http://www.optflux.org/wiki/api.php?action=feedcontributions&user=Admin&feedformat=atomOptflux - User contributions [en]2024-03-28T23:33:13ZUser contributionsMediaWiki 1.28.0http://www.optflux.org/wiki/index.php?title=CaseStudy&diff=2148CaseStudy2018-07-09T10:36:06Z<p>Admin: /* Case study files */</p>
<hr />
<div>== Case study files ==<br />
<br />
**[http://www.optflux.org/wiki/tutorial/gomGG.xml gomGG.xml gomGG Files]<br />
**[[Media:EcoliFlatFiles.zip| Reed's E.Coli files used on the OptFlux paper]]<br />
**[[Media:SimpEcoli.zip|Simplified Reed's E.Coli Model]]<br />
<br />
<!--<br />
== Older Version (for OptFlux 1.x) ==<br />
<br />
* This tutorial its based on '''OptFlux 1.35'''<br />
<br />
2003 Reed's E. coli files<br />
<br />
[[Media:ecoli.zip | Ecoli.zip]]<br />
<br />
Pyruvate Metabolism (CellDesigner format - for visualization only)<br />
<br />
[[Media:Pyruvate_metabolism.xml | Pyruvate Metabolism for visualization]]<br />
--></div>Adminhttp://www.optflux.org/wiki/index.php?title=BeginnersTutorial&diff=2147BeginnersTutorial2018-07-09T10:35:13Z<p>Admin: /* Older Versions */</p>
<hr />
<div>== New OptFlux 3 Tutorial ==<br />
<br />
*This tutorial it is based on '''OptFlux 3'''<br />
** [http://www.optflux.org/wiki/tutorial/TutorialOptFlux3.pdf OptFlux 3 Tutorial]<br />
** The files necessary to correctly follow the tutorial: [http://www.optflux.org/wiki/tutorial/gomGG.xml gomGG.xml] and [http://www.optflux.org/wiki/tutorial/ecoli_core_model.xml ecoli_core_model.xml]<br />
<br />
== Older Versions ==<br />
<br />
* This tutorial it is based on '''OptFlux 2'''<br />
** [http://www.optflux.org/wiki/tutorial/old/Tutorial_OptFlux2.pdf OptFlux 2 Tutorial]<br />
** The files necessary to correctly follow the tutorial: [http://www.optflux.org/wiki/tutorial/gomGG.xml gomGG.xml]<br />
<br />
* This is version 1.2 and it is based on '''OptFlux v1.35'''<br />
** [http://www.optflux.org/wiki/tutorial/old/TutorialOptFlux_v1.2.pdf Tutorial_v1.2.pdf]<br />
** The files necessary to correctly follow the tutorial: [http://www.optflux.org/wiki/tutorial/old/smallSC.zip smallSC.zip]</div>Adminhttp://www.optflux.org/wiki/index.php?title=BeginnersTutorial&diff=2142BeginnersTutorial2018-07-09T10:34:22Z<p>Admin: /* Older Versions */</p>
<hr />
<div>== New OptFlux 3 Tutorial ==<br />
<br />
*This tutorial it is based on '''OptFlux 3'''<br />
** [http://www.optflux.org/wiki/tutorial/TutorialOptFlux3.pdf OptFlux 3 Tutorial]<br />
** The files necessary to correctly follow the tutorial: [http://www.optflux.org/wiki/tutorial/gomGG.xml gomGG.xml] and [http://www.optflux.org/wiki/tutorial/ecoli_core_model.xml ecoli_core_model.xml]<br />
<br />
== Older Versions ==<br />
<br />
* This tutorial it is based on '''OptFlux 2'''<br />
** [http://www.optflux.org/wiki/tutorial/old/Tutorial_OptFlux2.pdf OptFlux 2 Tutorial]<br />
** The files necessary to correctly follow the tutorial: [http://www.optflux.org/wiki/tutorial/old/gomGG.zip gomGG.zip]<br />
<br />
* This is version 1.2 and it is based on '''OptFlux v1.35'''<br />
** [http://www.optflux.org/wiki/tutorial/old/TutorialOptFlux_v1.2.pdf Tutorial_v1.2.pdf]<br />
** The files necessary to correctly follow the tutorial: [http://www.optflux.org/wiki/tutorial/old/smallSC.zip smallSC.zip]</div>Adminhttp://www.optflux.org/wiki/index.php?title=BeginnersTutorial&diff=2138BeginnersTutorial2018-07-09T10:32:34Z<p>Admin: /* New OptFlux 3 Tutorial */</p>
<hr />
