Repository
» Data AccessID 42 » Model AccessID 19
Detail View - Model AccessID 19
Back
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 | first 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 KIMOMODELID19.xml
(2014-04-11 17:25:43 UTC
by Administrator KiMoSys
)
Preview
Preview file KIMOMODELID19.xml<?xml version='1.0' encoding='UTF-8'?>
<!-- Created by Sara Jabbari (sara.jabbari@nottingham.ac.uk) using 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'/>
</listOfCompartments>
<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='42.65' 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='5.63' name='En'/>
<species compartment='compartment' id='B' initialConcentration='55.83' name='B'/>
<species compartment='compartment' id='BC' initialConcentration='0' name='BC'/>
<species compartment='compartment' id='An' initialConcentration='2.66' name='An'/>
<species compartment='compartment' id='Bn' initialConcentration='0' name='Bn'/>
<species compartment='compartment' id='Ad' initialConcentration='0' name='Ad'/>
<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'/>
</listOfParameters>
<listOfReactions>
<reaction id='_1' name='v1'>
<listOfReactants>
<speciesReference species='extVariable'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='AC'/>
</listOfProducts>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<divide/>
<apply>
<times/>
<cn type='integer'> 2 </cn>
<ci> V1 </ci>
<ci> G </ci>
</apply>
<apply>
<plus/>
<ci> K1 </ci>
<ci> G </ci>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_2' name='v2'>
<listOfReactants>
<speciesReference species='AC'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='A'/>
</listOfProducts>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<divide/>
<apply>
<times/>
<ci> V2 </ci>
<ci> AC </ci>
</apply>
<apply>
<plus/>
<ci> K2 </ci>
<ci> AC </ci>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_3' name='v3'>
<listOfReactants>
<speciesReference species='A'/>
<speciesReference species='AaC'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='AC'/>
<speciesReference species='Aa'/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species='Cf'/>
</listOfModifiers>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<times/>
<ci> alpha3 </ci>
<ci> A </ci>
<ci> AaC </ci>
<ci> Cf </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_4' name='v4'>
<listOfReactants>
<speciesReference species='AC'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='AaC'/>
</listOfProducts>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<divide/>
<apply>
<times/>
<ci> V4 </ci>
<ci> AC </ci>
</apply>
<apply>
<plus/>
<ci> K4 </ci>
<ci> AC </ci>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_5' name='v5'>
<listOfReactants>
<speciesReference species='AC'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='En'/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species='Ah'/>
</listOfModifiers>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<times/>
<ci> alpha5 </ci>
<ci> AC </ci>
<ci> Ah </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_6' name='v6'>
<listOfReactants>
<speciesReference species='AaC'/>
<speciesReference species='B'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='Aa'/>
<speciesReference species='BC'/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species='Cf'/>
</listOfModifiers>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<times/>
<ci> alpha6 </ci>
<ci> B </ci>
<ci> AaC </ci>
<ci> Cf </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_7' name='v7'>
<listOfReactants>
<speciesReference species='Aa'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='An'/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species='Ad'/>
</listOfModifiers>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<times/>
<ci> alpha7 </ci>
<ci> Aa </ci>
<ci> Ad </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_8' name='v8'>
<listOfReactants>
<speciesReference species='BC'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='B'/>
</listOfProducts>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<divide/>
<apply>
<times/>
<ci> V8 </ci>
<ci> BC </ci>
</apply>
<apply>
<plus/>
<ci> K8 </ci>
<ci> BC </ci>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_9' name='v9'>
<listOfReactants>
<speciesReference species='BC'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='Bn'/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species='Ah'/>
</listOfModifiers>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<times/>
<ci> alpha9 </ci>
<ci> BC </ci>
<ci> Ah </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_10' name='v10'>
<listOfReactants>
<speciesReference species='extVariable'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='Ad'/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species='Tanh'/>
<modifierSpeciesReference species='t'/>
</listOfModifiers>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<minus/>
<apply>
<plus/>
<ci> rAd </ci>
<apply>
<times/>
<ci> rAdplus </ci>
<apply>
<minus/>
<cn type='integer'> 1 </cn>
<apply>
<tanh/>
<apply>
<times/>
<ci> n </ci>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<minus/>
<cn> 5.7 </cn>
<apply>
<times/>
<cn> 0.6 </cn>
<apply>
<tanh/>
<apply>
<times/>
<cn> 141.9436 </cn>
<cn> 0.1846 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<times/>
<cn> 0.6 </cn>
<apply>
<tanh/>
<apply>
<times/>
<cn> -0.1846 </cn>
<apply>
<minus/>
<ci> t </ci>
<cn> 141.9436 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<ci> pstar </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci> Dvar </ci>
<ci> Ad </ci>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_11' name='v11'>
<listOfReactants>
<speciesReference species='extVariable'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='Cf'/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species='Tanh'/>
<modifierSpeciesReference species='t'/>
</listOfModifiers>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<minus/>
<apply>
<plus/>
<ci> rCf </ci>
<apply>
<times/>
<ci> rCfplus </ci>
<apply>
<minus/>
<cn type='integer'> 1 </cn>
<apply>
<tanh/>
<apply>
<times/>
<ci> n </ci>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<minus/>
