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fix: rename anaerobicModel
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A yeast-GEM-specific script that ideally should be refactored. For now, just rename to avoid conflict with the function in yeast-GEM repository
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@edkerk
edkerk committed Sep 22, 2024
1 parent 8af53fb commit 072e952
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2 changes: 1 addition & 1 deletion doc/index.html
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Expand Up @@ -25,7 +25,7 @@ <h2>Matlab Files found in these Directories</h2>
<td><a href="src/geckomat/model_adapter/adapterTemplate.html" title="src\geckomat\model_adapter">adapterTemplate</a></td> <td><a href="src/geckomat/limit_proteins/fillEnzConcs.html" title="src\geckomat\limit_proteins">fillEnzConcs</a></td> <td><a href="src/geckomat/kcat_sensitivity_analysis/Bayesian/getrSample.html" title="src\geckomat\kcat_sensitivity_analysis\Bayesian">getrSample</a></td> <td><a href="src/geckomat/kcat_sensitivity_analysis/sensitivityTuning.html" title="src\geckomat\kcat_sensitivity_analysis">sensitivityTuning</a></td> </tr> <tr>
<td><a href="src/geckomat/kcat_sensitivity_analysis/Bayesian/addCarbonNum.html" title="src\geckomat\kcat_sensitivity_analysis\Bayesian">addCarbonNum</a></td> <td><a href="src/geckomat/get_enzyme_data/findECInDB.html" title="src\geckomat\get_enzyme_data">findECInDB</a></td> <td><a href="src/geckomat/get_enzyme_data/loadBRENDAdata.html" title="src\geckomat\get_enzyme_data">loadBRENDAdata</a></td> <td><a href="src/geckomat/change_model/setKcatForReactions.html" title="src\geckomat\change_model">setKcatForReactions</a></td> </tr> <tr>
<td><a href="src/geckomat/utilities/addNewRxnsToEC.html" title="src\geckomat\utilities">addNewRxnsToEC</a></td> <td><a href="src/geckomat/utilities/findGECKOroot.html" title="src\geckomat\utilities">findGECKOroot</a></td> <td><a href="src/geckomat/utilities/loadConventionalGEM.html" title="src\geckomat\utilities">loadConventionalGEM</a></td> <td><a href="src/geckomat/change_model/setProtPoolSize.html" title="src\geckomat\change_model">setProtPoolSize</a></td> </tr> <tr>
<td><a href="src/geckomat/kcat_sensitivity_analysis/Bayesian/anaerobicModel.html" title="src\geckomat\kcat_sensitivity_analysis\Bayesian">anaerobicModel</a></td> <td><a href="src/geckomat/kcat_sensitivity_analysis/findMaxValue.html" title="src\geckomat\kcat_sensitivity_analysis">findMaxValue</a></td> <td><a href="src/geckomat/get_enzyme_data/loadDatabases.html" title="src\geckomat\get_enzyme_data">loadDatabases</a></td> <td><a href="src/geckomat/kcat_sensitivity_analysis/sigmaFitter.html" title="src\geckomat\kcat_sensitivity_analysis">sigmaFitter</a></td> </tr> <tr>
<td><a href="src/geckomat/kcat_sensitivity_analysis/Bayesian/anaerobicModel_GECKO.html" title="src\geckomat\kcat_sensitivity_analysis\Bayesian">anaerobicModel_GECKO</a></td> <td><a href="src/geckomat/kcat_sensitivity_analysis/findMaxValue.html" title="src\geckomat\kcat_sensitivity_analysis">findMaxValue</a></td> <td><a href="src/geckomat/get_enzyme_data/loadDatabases.html" title="src\geckomat\get_enzyme_data">loadDatabases</a></td> <td><a href="src/geckomat/kcat_sensitivity_analysis/sigmaFitter.html" title="src\geckomat\kcat_sensitivity_analysis">sigmaFitter</a></td> </tr> <tr>
<td><a href="src/geckomat/change_model/applyComplexData.html" title="src\geckomat\change_model">applyComplexData</a></td> <td><a href="src/geckomat/change_model/findMetSmiles.html" title="src\geckomat\change_model">findMetSmiles</a></td> <td><a href="src/geckomat/utilities/loadEcModel.html" title="src\geckomat\utilities">loadEcModel</a></td> <td><a href="src/geckomat/utilities/startGECKOproject.html" title="src\geckomat\utilities">startGECKOproject</a></td> </tr> <tr>
<td><a href="src/geckomat/change_model/applyCustomKcats.html" title="src\geckomat\change_model">applyCustomKcats</a></td> <td><a href="src/geckomat/limit_proteins/flexibilizeEnzConcs.html" title="src\geckomat\limit_proteins">flexibilizeEnzConcs</a></td> <td><a href="src/geckomat/utilities/loadFluxData.html" title="src\geckomat\utilities">loadFluxData</a></td> <td><a href="src/geckomat/kcat_sensitivity_analysis/truncateValues.html" title="src\geckomat\kcat_sensitivity_analysis">truncateValues</a></td> </tr> <tr>