<div>== New OptFlux 3 Tutorial ==<br />
<br />
*This tutorial it is based on '''OptFlux 3'''<br />
** [http://www.optflux.org/wiki/tutorial/TutorialOptFlux3.pdf OptFlux 3 Tutorial]<br />
** The files necessary to correctly follow the tutorial: [http://www.optflux.org/wiki/tutorial/gomGG.xml gomGG.xml] and [http://www.optflux.org/wiki/tutorial/ecoli_core_model.xml ecoli_core_model.xml]<br />
<br />
== Older Versions ==<br />
<br />
* This tutorial it is based on '''OptFlux 2'''<br />
** [http://darwin.di.uminho.pt/optflux/downloads/documentation/Tutorial_OptFlux2.pdf OptFlux 2 Tutorial]<br />
** The files necessary to correctly follow the tutorial: [http://darwin.di.uminho.pt/optflux/tutorial/gomGG.zip gomGG.zip]<br />
<br />
* This is version 1.2 and it is based on '''OptFlux v1.35'''<br />
** [http://darwin.di.uminho.pt/optflux/downloads/documentation/TutorialOptFlux_v1.2.pdf Tutorial_v1.2.pdf]<br />
** The files necessary to correctly follow the tutorial: [http://darwin.di.uminho.pt/optflux/downloads/documentation/smallSC.zip smallSC.zip]</div>Adminhttp://www.optflux.org/wiki/index.php?title=BeginnersTutorial&diff=2136BeginnersTutorial2018-07-09T10:32:09Z<p>Admin: /* New OptFlux 3 Tutorial */</p>
<hr />
<div>== New OptFlux 3 Tutorial ==<br />
<br />
*This tutorial it is based on '''OptFlux 3'''<br />
** [http://www.optflux.org/wiki/tutorial/TutorialOptFlux3.pdf OptFlux 3 Tutorial]<br />
** The files necessary to correctly follow the tutorial: [http://www.optflux.org/tutorial/gomGG.xml gomGG.xml] and [http://www.optflux.org/tutorial/ecoli_core_model.xml ecoli_core_model.xml]<br />
<br />
== Older Versions ==<br />
<br />
* This tutorial it is based on '''OptFlux 2'''<br />
** [http://darwin.di.uminho.pt/optflux/downloads/documentation/Tutorial_OptFlux2.pdf OptFlux 2 Tutorial]<br />
** The files necessary to correctly follow the tutorial: [http://darwin.di.uminho.pt/optflux/tutorial/gomGG.zip gomGG.zip]<br />
<br />
* This is version 1.2 and it is based on '''OptFlux v1.35'''<br />
** [http://darwin.di.uminho.pt/optflux/downloads/documentation/TutorialOptFlux_v1.2.pdf Tutorial_v1.2.pdf]<br />
** The files necessary to correctly follow the tutorial: [http://darwin.di.uminho.pt/optflux/downloads/documentation/smallSC.zip smallSC.zip]</div>Adminhttp://www.optflux.org/wiki/index.php?title=Cplex_Configuration:Preferences&diff=2094Cplex Configuration:Preferences2016-12-21T10:22:55Z<p>Admin: </p>
<hr />
<div>{{DISPLAYTITLE: CPLEX Configuration}}<br />
OptFlux allows the user to use CPLEX in the simulations.<br><br />
Follow this [https://vimeo.com/124835561 link] to watch a video with the tutorial.</div>Adminhttp://www.optflux.org/wiki/index.php?title=Cplex_Configuration:Preferences&diff=2093Cplex Configuration:Preferences2016-12-21T10:21:53Z<p>Admin: Created page with "{{DISPLAYTITLE: CPLEX Configuration}} OptFlux allows the user to use CPLEX in the simulations.<br> Follow this [https://vimeo.com/124835561 link] to watch a video with the tut..."</p>
<hr />
<div>{{DISPLAYTITLE: CPLEX Configuration}}<br />
OptFlux allows the user to use CPLEX in the simulations.<br><br />
Follow this [https://vimeo.com/124835561 link] to watch a video with the tutorial</div>Adminhttp://www.optflux.org/wiki/index.php?title=HowTos:OptFlux3&diff=2092HowTos:OptFlux32016-12-21T10:16:38Z<p>Admin: /* Help */</p>
