https://wiki.biouml.org/index.php?action=history&feed=atom&title=Flux_Balance_Constraint_%28analysis%29 2026-04-13T07:59:54Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=Flux_Balance_Constraint_(analysis)&diff=8773&oldid=prev 2020-12-09T11:14:49Z

<p>Automatic synchronization with BioUML</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 11:14, 9 December 2020</td> </tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Analysis title</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Analysis title</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:[[File:<del class="diffchange diffchange-inline">DAE</del>-<del class="diffchange diffchange-inline">models</del>-Flux-Balance-Constraint-icon.png]] Flux Balance Constraint</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:[[File:<ins class="diffchange diffchange-inline">Differential</ins>-<ins class="diffchange diffchange-inline">algebraic-equations</ins>-Flux-Balance-Constraint-icon.png]] Flux Balance Constraint</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Provider</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Provider</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Institute of Systems Biology]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Institute of Systems Biology]]</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 29:</td> <td colspan="2" class="diff-lineno">Line 29:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>FBC syntax example: a simple four reaction pathway. The reactions are ''R1, R2, X1, X2'' with fixed species ''IN, OUT, ATP, NADH'' and variable species ''A, B''.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>FBC syntax example: a simple four reaction pathway. The reactions are ''R1, R2, X1, X2'' with fixed species ''IN, OUT, ATP, NADH'' and variable species ''A, B''.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:: [[File:<del class="diffchange diffchange-inline">DAE</del>-<del class="diffchange diffchange-inline">models</del>-Flux-Balance-Constraint-fbc_1.png]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:: [[File:<ins class="diffchange diffchange-inline">Differential</ins>-<ins class="diffchange diffchange-inline">algebraic-equations</ins>-Flux-Balance-Constraint-fbc_1.png]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Using the reagent identity and stoichiometry it is possible to compactly describe this network in terms of its reaction stoichiometry:</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Using the reagent identity and stoichiometry it is possible to compactly describe this network in terms of its reaction stoichiometry:</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:: [[File:<del class="diffchange diffchange-inline">DAE</del>-<del class="diffchange diffchange-inline">models</del>-Flux-Balance-Constraint-fbc_2.png]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:: [[File:<ins class="diffchange diffchange-inline">Differential</ins>-<ins class="diffchange diffchange-inline">algebraic-equations</ins>-Flux-Balance-Constraint-fbc_2.png]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:: [[File:<del class="diffchange diffchange-inline">DAE</del>-<del class="diffchange diffchange-inline">models</del>-Flux-Balance-Constraint-fbc_3.png]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:: [[File:<ins class="diffchange diffchange-inline">Differential</ins>-<ins class="diffchange diffchange-inline">algebraic-equations</ins>-Flux-Balance-Constraint-fbc_3.png]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>There are capacity constraints in this example:</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>There are capacity constraints in this example:</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:: [[File:<del class="diffchange diffchange-inline">DAE</del>-<del class="diffchange diffchange-inline">models</del>-Flux-Balance-Constraint-fbc_4.png]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:: [[File:<ins class="diffchange diffchange-inline">Differential</ins>-<ins class="diffchange diffchange-inline">algebraic-equations</ins>-Flux-Balance-Constraint-fbc_4.png]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>In this example the flux through reaction ''R2'' will be maximized. Solving this we find that maximization of flux through ''R2'' gives an optimal solution ''R2 = 1'' with one possible solution for ''v''.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>In this example the flux through reaction ''R2'' will be maximized. Solving this we find that maximization of flux through ''R2'' gives an optimal solution ''R2 = 1'' with one possible solution for ''v''.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:: [[File:<del class="diffchange diffchange-inline">DAE</del>-<del class="diffchange diffchange-inline">models</del>-Flux-Balance-Constraint-fbc_5.png]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:: [[File:<ins class="diffchange diffchange-inline">Differential</ins>-<ins class="diffchange diffchange-inline">algebraic-equations</ins>-Flux-Balance-Constraint-fbc_5.png]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div># Jeffrey D. Orth, Ines Thiele and Bernhard O. Palsson, &quot;What is flux balance analysis?&quot;. Nature Biotechnology 28, 245-248 2010.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div># Jeffrey D. Orth, Ines Thiele and Bernhard O. Palsson, &quot;What is flux balance analysis?&quot;. Nature Biotechnology 28, 245-248 2010.</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 49:</td> <td colspan="2" class="diff-lineno">Line 49:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Analyses]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Analyses]]</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Category:<del class="diffchange diffchange-inline">DAE models </del>(analyses group)]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Category:<ins class="diffchange diffchange-inline">Differential algebraic equations </ins>(analyses group)]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:ISB analyses]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:ISB analyses]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Autogenerated pages]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Autogenerated pages]]</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=Flux_Balance_Constraint_(analysis)&diff=6972&oldid=prev 2017-02-13T12:00:27Z