<td><a href="src/geckomat/change_model/applyKcatConstraints.html" title="src\geckomat\change_model">applyKcatConstraints</a></td> <td><a href="src/geckomat/gather_kcats/fuzzyKcatMatching.html" title="src\geckomat\gather_kcats">fuzzyKcatMatching</a></td> <td><a href="src/geckomat/utilities/loadProtData.html" title="src\geckomat\utilities">loadProtData</a></td> <td><a href="src/geckomat/utilities/updateGECKOdoc.html" title="src\geckomat\utilities">updateGECKOdoc</a></td> </tr> <tr>
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4 changes: 2 additions & 2 deletions doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/abc_max.html
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Expand Up @@ -54,7 +54,7 @@ <h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="
<h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^" border="0" src="../../../../up.png"></a></h2>
This function calls:
<ul style="list-style-image:url(../../../../matlabicon.gif)">
<li><a href="addCarbonNum.html" class="code" title="function model = addCarbonNum(model)">addCarbonNum</a> addCarbonNum</li><li><a href="anaerobicModel.html" class="code" title="function model = anaerobicModel(model)">anaerobicModel</a> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</li><li><a href="changeMedia.html" class="code" title="function [model,pos] = changeMedia(model,c_source,media,anox,flux)">changeMedia</a> changeMedia</li></ul>
<li><a href="addCarbonNum.html" class="code" title="function model = addCarbonNum(model)">addCarbonNum</a> addCarbonNum</li><li><a href="anaerobicModel_GECKO.html" class="code" title="function model = anaerobicModel_GECKO(model)">anaerobicModel_GECKO</a> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</li><li><a href="changeMedia.html" class="code" title="function [model,pos] = changeMedia(model,c_source,media,anox,flux)">changeMedia</a> changeMedia</li></ul>
This function is called by:
<ul style="list-style-image:url(../../../../matlabicon.gif)">
<li><a href="bayesianSensitivityTuning.html" class="code" title="function ecModel = bayesianSensitivityTuning(ecModel,modelAdapter,maxIterations)">bayesianSensitivityTuning</a> bayesianSensitivityTuning</li></ul>
Expand Down Expand Up @@ -152,7 +152,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0085 model_tmp = changeRxnBounds(model_tmp,<span class="string">'r_1631'</span>,0,<span class="string">'b'</span>);
0086
0087 <span class="keyword">if</span> strcmp(data(i,14),<span class="string">'anaerobic'</span>) ||strcmp(data(i,14),<span class="string">'limited'</span>)
0088 model_tmp = <a href="anaerobicModel.html" class="code" title="function model = anaerobicModel(model)">anaerobicModel</a>(model_tmp);
0088 model_tmp = <a href="anaerobicModel_GECKO.html" class="code" title="function model = anaerobicModel_GECKO(model)">anaerobicModel_GECKO</a>(model_tmp);
0089 <span class="keyword">end</span>
0090 <span class="keyword">if</span> strcmp(data(i,14),<span class="string">'limited'</span>)
0091 model_tmp.lb(strcmp(model_tmp.rxnNames,<span class="string">'oxygen exchange'</span>)) = -5;<span class="comment">%TODO: Currently hard-coded for yeast</span>
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16 changes: 8 additions & 8 deletions ...ity_analysis/Bayesian/anaerobicModel.html → ...alysis/Bayesian/anaerobicModel_GECKO.html
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"http://www.w3.org/TR/REC-html40/loose.dtd">
<html>
<head>
<title>Description of anaerobicModel</title>
<meta name="keywords" content="anaerobicModel">
<title>Description of anaerobicModel_GECKO</title>
<meta name="keywords" content="anaerobicModel_GECKO">
<meta name="description" content="%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%">
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<meta name="generator" content="m2html v1.5 &copy; 2003-2005 Guillaume Flandin">
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</head>
<body>
<a name="_top"></a>
<div><a href="../../../../index.html">Home</a> &gt; <a href="#">src</a> &gt; <a href="#">geckomat</a> &gt; <a href="../index.html">kcat_sensitivity_analysis</a> &gt; <a href="index.html">Bayesian</a> &gt; anaerobicModel.m</div>
<div><a href="../../../../index.html">Home</a> &gt; <a href="#">src</a> &gt; <a href="#">geckomat</a> &gt; <a href="../index.html">kcat_sensitivity_analysis</a> &gt; <a href="index.html">Bayesian</a> &gt; anaerobicModel_GECKO.m</div>