<hr />
<div>{{DISPLAYTITLE:How Tos for Optflux 3}}<br />
<br />
== Project And Model Handling==<br />
*[[OptFlux3:CORE:NewProject|New project]]<br />
**[[CORE:Readers:Drains | Drains Definition]]<br />
**[[OptFlux Readers]]<br />
***[[SBML Reader]]<br />
***[[Flat Files Reader]]<br />
***[[Metatool]]<br />
***[[OptFlux3:MR | OptFlux Repository]]<br />
***[[Table format Reader]]<br />
***[[Cell Designer Reader]]<br />
*[[OptFlux3:CORE:ImportProject | Import Project]]<br />
*[[OptFlux3:SMP |Model Simplification]]<br />
<br />
=== Model Handling ===<br />
<br />
*[[Create Environmental conditions]]<br />
<br />
== Simulation ==<br />
*[[OptFlux3:SIM:WildType | Wild Type]]<br />
*[[OptFlux3:SIM:Knockouts | Knockouts]]<br />
*[[OptFlux3:SIM:UnderOverExpression | Under-Over Expression]]<br />
<br />
== Analysis ==<br />
*[[OptFlux3:OPT:Critical | Critical Genes/Reactions]]<br />
*[[OptFlux3:BC:balancechecker | Balance Checker]]<br />
*Flux Variability Analysis<br />
**[[OptFlux3:SIM:ZeroFluxFVA | Zero-flux values]]<br />
**[[OptFlux3:SIM:VarPlot | Flux-variation plot]]<br />
**[[OptFlux3:SIM:FluxLim | Flux limits]]<br />
*Structural Analysis<br />
**[[OptFlux3:SIM:ZeroFluxStruc | Zero-flux values]]<br />
**[[OptFlux3:SIM:EquivalentFluxes | Equivalent-flux values]]<br />
<br />
== Optimization ==<br />
*[[OptFlux3:Evolutionary | Evolutionary]]<br />
*[[OptFlux3:OPK | Optknock]]<br />
<br />
== Help ==<br />
*Repository Manager<br />
**[[KnownProblems:RepositoryManager | Known Problems]]<br />
*Updates<br />
*Preferences<br />
**[[Cplex Configuration:Preferences | Cplex Configuration]]<br />
<br />
== Plugins ==<br />
*[[OptFlux3:CORE|Core]]<br />
*[[OptFlux3:MR | Model Repository]]<br />
*[[OptFlux3:SIM | Simulation]]<br />
*[[OptFlux3:Evolutionary | Optimization]]<br />
*[[OptFlux3:SMP | Simplification]]<br />
*[[OptFlux3:BC:balancechecker:hgfhgf | Mass Balance Validator]]<br />
*[[OptFlux3:OPK | OptKnock]]<br />
*[[OptFlux3:TNA | Network Topology Analysis (TNA)]]<br />
*[[OptFlux3:EFM | Elementary Flux Modes]]<br />
*[[OptFlux3:RT | Reg4OptFlux - Regulatory plugin]]<br />
*[[OptFlux3:METAVIZ | Metabolic Network Visualization Plugin]]<br />
*[[OptFlux3:MFA | Metabolic Flux Analysis]]<br />
*[[OptFlux3:COBRA | Cobra4OptFlux - Cobra plugin]]<br />
*[[OptFlux3:Serialization | Serialization plugin]]</div>Adminhttp://www.optflux.org/wiki/index.php?title=OptFlux3:Serialization&diff=2091OptFlux3:Serialization2016-06-03T10:23:54Z<p>Admin: /* 3.2.10 */</p>
<hr />
<div>{{DISPLAYTITLE: Serialization Plugin}}<br />
__TOC__<br />
=Purpose=<br />
Since the release of OptFlux 3.3.0 the workspace of previous version became deprecated and are not loaded by this or recent versions.<br><br />
The '''Serialization Plugin''' was developed for the OptFlux 3.2 version to garantee the backward compatible of pre-3.3.0 workspaces with newer OptFlux versions.<br><br />
This plugin can convert most of the workspace items that OptFlux v3.2 can generate. (Check [[OptFlux3:Serialization:NonBackwardCompatible|not backward compatible items]])<br />
*Backup the workspace before performing the conversion.<br />
<br />
=Installation=<br />
<br />
Before installing the 3.3.0 version, there are two ways to have the Serialization4OptFlux plugin. <br />
<br />
===3.2.10===<br />
Install the 3.2.10 version if you don't want to perform updates on your current version of OptFlux.<br />
