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stable/modules/analysis/FBA/index.html

@@ -335,7 +335,7 @@ <h1>The COBRA Toolbox</h1>
 </dd>
 <dt class="field-odd">OPTIONAL INPUTS</dt>
 <dd class="field-odd"><ul>
-<li><p><strong>osenseStr</strong> – Maximize (‘max’)/minimize (‘min’) (opt, default = ‘max’)</p></li>
+<li><p><strong>osenseStr</strong> – Maximize (‘max’)/minimize (‘min’) (opt, default = ‘min’)</p></li>
 <li><p><strong>minNorm</strong> – {(0), ‘one’, ‘zero’, &gt; 0 , <cite>n x 1</cite> vector}, where <cite>[m,n]=size(S)</cite>;
 0 - Default, normal LP,
 ‘one’  Minimise the Taxicab Norm using LP.</p>
@@ -450,6 +450,12 @@ <h1>The COBRA Toolbox</h1>
 <li><p>d - <cite>k x 1</cite> Right hand side of C*v &lt;= d</p></li>
 <li><p>ctrs <cite>k x 1</cite> Cell Array of Strings giving IDs of the coupling constraints</p></li>
 <li><p>dsense - <cite>k x 1</cite> character array with entries in {L,E,G}</p></li>
+<li><p><cite>.evars</cite> : evars x 1  Column Cell Array of Strings   IDs of the additional variables</p></li>
+<li><p><cite>.E</cite>     : n x evars  The additional Variable Matrix</p></li>
+<li><p><cite>.evarub</cite>: evars x 1  The upper bounds of the variables from E;</p></li>
+<li><p><cite>.evarlb</cite>: evars x 1  The lower bounds of the variables from E;</p></li>
+<li><p><cite>.evarc</cite> : evars x 1  The objective coefficients of the variables from E;</p></li>
+<li><p><cite>.D</cite>     : k x evars  The matrix coupling additional Constraints (form C), with additional Variables (from E);</p></li>
 <li><p>g0 - <cite>n x 1</cite> weights on zero norm, where positive is minimisation, negative is maximisation, zero is neither.</p></li>
 <li><p>g1 - <cite>n x 1</cite> weights on one norm, where positive is minimisation, negative is maximisation, zero is neither.</p></li>
 <li><p>g2 - <cite>n x 1</cite> weights on two norm</p></li>

stable/modules/analysis/exploration/index.html

@@ -974,13 +974,11 @@ <h1>The COBRA Toolbox</h1>
 reactionNames in the model (same order).</p></li>
 </ul>
 </dd>
-<dt class="field-even">USAGE</dt>
-<dd class="field-even"><ul class="simple">
-<li><p><strong>%Obtain all reactions with Glycolysis in their respective subSystems</strong> – field.</p></li>
-<li><p><strong>[reactionNames,rxnPos]  = findRxnsFromSubSystem</strong> (<em>model,’Glycolysis’</em>)</p></li>
-</ul>
-</dd>
 </dl>
+<p class="rubric">Example</p>
+<p>Obtain all reactions with Glycolysis in their respective subSystems
+field.
+[reactionNames,rxnPos]  = findRxnsFromSubSystem(model,’Glycolysis’)</p>
 </dd></dl>
 
 <dl class="mat function">
@@ -1161,7 +1159,7 @@ <h1>The COBRA Toolbox</h1>
 </dd>
 <dt class="field-even">USAGE</dt>
 <dd class="field-even"><ul class="simple">
-<li><p><strong>%Get all subSystems present in the model.</strong></p></li>
+<li><p><strong>Get all subSystems present in the model.</strong></p></li>
 <li><p><strong>[subSystems]  = getModelSubSystems</strong> (<em>model</em>)</p></li>
 </ul>
 </dd>
@@ -1218,12 +1216,12 @@ <h1>The COBRA Toolbox</h1>
 <dd><p>Determine whether a reaction is in a given subSystem.</p>
 <dl class="field-list simple">
 <dt class="field-odd">USAGE</dt>
-<dd class="field-odd"><p><strong>[subSystems]  = getModelSubSystems</strong> (<em>model</em>)</p>
+<dd class="field-odd"><p><strong>[present]  = isReactionInSubSystem</strong> (<em>model,reactions,subSystem</em>)</p>
 </dd>
 <dt class="field-even">INPUT</dt>
 <dd class="field-even"><ul class="simple">
 <li><p><strong>model</strong> – A COBRA model struct with at least rxns and
-subSystems fields</p></li>
+subSystems or rxn2subSystem(COBRA V4) fields</p></li>
 <li><p><strong>reactions</strong> – Either a string identifying a reaction, or a
 cell array of strings identifying multiple
 reactions, or a double vector identifying the
@@ -1234,12 +1232,6 @@ <h1>The COBRA Toolbox</h1>
 <dt class="field-odd">OUTPUT</dt>
 <dd class="field-odd"><p><strong>present</strong> – a boolean vector for each provided reaction.</p>
 </dd>
-<dt class="field-even">USAGE</dt>
-<dd class="field-even"><ul class="simple">
-<li><p><strong>%Get all subSystems present in the model.</strong></p></li>
-<li><p><strong>[subSystems]  = getModelSubSystems</strong> (<em>model</em>)</p></li>
-</ul>
-</dd>
 </dl>
 </dd></dl>
 

stable/modules/analysis/index.html

@@ -353,6 +353,7 @@ <h1>Analysis<a class="headerlink" href="#id1" title="Permalink to this heading">
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="wholeBody/index.html">Wholebody</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="wholeBody/io/index.html">Io</a></li>
 <li class="toctree-l2"><a class="reference internal" href="wholeBody/PSCMToolbox/index.html">Pscmtoolbox</a></li>
 <li class="toctree-l2"><a class="reference internal" href="wholeBody/Nutrition_Modelling_Toolbox/index.html">Nutrition_modelling_toolbox</a></li>
 </ul>