<cn> 5.7 </cn>
<apply>
<times/>
<cn> 0.6 </cn>
<apply>
<tanh/>
<apply>
<times/>
<cn> 141.9436 </cn>
<cn> 0.1846 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<times/>
<cn> 0.6 </cn>
<apply>
<tanh/>
<apply>
<times/>
<cn> -0.1846 </cn>
<apply>
<minus/>
<ci> t </ci>
<cn> 141.9436 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<ci> pstar </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci> Dvar </ci>
<ci> Cf </ci>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_12' name='v12'>
<listOfReactants>
<speciesReference species='extVariable'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='Ah'/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species='Tanh'/>
<modifierSpeciesReference species='t'/>
</listOfModifiers>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<minus/>
<apply>
<plus/>
<ci> rAh </ci>
<apply>
<times/>
<ci> rAhplus </ci>
<apply>
<minus/>
<cn type='integer'> 1 </cn>
<apply>
<tanh/>
<apply>
<times/>
<ci> n </ci>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<minus/>
<cn> 5.7 </cn>
<apply>
<times/>
<cn> 0.6 </cn>
<apply>
<tanh/>
<apply>
<times/>
<cn> 141.9436 </cn>
<cn> 0.1846 </cn>
</apply>
</apply>
</apply>
</apply>
<apply>
<times/>
<cn> 0.6 </cn>
<apply>
<tanh/>
<apply>
<times/>
<cn> -0.1846 </cn>
<apply>
<minus/>
<ci> t </ci>
<cn> 141.9436 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<ci> pstar </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci> Dvar </ci>
<ci> Ah </ci>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_13' name='v13'>
<listOfReactants>
<speciesReference species='AaC'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='BC'/>
</listOfProducts>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<divide/>
<apply>
<times/>
<ci> V10 </ci>
<ci> AaC </ci>
</apply>
<apply>
<plus/>
<ci> K10 </ci>
<ci> AaC </ci>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_14' name='v14'>
<listOfReactants>
<speciesReference species='AC'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='extVariable'/>
</listOfProducts>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<times/>
<ci> Dvar </ci>
<ci> AC </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_15' name='v15'>
<listOfReactants>
<speciesReference species='A'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='extVariable'/>
</listOfProducts>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<times/>
<ci> Dvar </ci>
<ci> A </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_16' name='v16'>
<listOfReactants>
<speciesReference species='En'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='extVariable'/>
</listOfProducts>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<times/>
<ci> Dvar </ci>
<ci> En </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_17' name='v17'>
<listOfReactants>
<speciesReference species='AaC'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='extVariable'/>
</listOfProducts>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<times/>
<ci> Dvar </ci>
<ci> AaC </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_18' name='v18'>
<listOfReactants>
<speciesReference species='Aa'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='extVariable'/>
</listOfProducts>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<times/>
<ci> Dvar </ci>
<ci> Aa </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_19' name='v19'>
<listOfReactants>
<speciesReference species='BC'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='extVariable'/>
</listOfProducts>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<times/>
<ci> Dvar </ci>
<ci> BC </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_20' name='v20'>
<listOfReactants>
<speciesReference species='B'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='extVariable'/>
</listOfProducts>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<times/>
<ci> Dvar </ci>
<ci> B </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_21' name='v21'>
<listOfReactants>
<speciesReference species='An'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='extVariable'/>
</listOfProducts>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<times/>
<ci> Dvar </ci>
<ci> An </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='_22' name='v22'>
<listOfReactants>
<speciesReference species='Bn'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='extVariable'/>
</listOfProducts>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<times/>
<ci> Dvar </ci>
<ci> Bn </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model></sbml>
Simulation of KIMOMODELID19.xml |
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Notes |
not specified
|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Software | http://www.sbtoolbox.org (SBToolbox) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| BioModels or JWS Online ID | — | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Export metadata |
RDF:
metadataModelEntryID19.rdf
XML: metadataModelEntryID19.xml Plain text: metadataModelEntryID19.txt |
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AC
Share
|
Cite Model EntryID 19
Cite Model EntryID 19
| APA |
KiMoSys (https://kimosys.org). (2018, December 21). Model EntryID 19 (Clostridium acetobutylicum). https://kimosys.org/repository/42/associated_models/19
|
|
| MLA |
KiMoSys (https://kimosys.org). "Model EntryID 19 (Clostridium acetobutylicum)." 2024, kimosys.org/repository/42/associated_models/19.
|
|
| ISO-690 |
KiMoSys (https://kimosys.org). Model EntryID 19 (Clostridium acetobutylicum). [online], [Accessed 21 December 2024]. Available from: https://kimosys.org/repository/42/associated_models/19
|
|
| BibTeX |
@misc{ KiMoSysModelEntryID19,
author = "{KiMoSys (https://kimosys.org)}",
title = "Model EntryID 19 (Clostridium acetobutylicum)",
url = "https://kimosys.org/repository/42/associated_models/19",
note = "[Online; accessed 21-December-2024]"
}
|
|
Related Model(s): AccessID 20 | 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 13:15:51 UTC
Updated: 2018-07-21 14:49:30 UTC
Version: 0
Status: (reviewed) 2013-12-06 18:05:50 UTC
Views: 202
Downloads: 69