<p>Automatic synchronization with BioUML</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 12:00, 13 February 2017</td> </tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Analysis title</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Analysis title</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:[[File:<del class="diffchange diffchange-inline">Default</del>-<del class="diffchange diffchange-inline">analysis</del>-icon.png]] Flux Balance Constraint</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:[[File:<ins class="diffchange diffchange-inline">DAE</ins>-<ins class="diffchange diffchange-inline">models-Flux-Balance-Constraint</ins>-icon.png]] Flux Balance Constraint</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Provider</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Provider</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Institute of Systems Biology]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Institute of Systems Biology]]</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 8:</td> <td colspan="2" class="diff-lineno">Line 8:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Biouml.plugins.fbc (plugin)|biouml.plugins.fbc (Flux Balance)]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Biouml.plugins.fbc (plugin)|biouml.plugins.fbc (Flux Balance)]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>=== Flux <del class="diffchange diffchange-inline">balance </del>Analysis ===</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>=== Flux <ins class="diffchange diffchange-inline">Balance </ins>Analysis ===</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Flux balance analysis is a mathematical approach for analyzing the flow of metabolites through a metabolic network.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Flux balance analysis is a mathematical approach for analyzing the flow of metabolites through a metabolic network.</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 16:</td> <td colspan="2" class="diff-lineno">Line 16:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Parameters: ====</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Parameters: ====</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* '''Diagram <del class="diffchange diffchange-inline">path</del>''' – Path to input diagram</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* '''Diagram''' – Path to input diagram</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* '''Data <del class="diffchange diffchange-inline">Table Path</del>''' – Path to FBC data <del class="diffchange diffchange-inline">table</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* '''Data <ins class="diffchange diffchange-inline">table</ins>''' – Path to <ins class="diffchange diffchange-inline">the table with initial </ins>FBC data <ins class="diffchange diffchange-inline">(bounds, objective function coefficients)</ins></div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* '''<del class="diffchange diffchange-inline">Result </del>path''' – Path to <del class="diffchange diffchange-inline">resulting element</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* '''<ins class="diffchange diffchange-inline">Output </ins>path''' – Path to <ins class="diffchange diffchange-inline">table with fluxes values</ins></div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* '''<del class="diffchange diffchange-inline">Type Objective Function</del>''' (expert) – Type <del class="diffchange diffchange-inline">Objective Function</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* '''<ins class="diffchange diffchange-inline">Optimization type</ins>''' (expert) – Type <ins class="diffchange diffchange-inline">of objective function optimization which will be used (maximize or minimize)</ins></div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* '''Solver type''' (expert) – <del class="diffchange diffchange-inline">Solver type</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* '''Solver type''' (expert) – <ins class="diffchange diffchange-inline">Type of the solver which will be used to find fluxes</ins></div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">*</del>* '''Max iter''' – <del class="diffchange diffchange-inline">Iterations limit</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* '''Max iter''' <ins class="diffchange diffchange-inline">(expert) </ins>– <ins class="diffchange diffchange-inline">Maximal iteration number</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160;</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">One should use '''Building Flux Balance DataTable''' or '''Score based FBC table builder''' analyses to generate FBC data table.</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Example ====</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Example ====</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=Flux_Balance_Constraint_(analysis)&diff=6442&oldid=prev 2015-08-25T05:20:15Z

<p>Automatic synchronization with BioUML</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 05:20, 25 August 2015</td> </tr><tr><td colspan="2" class="diff-lineno">Line 21:</td> <td colspan="2" class="diff-lineno">Line 21:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Type Objective Function''' (expert) – Type Objective Function</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Type Objective Function''' (expert) – Type Objective Function</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Solver type''' (expert) – Solver type</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Solver type''' (expert) – Solver type</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">** '''Max iter''' – Iterations limit</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Example ====</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Example ====</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 42:</td> <td colspan="2" class="diff-lineno">Line 43:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:: [[File:DAE-models-Flux-Balance-Constraint-fbc_5.png]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:: [[File:DAE-models-Flux-Balance-Constraint-fbc_5.png]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div># Jeffrey D. Orth, Ines Thiele and Bernhard O. Palsson, &quot;What is flux balance analysis?&quot;. Nature Biotechnology 28, <del class="diffchange diffchange-inline">245�248 </del>2010.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># Jeffrey D. Orth, Ines Thiele and Bernhard O. Palsson, &quot;What is flux balance analysis?&quot;. Nature Biotechnology 28, <ins class="diffchange diffchange-inline">245-248 </ins>2010.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div># [http://identifiers.org/combine.specifications/sbml.level-3.version-1.fbc.version-1.release-1 SBML Level 3 Package Specification]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div># [http://identifiers.org/combine.specifications/sbml.level-3.version-1.fbc.version-1.release-1 SBML Level 3 Package Specification]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=Flux_Balance_Constraint_(analysis)&diff=5816&oldid=prev 2014-12-11T09:17:38Z