<!--<table width="100%"><tr><td align="left"><a href="../../../../index.html"><img alt="<" border="0" src="../../../../left.png">&nbsp;Master index</a></td>
<td align="right"><a href="index.html">Index for src\geckomat\kcat_sensitivity_analysis\Bayesian&nbsp;<img alt=">" border="0" src="../../../../right.png"></a></td></tr></table>-->

<h1>anaerobicModel
<h1>anaerobicModel_GECKO
</h1>

<h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../../../../up.png"></a></h2>
<div class="box"><strong>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</strong></div>

<h2><a name="_synopsis"></a>SYNOPSIS <a href="#_top"><img alt="^" border="0" src="../../../../up.png"></a></h2>
<div class="box"><strong>function model = anaerobicModel(model) </strong></div>
<div class="box"><strong>function model = anaerobicModel_GECKO(model) </strong></div>

<h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="0" src="../../../../up.png"></a></h2>
<div class="fragment"><pre class="comment">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
anaerobicModel.m
anaerobicModel_GECKO.m
Converts model to anaerobic

Benjamin J. Sanchez
Expand All @@ -52,14 +52,14 @@ <h2><a name="_subfunctions"></a>SUBFUNCTIONS <a href="#_top"><img alt="^" border

<h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="../../../../up.png"></a></h2>
<div class="fragment"><pre>0001 <span class="comment">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span>
0002 <span class="comment">% anaerobicModel.m</span>
0002 <span class="comment">% anaerobicModel_GECKO.m</span>
0003 <span class="comment">% Converts model to anaerobic</span>
0004 <span class="comment">%</span>
0005 <span class="comment">% Benjamin J. Sanchez</span>
0006 <span class="comment">% Feiran Li - 2019-09-24</span>
0007 <span class="comment">% Feiran Li - Last update: 2019-10-02 modify the order of changes</span>
0008 <span class="comment">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span>
0009 <a name="_sub0" href="#_subfunctions" class="code">function model = anaerobicModel(model)</a>
0009 <a name="_sub0" href="#_subfunctions" class="code">function model = anaerobicModel_GECKO(model)</a>
0010
0011 <span class="comment">%1th change: Refit GAM and NGAM to exp. data, change biomass composition</span>
0012 GAM = 58.1988; <span class="comment">%Data from Nissen et al. 1997</span>
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4 changes: 2 additions & 2 deletions doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/changeMedia.html
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Expand Up @@ -54,7 +54,7 @@ <h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="
<h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^" border="0" src="../../../../up.png"></a></h2>
This function calls:
<ul style="list-style-image:url(../../../../matlabicon.gif)">
<li><a href="anaerobicModel.html" class="code" title="function model = anaerobicModel(model)">anaerobicModel</a> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</li></ul>
<li><a href="anaerobicModel_GECKO.html" class="code" title="function model = anaerobicModel_GECKO(model)">anaerobicModel_GECKO</a> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</li></ul>
This function is called by:
<ul style="list-style-image:url(../../../../matlabicon.gif)">
<li><a href="abc_max.html" class="code" title="function [rmse_final,exp,simulated,growthdata,max_growth]=abc_max(ecModel,kcat_random_all,growthdata,max_growth,proc,sample_generation,j,rxn2block)">abc_max</a> setProtPoolSize</li></ul>
Expand Down Expand Up @@ -180,7 +180,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0113 <span class="comment">% change aeerobic or anaerobic</span>
0114 <span class="keyword">if</span> strcmp(anox,<span class="string">'anaerobic'</span>)
0115 1
0116 model = <a href="anaerobicModel.html" class="code" title="function model = anaerobicModel(model)">anaerobicModel</a>(model);
0116 model = <a href="anaerobicModel_GECKO.html" class="code" title="function model = anaerobicModel_GECKO(model)">anaerobicModel_GECKO</a>(model);
0117 <span class="keyword">end</span>
0118 <span class="keyword">end</span>
0119
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2 changes: 1 addition & 1 deletion doc/src/geckomat/kcat_sensitivity_analysis/Bayesian/index.html
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Expand Up @@ -19,7 +19,7 @@ <h1>Index for src\geckomat\kcat_sensitivity_analysis\Bayesian</h1>

