KiMoSys
)
Preview
Preview file KIMOMODELID20.xml<?xml version='1.0' encoding='UTF-8'?>
<!-- Created by JWS2SBML on 2010/10/08 16:38:37-->
<!-- A Systems Biology Approach to Investigate the Effect of pH-induced Gene Regulation on Solvent Production by Clostridium acetobutylicum in Continuous Culture
Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John King, Olaf Wolkenhauer
BMC Systems Biology (2010)
Corresponding author:
Sara Jabbari
sara.jabbari@nottingham.ac.uk
-->
<sbml level='2' version='4' xmlns='http://www.sbml.org/sbml/level2/version4'>
<model name='pH_shift_forward_3'>
<listOfCompartments>
<compartment id='compartment' name='compartment' size='1'/>
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<listOfSpecies>
<species boundaryCondition='true' compartment='compartment' constant='true' id='extVariable' initialConcentration='0' name='extVariable'/>
<species compartment='compartment' id='AC' initialConcentration='0' name='AC'/>
<species compartment='compartment' id='A' initialConcentration='13.73' name='A'/>
<species compartment='compartment' id='AaC' initialConcentration='0' name='AaC'/>
<species compartment='compartment' id='Aa' initialConcentration='0' name='Aa'/>
<species compartment='compartment' id='En' initialConcentration='3.02' name='En'/>
<species compartment='compartment' id='B' initialConcentration='8.81' name='B'/>
<species compartment='compartment' id='BC' initialConcentration='0' name='BC'/>
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<species compartment='compartment' id='Bn' initialConcentration='0' name='Bn'/>
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<species compartment='compartment' id='Cf' initialConcentration='0' name='Cf'/>
<species compartment='compartment' id='Ah' initialConcentration='0' name='Ah'/>
</listOfSpecies>
<listOfParameters>
<parameter id='k0' name='k0' value='0'/>
<parameter id='G' name='G' value='40'/>
<parameter id='Dvar' name='Dvar' value='0.075'/>
<parameter id='V1' name='V1' value='4.94'/>
<parameter id='V2' name='V2' value='2.92'/>
<parameter id='V4' name='V4' value='22.8'/>
<parameter id='V8' name='V8' value='64.8'/>
<parameter id='V10' name='V10' value='4.75'/>
<parameter id='K1' name='K1' value='0.00158'/>
<parameter id='K2' name='K2' value='0.00181'/>
<parameter id='K4' name='K4' value='1.87'/>
<parameter id='K8' name='K8' value='7.92e-06'/>
<parameter id='K10' name='K10' value='1.4e-05'/>
<parameter id='alpha3' name='alpha3' value='0.00517'/>
<parameter id='alpha5' name='alpha5' value='0.014'/>
<parameter id='alpha6' name='alpha6' value='0.00537'/>
<parameter id='alpha7' name='alpha7' value='4790'/>
<parameter id='alpha9' name='alpha9' value='347000'/>
<parameter id='rAd' name='rAd' value='0.00547'/>
<parameter id='rCf' name='rCf' value='0.000324'/>
<parameter id='rAh' name='rAh' value='0.289'/>
<parameter id='rAdplus' name='rAdplus' value='0.1037'/>
<parameter id='rCfplus' name='rCfplus' value='1.063'/>
<parameter id='rAhplus' name='rAhplus' value='2.5594'/>
<parameter id='n' name='n' value='485'/>
<parameter id='pstar' name='pstar' value='4.5'/>
<parameter id='Chemostat' name='Chemostat' value='1'/>
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<listOfReactions>
<reaction id='_1' name='v1'>
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Simulation of KIMOMODELID20.xml |
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| Notes |
not specified
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| Software | http://www.sbtoolbox.org (SBToolbox) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| BioModels or JWS Online ID | — | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Export metadata |
RDF:
metadataModelEntryID20.rdf
XML: metadataModelEntryID20.xml Plain text: metadataModelEntryID20.txt |
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AC
Share
|
Cite Model EntryID 20
Cite Model EntryID 20
| APA |
KiMoSys (https://kimosys.org). (2014, November 21). Model EntryID 20 (Clostridium acetobutylicum). https://kimosys.org/repository/42/associated_models/20
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| MLA |
KiMoSys (https://kimosys.org). "Model EntryID 20 (Clostridium acetobutylicum)." 2024, kimosys.org/repository/42/associated_models/20.
|
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| ISO-690 |
KiMoSys (https://kimosys.org). Model EntryID 20 (Clostridium acetobutylicum). [online], [Accessed 21 November 2024]. Available from: https://kimosys.org/repository/42/associated_models/20
|
|
| BibTeX |
@misc{ KiMoSysModelEntryID20,
author = "{KiMoSys (https://kimosys.org)}",
title = "Model EntryID 20 (Clostridium acetobutylicum)",
url = "https://kimosys.org/repository/42/associated_models/20",
note = "[Online; accessed 21-November-2024]"
}
|
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Related Model(s): AccessID 19 | AccessID 21 | AccessID 22
Submission and curation
Entered by:
Administrator KiMoSysFirst name: Administrator
Affiliation: INESC-ID/IST
Homepage: http://kdbio.inesc-id.pt/kimosys
Interests: mathematical modeling, accessible data, use of data
Created: 2013-05-03 13:24:53 UTC
Updated: 2014-06-30 20:39:10 UTC
Version: 0
Status: (reviewed) 2013-12-06 18:05:50 UTC
Views: 171
Downloads: 76