<p>Automatic synchronization with BioUML</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 09:17, 11 December 2014</td> </tr><tr><td colspan="2" class="diff-lineno">Line 19:</td> <td colspan="2" class="diff-lineno">Line 19:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Data Table Path''' – Path to FBC data table</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Data Table Path''' – Path to FBC data table</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Result path''' – Path to resulting element</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Result path''' – Path to resulting element</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* '''Type Objective Function''' (expert) – <del class="diffchange diffchange-inline">TypeObjectiveFunction</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* '''Type Objective Function''' (expert) – <ins class="diffchange diffchange-inline">Type Objective Function</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* '''Solver type''' (expert) – Solver type</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Example ====</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Example ====</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=Flux_Balance_Constraint_(analysis)&diff=5334&oldid=prev 2013-11-18T07:59:50Z

<p>Automatic synchronization with BioUML</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 07:59, 18 November 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 41:</td> <td colspan="2" class="diff-lineno">Line 41:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:: [[File:DAE-models-Flux-Balance-Constraint-fbc_5.png]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:: [[File:DAE-models-Flux-Balance-Constraint-fbc_5.png]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div># Jeffrey D. Orth, Ines Thiele and Bernhard O. Palsson, &quot;What is flux balance analysis?&quot;. Nature Biotechnology 28, <del class="diffchange diffchange-inline">245–248 </del>2010.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># Jeffrey D. Orth, Ines Thiele and Bernhard O. Palsson, &quot;What is flux balance analysis?&quot;. Nature Biotechnology 28, <ins class="diffchange diffchange-inline">245�248 </ins>2010.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div># [http://identifiers.org/combine.specifications/sbml.level-3.version-1.fbc.version-1.release-1 SBML Level 3 Package Specification]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div># [http://identifiers.org/combine.specifications/sbml.level-3.version-1.fbc.version-1.release-1 SBML Level 3 Package Specification]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=Flux_Balance_Constraint_(analysis)&diff=4497&oldid=prev 2013-06-14T11:07:31Z

<p>Default analysis icon as separate file</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 11:07, 14 June 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Analysis title</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Analysis title</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:[[File:<del class="diffchange diffchange-inline">DAE</del>-<del class="diffchange diffchange-inline">models-Flux-Balance-Constraint</del>-icon.png]] Flux Balance Constraint</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:[[File:<ins class="diffchange diffchange-inline">Default</ins>-<ins class="diffchange diffchange-inline">analysis</ins>-icon.png]] Flux Balance Constraint</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Provider</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Provider</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Institute of Systems Biology]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Institute of Systems Biology]]</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=Flux_Balance_Constraint_(analysis)&diff=3957&oldid=prev 2013-05-31T04:14:21Z

<p>Class name added</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 04:14, 31 May 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 3:</td> <td colspan="2" class="diff-lineno">Line 3:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Provider</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Provider</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Institute of Systems Biology]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Institute of Systems Biology]]</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">;Class</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">:{{Class|biouml.plugins.fbc.analysis.FbcAnalysis}}</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Plugin</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Plugin</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Biouml.plugins.fbc (plugin)|biouml.plugins.fbc (Flux Balance)]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Biouml.plugins.fbc (plugin)|biouml.plugins.fbc (Flux Balance)]]</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=Flux_Balance_Constraint_(analysis)&diff=3441&oldid=prev 2013-05-16T05:40:39Z

<p>Mistaken file names update reverted</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 05:40, 16 May 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Analysis title</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Analysis title</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:[[File:Flux-Balance-Constraint<del class="diffchange diffchange-inline">-analysis</del>-icon.png]] Flux Balance Constraint</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:[[File:<ins class="diffchange diffchange-inline">DAE-models-</ins>Flux-Balance-Constraint-icon.png]] Flux Balance Constraint</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Provider</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Provider</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Institute of Systems Biology]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Institute of Systems Biology]]</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=Flux_Balance_Constraint_(analysis)&diff=3356&oldid=prev 2013-05-16T05:36:42Z

