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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

Number of species

Number of regulators

not specified

Number of parameters

Number of compartments

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

<?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'/>
  </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='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'/>
    <species compartment='compartment' id='An' initialConcentration='1.82' 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> 144.4033 </cn>
				  <cn> 0.1071 </cn>
                                </apply>
                              </apply>
                            </apply>
                          </apply>
                          <apply>
                            <times/>
                            <cn> 0.6 </cn>
                            <apply>
                              <tanh/>
                              <apply>
                                <times/>
				<cn> -0.1071 </cn>
                                <apply>
                                  <minus/>
                                  <ci> t </ci>
				  <cn> 144.4033 </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> 144.4033 </cn>
				  <cn> 0.1071 </cn>
                                </apply>
                              </apply>
                            </apply>
                          </apply>
                          <apply>
                            <times/>
                            <cn> 0.6 </cn>
                            <apply>
                              <tanh/>
                              <apply>
                                <times/>
				<cn> -0.1071 </cn>
                                <apply>
                                  <minus/>
                                  <ci> t </ci>
				  <cn> 144.4033 </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> 144.4033 </cn>
				  <cn> 0.1071 </cn>
                                </apply>
                              </apply>
                            </apply>
                          </apply>
                          <apply>
                            <times/>
                            <cn> 0.6 </cn>
                            <apply>
                              <tanh/>
                              <apply>
                                <times/>
				<cn> -0.1071 </cn>
                                <apply>
                                  <minus/>
                                  <ci> t </ci>
				  <cn> 144.4033 </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>

Specie	Initial concentration
extVariable	0 mmol
AC	0 mmol
A	13.73 mmol
AaC	0 mmol
Aa	0 mmol
En	3.02 mmol
B	8.81 mmol
BC	0 mmol
An	1.82 mmol
Bn	0 mmol
Ad	0 mmol
Cf	0 mmol
Ah	0 mmol

Reaction	Equation	Parameters
extVariable AC	$2 V1 G K1 G$	No information available
AC A	$V2 AC K2 AC$	No information available
A + AaC AC + Aa	$alpha3 A AaC Cf$	No information available
AC AaC	$V4 AC K4 AC$	No information available
AC En	$alpha5 AC Ah$	No information available
AaC + B Aa + BC	$alpha6 B AaC Cf$	No information available
Aa An	$alpha7 Aa Ad$	No information available
BC B	$V8 BC K8 BC$	No information available
BC Bn	$alpha9 BC Ah$	No information available
extVariable Ad	$rAd rAdplus 1 n 5.7 0.6 144.4033 0.1071 0.6 -0.1071 t 144.4033 pstar Dvar Ad$	No information available
extVariable Cf	$rCf rCfplus 1 n 5.7 0.6 144.4033 0.1071 0.6 -0.1071 t 144.4033 pstar Dvar Cf$	No information available
extVariable Ah	$rAh rAhplus 1 n 5.7 0.6 144.4033 0.1071 0.6 -0.1071 t 144.4033 pstar Dvar Ah$	No information available
AaC BC	$V10 AaC K10 AaC$	No information available
AC extVariable	$Dvar AC$	No information available
A extVariable	$Dvar A$	No information available
En extVariable	$Dvar En$	No information available
AaC extVariable	$Dvar AaC$	No information available
Aa extVariable	$Dvar Aa$	No information available
BC extVariable	$Dvar BC$	No information available
B extVariable	$Dvar B$	No information available
An extVariable	$Dvar An$	No information available
Bn extVariable	$Dvar Bn$	No information available

Simulate

Notes

not specified

Software

http://www.sbtoolbox.org (SBToolbox)

BioModels or JWS Online ID

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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: 174

Downloads: 76

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APA	KiMoSys (https://kimosys.org). (2014, April 4). Model EntryID 20 (Clostridium acetobutylicum). https://kimosys.org/repository/42/associated_models/20
MLA	KiMoSys (https://kimosys.org). "Model EntryID 20 (Clostridium acetobutylicum)." 2025, kimosys.org/repository/42/associated_models/20.
ISO-690	KiMoSys (https://kimosys.org). Model EntryID 20 (Clostridium acetobutylicum). [online], [Accessed 4 April 2025]. 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 4-April-2025]" }