<br>In this version all the plugins, along with the Serialization4OptFlux, will already be installed.<br />
* Download link [https://sourceforge.net/projects/optflux/files/History/3.2.10/Installers/ here].<br />
<br />
===3.2.7===<br />
<br />
Install the 3.2.7 version of OptFlux and perform all updates, the Serialization4OptFlux plugin can be installed through the repository manager operation.<br />
*You can access the '''Repository''' option under the '''Help -> Repository Manager''' menu.<br><br />
*See also [[KnownProblems:RepositoryManager|Problem with Repository Manager in 3.2 versions]]<br />
<br />
[[Image:PluginManager2.jpg|800px]]<br />
<br />
<br />
After the restart check if the plugin is installed by opening the '''Repository Manager'''.<br><br />
<br />
*'''Special Case:''' Sometimes some plugins may be disabled which results in a disabled '''Serialization Plugin'''. If that happens make sure all plugins are enabled.<br />
<br />
[[Image:PluginManager4.png|800px]]<br />
<br />
<br />
If all the plugins are installed and enabled the '''Serialization Plugin''' will also be enabled and the '''Repository Manager''' will be present like the following image<br />
<br />
[[Image:PluginManager5.jpg|800px]]<br />
<br />
=How to Use=<br />
<br />
==Convert Workspace==<br />
Clipboard must have at least one project to enable operation.<br><br />
*Projects can be either open or closed.<br />
[[Image:Serialization1.jpg|800px]]<br />
<br />
Select '''File -> Workspace -> Convert Workspace...'''<br />
<br />
<br>The '''Convert Workspace''' window will be present.<br><br />
Select a folder that will be the workspace folder for the '''OptFlux v3.3 or newer'''.<br />
*Folder must be empty.<br />
[[Image:Serialization2.jpg|800px]]<br />
<br />
<br>If everything went as expected the converter will present a successful message similar to the following image.<br />
<br />
[[Image:Serialization3.jpg|550px]]<br />
<br />
==Special cases==<br />
Since there are some items that are [[OptFlux3:Serialization:NonBackwardCompatible|not backward compatible]] the converter will not present the previous successfull message.<br><br />
For that cases a message similar to the following image is present.<br><br />
*In this particular case the TNA items were not successfull converted.<br />
[[Image:SerializationExtra.jpg|800px]]<br />
<br />
==Workspace after conversion==<br />
After a successfull conversion the new workspace will only be loaded by OptFlux v3.3 or newer and it will be similar to the original workspace.<br />
*The following image represents the converted workspace loaded by the '''OptFlux 3.3.0''' version.<br />
[[Image:SerializationFinal.jpg|800px]]</div>Adminhttp://www.optflux.org/wiki/index.php?title=OptFlux3:Serialization&diff=2090OptFlux3:Serialization2016-06-02T14:26:49Z<p>Admin: /* Installation */</p>
<hr />
<div>{{DISPLAYTITLE: Serialization Plugin}}<br />
__TOC__<br />
=Purpose=<br />
Since the release of OptFlux 3.3.0 the workspace of previous version became deprecated and are not loaded by this or recent versions.<br><br />
The '''Serialization Plugin''' was developed for the OptFlux 3.2 version to garantee the backward compatible of pre-3.3.0 workspaces with newer OptFlux versions.<br><br />
This plugin can convert most of the workspace items that OptFlux v3.2 can generate. (Check [[OptFlux3:Serialization:NonBackwardCompatible|not backward compatible items]])<br />