<p>Automatic synchronization with BioUML</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 05:36, 16 May 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 23:</td> <td colspan="2" class="diff-lineno">Line 23:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>FBC syntax example: a simple four reaction pathway. The reactions are ''R1, R2, X1, X2'' with fixed species ''IN, OUT, ATP, NADH'' and variable species ''A, B''.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>FBC syntax example: a simple four reaction pathway. 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Solving this we find that maximization of flux through ''R2'' gives an optimal solution ''R2 = 1'' with one possible solution for ''v''.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>In this example the flux through reaction ''R2'' will be maximized. Solving this we find that maximization of flux through ''R2'' gives an optimal solution ''R2 = 1'' with one possible solution for ''v''.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:: [[File:Flux-Balance-Constraint<del class="diffchange diffchange-inline">-analysis</del>-fbc_5.png]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:: [[File:<ins class="diffchange diffchange-inline">DAE-models-</ins>Flux-Balance-Constraint-fbc_5.png]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div># Jeffrey D. Orth, Ines Thiele and Bernhard O. Palsson, &quot;What is flux balance analysis?&quot;. Nature Biotechnology 28, 245–248 2010.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div># Jeffrey D. Orth, Ines Thiele and Bernhard O. Palsson, &quot;What is flux balance analysis?&quot;. Nature Biotechnology 28, 245–248 2010.</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=Flux_Balance_Constraint_(analysis)&diff=3331&oldid=prev 2013-05-16T05:32:41Z

<p>Automatic synchronization with BioUML</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 05:32, 16 May 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Analysis title</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Analysis title</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:[[File:<del class="diffchange diffchange-inline">DAE-models-</del>Flux-Balance-Constraint-icon.png]] Flux Balance Constraint</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:[[File:Flux-Balance-Constraint<ins class="diffchange diffchange-inline">-analysis</ins>-icon.png]] Flux Balance Constraint</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Provider</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Provider</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Institute of Systems Biology]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Institute of Systems Biology]]</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 23:</td> <td colspan="2" class="diff-lineno">Line 23:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>FBC syntax example: a simple four reaction pathway. The reactions are ''R1, R2, X1, X2'' with fixed species ''IN, OUT, ATP, NADH'' and variable species ''A, B''.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>FBC syntax example: a simple four reaction pathway. The reactions are ''R1, R2, X1, X2'' with fixed species ''IN, OUT, ATP, NADH'' and variable species ''A, B''.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:: [[File:<del class="diffchange diffchange-inline">DAE-models-</del>Flux-Balance-Constraint-fbc_1.png]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:: [[File:Flux-Balance-Constraint<ins class="diffchange diffchange-inline">-analysis</ins>-fbc_1.png]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Using the reagent identity and stoichiometry it is possible to compactly describe this network in terms of its reaction stoichiometry:</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Using the reagent identity and stoichiometry it is possible to compactly describe this network in terms of its reaction stoichiometry:</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:: [[File:<del class="diffchange diffchange-inline">DAE-models-</del>Flux-Balance-Constraint-fbc_2.png]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:: [[File:Flux-Balance-Constraint<ins class="diffchange diffchange-inline">-analysis</ins>-fbc_2.png]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:: [[File:<del class="diffchange diffchange-inline">DAE-models-</del>Flux-Balance-Constraint-fbc_3.png]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:: [[File:Flux-Balance-Constraint<ins class="diffchange diffchange-inline">-analysis</ins>-fbc_3.png]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>There are capacity constraints in this example:</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>There are capacity constraints in this example:</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:: [[File:<del class="diffchange diffchange-inline">DAE-models-</del>Flux-Balance-Constraint-fbc_4.png]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:: [[File:Flux-Balance-Constraint<ins class="diffchange diffchange-inline">-analysis</ins>-fbc_4.png]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>In this example the flux through reaction ''R2'' will be maximized. Solving this we find that maximization of flux through ''R2'' gives an optimal solution ''R2 = 1'' with one possible solution for ''v''.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>In this example the flux through reaction ''R2'' will be maximized. Solving this we find that maximization of flux through ''R2'' gives an optimal solution ''R2 = 1'' with one possible solution for ''v''.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:: [[File:<del class="diffchange diffchange-inline">DAE-models-</del>Flux-Balance-Constraint-fbc_5.png]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:: [[File:Flux-Balance-Constraint<ins class="diffchange diffchange-inline">-analysis</ins>-fbc_5.png]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div># Jeffrey D. Orth, Ines Thiele and Bernhard O. Palsson, &quot;What is flux balance analysis?&quot;. Nature Biotechnology 28, 245–248 2010.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div># Jeffrey D. Orth, Ines Thiele and Bernhard O. Palsson, &quot;What is flux balance analysis?&quot;. Nature Biotechnology 28, 245–248 2010.</div></td></tr> </table>

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