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latest/modules/analysis/multiSpecies/microbiomeModelingToolbox/mgPipe/index.html

@@ -381,7 +381,7 @@ <h1>The COBRA Toolbox</h1>
 
 <dl class="mat function">
 <dt class="sig sig-object mat" id="src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe.createPanModels">
-<span class="sig-name descname"><span class="pre">createPanModels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">agoraPath</span></em>, <em class="sig-param"><span class="pre">panPath</span></em>, <em class="sig-param"><span class="pre">taxonLevel</span></em>, <em class="sig-param"><span class="pre">agoraVersion</span></em>, <em class="sig-param"><span class="pre">numWorkers</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/opencobra/cobratoolbox/blob/master/src/analysis/multiSpecies/microbiomeModelingToolbox/mgPipe/createPanModels.m"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe.createPanModels" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">createPanModels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">agoraPath</span></em>, <em class="sig-param"><span class="pre">panPath</span></em>, <em class="sig-param"><span class="pre">taxonLevel</span></em>, <em class="sig-param"><span class="pre">agoraVersion</span></em>, <em class="sig-param"><span class="pre">numWorkers</span></em>, <em class="sig-param"><span class="pre">builtTaxa</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/opencobra/cobratoolbox/blob/master/src/analysis/multiSpecies/microbiomeModelingToolbox/mgPipe/createPanModels.m"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe.createPanModels" title="Permalink to this definition">¶</a></dt>
 <dd><p>This function creates pan-models for all unique taxa (e.g., species)
 included in the AGORA resource. If reconstructions of multiple strains
 in a given taxon are present, the reactions in these reconstructions will
@@ -403,12 +403,18 @@ <h1>The COBRA Toolbox</h1>
 <li><p><strong>agoraPath     String containing the path to the AGORA reconstructions.</strong> – Must end with a file separator.</p></li>
 <li><p><strong>panPath       String containing the path to an empty folder that the</strong> – created pan-models will be stored in. Must end with a file separator.</p></li>
 <li><p><strong>taxonLevel    String with desired taxonomical level of the pan-models.</strong> – Allowed inputs are ‘Species’,’Genus’,’Family’,’Order’, ‘Class’,’Phylum’.</p></li>
-<li><p><strong>agoraVersion  Version of AGORA that will be used (allowed inputs</strong> – ‘AGORA’, ‘AGORA2’)</p></li>
+<li><p><strong>agoraVersion  Version of AGORA that will be used (allowed inputs</strong> – ‘AGORA’, ‘AGORA2’,
+alternatively: path to custom table with reconstruction information)</p></li>
 </ul>
 </dd>
 </dl>
-<dl class="simple">
-<dt>OPTIONAL INPUTS</dt><dd><p>numWorkers    Number of workers for parallel pool (default: no pool)</p>
+<dl>
+<dt>OPTIONAL INPUTS</dt><dd><p>numWorkers    Number of workers for parallel pool (default: no pool)
+builtTaxa     Names of taxa in table that will be built (default:</p>
+<blockquote>
+<div><p>all). Need to be entered as a cell array of strings with names written
+exactly as in the corresponding column in the table.</p>
+</div></blockquote>
 </dd>
 </dl>
 </dd></dl>

latest/modules/base/solvers/getSetSolver/index.html

@@ -244,7 +244,7 @@ <h1>The COBRA Toolbox</h1>
 <dd><p>Changes the Cobra Toolbox optimization solver(s)</p>
 <dl class="field-list simple">
 <dt class="field-odd">USAGE</dt>
-<dd class="field-odd"><p><strong>[solverOK, solverInstalled] = changeCobraSolver</strong> (<em>solverName, solverType, printLevel, validationLevel</em>)</p>
+<dd class="field-odd"><p><strong>[solverOK, solverInstalled] = changeCobraSolver</strong> (<em>solverName, problemType, printLevel, validationLevel</em>)</p>
 </dd>
 <dt class="field-even">INPUTS</dt>
 <dd class="field-even"><ul class="simple">