*Backup the workspace before performing the conversion.<br />
<br />
=Installation=<br />
<br />
Before installing the 3.3.0 version, there are two ways to have the Serialization4OptFlux plugin. <br />
<br />
===3.2.10===<br />
Install the 3.2.10 version if you don't want to perform updates on your current version of OptFlux.<br />
<br>In this version all the plugins, along with the Serialization4OptFlux, will already be installed.<br />
* Download link [https://sourceforge.net/projects/optflux/files/History/3.2.10/Installers/ here]. At the moment there is no MacOS version.<br />
<br />
===3.2.7===<br />
<br />
Install the 3.2.7 version of OptFlux and perform all updates, the Serialization4OptFlux plugin can be installed through the repository manager operation.<br />
*You can access the '''Repository''' option under the '''Help -> Repository Manager''' menu.<br><br />
*See also [[KnownProblems:RepositoryManager|Problem with Repository Manager in 3.2 versions]]<br />
<br />
[[Image:PluginManager2.jpg|800px]]<br />
<br />
<br />
After the restart check if the plugin is installed by opening the '''Repository Manager'''.<br><br />
<br />
*'''Special Case:''' Sometimes some plugins may be disabled which results in a disabled '''Serialization Plugin'''. If that happens make sure all plugins are enabled.<br />
<br />
[[Image:PluginManager4.png|800px]]<br />
<br />
<br />
If all the plugins are installed and enabled the '''Serialization Plugin''' will also be enabled and the '''Repository Manager''' will be present like the following image<br />
<br />
[[Image:PluginManager5.jpg|800px]]<br />
<br />
=How to Use=<br />
<br />
==Convert Workspace==<br />
Clipboard must have at least one project to enable operation.<br><br />
*Projects can be either open or closed.<br />
[[Image:Serialization1.jpg|800px]]<br />
<br />
Select '''File -> Workspace -> Convert Workspace...'''<br />
<br />
<br>The '''Convert Workspace''' window will be present.<br><br />
Select a folder that will be the workspace folder for the '''OptFlux v3.3 or newer'''.<br />
*Folder must be empty.<br />
[[Image:Serialization2.jpg|800px]]<br />
<br />
<br>If everything went as expected the converter will present a successful message similar to the following image.<br />
<br />
[[Image:Serialization3.jpg|550px]]<br />
<br />
==Special cases==<br />
Since there are some items that are [[OptFlux3:Serialization:NonBackwardCompatible|not backward compatible]] the converter will not present the previous successfull message.<br><br />
For that cases a message similar to the following image is present.<br><br />
*In this particular case the TNA items were not successfull converted.<br />
[[Image:SerializationExtra.jpg|800px]]<br />
<br />
==Workspace after conversion==<br />
After a successfull conversion the new workspace will only be loaded by OptFlux v3.3 or newer and it will be similar to the original workspace.<br />
*The following image represents the converted workspace loaded by the '''OptFlux 3.3.0''' version.<br />
[[Image:SerializationFinal.jpg|800px]]</div>Adminhttp://www.optflux.org/wiki/index.php?title=OptFlux3:Serialization&diff=2089OptFlux3:Serialization2016-06-01T14:21:44Z<p>Admin: /* Installation */</p>
<hr />
<div>{{DISPLAYTITLE: Serialization Plugin}}<br />
__TOC__<br />
=Purpose=<br />