<h2>Matlab files in this directory:</h2>
<table>
<tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="abc_max.html">abc_max</a></td><td>setProtPoolSize </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="addCarbonNum.html">addCarbonNum</a></td><td>addCarbonNum </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="anaerobicModel.html">anaerobicModel</a></td><td>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="bayesianSensitivityTuning.html">bayesianSensitivityTuning</a></td><td>bayesianSensitivityTuning </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="changeMedia.html">changeMedia</a></td><td>changeMedia </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="getcarbonnum.html">getcarbonnum</a></td><td>getcarbonnum </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="getrSample.html">getrSample</a></td><td>getrSample </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="updateprior.html">updateprior</a></td><td>updateprior </td></tr></table>
<tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="abc_max.html">abc_max</a></td><td>setProtPoolSize </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="addCarbonNum.html">addCarbonNum</a></td><td>addCarbonNum </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="anaerobicModel_GECKO.html">anaerobicModel_GECKO</a></td><td>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="bayesianSensitivityTuning.html">bayesianSensitivityTuning</a></td><td>bayesianSensitivityTuning </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="changeMedia.html">changeMedia</a></td><td>changeMedia </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="getcarbonnum.html">getcarbonnum</a></td><td>getcarbonnum </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="getrSample.html">getrSample</a></td><td>getrSample </td></tr><tr><td><img src="../../../../matlabicon.gif" alt="" border="">&nbsp;<a href="updateprior.html">updateprior</a></td><td>updateprior </td></tr></table>



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2 changes: 1 addition & 1 deletion src/geckomat/kcat_sensitivity_analysis/Bayesian/abc_max.m
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Expand Up @@ -85,7 +85,7 @@
model_tmp = changeRxnBounds(model_tmp,'r_1631',0,'b');

if strcmp(data(i,14),'anaerobic') ||strcmp(data(i,14),'limited')
model_tmp = anaerobicModel(model_tmp);
model_tmp = anaerobicModel_GECKO(model_tmp);
end
if strcmp(data(i,14),'limited')
model_tmp.lb(strcmp(model_tmp.rxnNames,'oxygen exchange')) = -5;%TODO: Currently hard-coded for yeast
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4 changes: 2 additions & 2 deletions ...tivity_analysis/Bayesian/anaerobicModel.m → ..._analysis/Bayesian/anaerobicModel_GECKO.m
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@@ -1,12 +1,12 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% anaerobicModel.m
% anaerobicModel_GECKO.m
% Converts model to anaerobic
%
% Benjamin J. Sanchez
% Feiran Li - 2019-09-24
% Feiran Li - Last update: 2019-10-02 modify the order of changes
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function model = anaerobicModel(model)
function model = anaerobicModel_GECKO(model)

%1th change: Refit GAM and NGAM to exp. data, change biomass composition
GAM = 58.1988; %Data from Nissen et al. 1997
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2 changes: 1 addition & 1 deletion src/geckomat/kcat_sensitivity_analysis/Bayesian/changeMedia.m
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Expand Up @@ -113,7 +113,7 @@
% change aeerobic or anaerobic
if strcmp(anox,'anaerobic')
1
model = anaerobicModel(model);
model = anaerobicModel_GECKO(model);
end
end

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