latest/modules/dataIntegration/XomicsToModel/analysis/index.html

@@ -342,7 +342,7 @@ <h1>The COBRA Toolbox</h1>
 pipeline</p>
 </div>
 <dl class="simple">
-<dt>Author(s): - Xi Luo</dt><dd><ul class="simple">
+<dt>Author(s): - Xi Luo, update at 2024/10</dt><dd><ul class="simple">
 <li><p>Hanneke Leegwater (2022)</p></li>
 </ul>
 </dd>
@@ -554,22 +554,26 @@ <h1>The COBRA Toolbox</h1>
 <dl class="mat function">
 <dt class="sig sig-object mat" id="src.dataIntegration.XomicsToModel.analysis.plotOverlapResults">
 <span class="sig-name descname"><span class="pre">plotOverlapResults</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">overlapresults</span></em>, <em class="sig-param"><span class="pre">statistic</span></em>, <em class="sig-param"><span class="pre">savepath</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/opencobra/cobratoolbox/blob/master/src/dataIntegration/XomicsToModel/analysis/plotOverlapResults.m"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#src.dataIntegration.XomicsToModel.analysis.plotOverlapResults" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list">
+<dd><dl class="field-list simple">
 <dt class="field-odd">USAGE</dt>
 <dd class="field-odd"><p><strong>plot the overlapped heatmap for each model with proportion text labels</strong></p>
-<dl class="simple">
-<dt>Input:</dt><dd><p>overlapresults: from compareXomicsModels.m
-statistic:  from compareXomicsModels.m
-savepath (optional): the path to save the plot</p>
 </dd>
-<dt>Output:</dt><dd><p>a heat map plot</p>
+<dt class="field-even">Input</dt>
+<dd class="field-even"><ul class="simple">
+<li><p><strong>overlapresults</strong> – from compareXomicsModels.m</p></li>
+<li><p><strong>statistic</strong> – from compareXomicsModels.m</p></li>
+<li><p><strong>savepath</strong> (<em>optional</em>) – the path to save the plot</p></li>
+</ul>
 </dd>
-<dt>Author(s):</dt><dd><p>Xi Luo, 2023/02</p>
+<dt class="field-odd">Output</dt>
+<dd class="field-odd"><p><strong>a heat map plot</strong></p>
 </dd>
 </dl>
+<dl class="simple">
+<dt>Author(s):</dt><dd><p>Xi Luo, update 2024/10</p>
 </dd>
 </dl>
-<p>use proportion to create map</p>
+<p>use proportion data to create map</p>
 </dd></dl>
 
 <dl class="mat function">

latest/modules/dataIntegration/metanetxMapper/index.html

@@ -226,18 +226,18 @@ <h1>The COBRA Toolbox</h1>
 <dd><p>This function maps metabolite IDs to each other using Beta MetaNetX database</p>
 <dl class="field-list simple">
 <dt class="field-odd">USAGE</dt>
-<dd class="field-odd"><p><strong>[metData] = metanetxMapper</strong> (<em>metInfo, varargin</em>)</p>
+<dd class="field-odd"><p><strong>[metData] = metanetxMapper</strong> (<em>metInfo, infoType</em>)</p>
 </dd>
 <dt class="field-even">INPUTS</dt>
 <dd class="field-even"><ul class="simple">
-<li><p><strong>name</strong> – string name of the metabolite (Common names, VMH names, CHEBI ids,</p></li>
-<li><p><strong>swiss lipids id, HMDB ids, and lipidmaps are supported)</strong></p></li>
+<li><p><strong>metInfo</strong> – string information of the metabolite (Common name, VMH name, CHEBI id,</p></li>
+<li><p><strong>Swiss Lipid id, HMDB id, Lipidmap, or InChIkey are supported)</strong></p></li>
 </ul>
 </dd>
 <dt class="field-odd">OPTIONAL INPUT</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>outputStyle</strong> – same as the input, choose an output option between</p></li>
-<li><p><strong>‘name’, ‘vmh’, and ‘chebi’ for more accurate respond</strong></p></li>
+<li><p><strong>infoType</strong> – In the cases of searching with common name, VMH, or ChEBI, use ‘name’, ‘vmh’,</p></li>
+<li><p><strong>or ‘chebi’ respectively as the identifier type for more accurate respond</strong></p></li>
 </ul>
 </dd>
 <dt class="field-even">OUTPUT</dt>

latest/modules/design/index.html

@@ -162,6 +162,7 @@ <h1>The COBRA Toolbox</h1>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">Design</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="optForceGAMS/index.html">Optforcegams</a></li>
 <li class="toctree-l3"><a class="reference internal" href="optForce/index.html">Optforce</a></li>
+<li class="toctree-l3"><a class="reference internal" href="optEnvelope/index.html">Optenvelope</a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="../reconstruction/index.html">Reconstruction</a></li>
@@ -226,6 +227,7 @@ <h1>Design<a class="headerlink" href="#id1" title="Permalink to this heading">¶
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="optForceGAMS/index.html">Optforcegams</a></li>
 <li class="toctree-l1"><a class="reference internal" href="optForce/index.html">Optforce</a></li>
+<li class="toctree-l1"><a class="reference internal" href="optEnvelope/index.html">Optenvelope</a></li>
 </ul>
 </div>
          </div>