Since the release of OptFlux 3.3.0 the workspace of previous version became deprecated and are not loaded by this or recent versions.<br><br />
The '''Serialization Plugin''' was developed for the OptFlux 3.2 version to garantee the backward compatible of pre-3.3.0 workspaces with newer OptFlux versions.<br><br />
This plugin can convert most of the workspace items that OptFlux v3.2 can generate. (Check [[OptFlux3:Serialization:NonBackwardCompatible|not backward compatible items]])<br />
*Backup the workspace before performing the conversion.<br />
<br />
=Installation=<br />
<br />
Before installing the 3.3.0 version, install the 3.2.7 version of OptFlux and perform all updates, the Serialization4OptFlux plugin can be installed through the repository manager operation.<br />
*You can access the '''Repository''' option under the '''Help -> Repository Manager''' menu.<br><br />
*See also [[KnownProblems:RepositoryManager|Problem with Repository Manager in 3.2 versions]]<br />
<br />
[[Image:PluginManager2.jpg|800px]]<br />
<br />
<br />
After the restart check if the plugin is installed by opening the '''Repository Manager'''.<br><br />
<br />
*'''Special Case:''' Sometimes some plugins may be disabled which results in a disabled '''Serialization Plugin'''. If that happens make sure all plugins are enabled.<br />
<br />
[[Image:PluginManager4.png|800px]]<br />
<br />
<br />
If all the plugins are installed and enabled the '''Serialization Plugin''' will also be enabled and the '''Repository Manager''' will be present like the following image<br />
<br />
[[Image:PluginManager5.jpg|800px]]<br />
<br />
=How to Use=<br />
<br />
==Convert Workspace==<br />
Clipboard must have at least one project to enable operation.<br><br />
*Projects can be either open or closed.<br />
[[Image:Serialization1.jpg|800px]]<br />
<br />
Select '''File -> Workspace -> Convert Workspace...'''<br />
<br />
<br>The '''Convert Workspace''' window will be present.<br><br />
Select a folder that will be the workspace folder for the '''OptFlux v3.3 or newer'''.<br />
*Folder must be empty.<br />
[[Image:Serialization2.jpg|800px]]<br />
<br />
<br>If everything went as expected the converter will present a successful message similar to the following image.<br />
<br />
[[Image:Serialization3.jpg|550px]]<br />
<br />
==Special cases==<br />
Since there are some items that are [[OptFlux3:Serialization:NonBackwardCompatible|not backward compatible]] the converter will not present the previous successfull message.<br><br />
For that cases a message similar to the following image is present.<br><br />
*In this particular case the TNA items were not successfull converted.<br />
[[Image:SerializationExtra.jpg|800px]]<br />
<br />
==Workspace after conversion==<br />
After a successfull conversion the new workspace will only be loaded by OptFlux v3.3 or newer and it will be similar to the original workspace.<br />
*The following image represents the converted workspace loaded by the '''OptFlux 3.3.0''' version.<br />
[[Image:SerializationFinal.jpg|800px]]</div>Adminhttp://www.optflux.org/wiki/index.php?title=File:PluginManager5.jpg&diff=2088File:PluginManager5.jpg2016-06-01T14:16:23Z<p>Admin: </p>
<hr />
<div></div>Adminhttp://www.optflux.org/wiki/index.php?title=OptFlux3:Serialization&diff=2087OptFlux3:Serialization2016-06-01T13:24:34Z<p>Admin: /* Installation */</p>
<hr />
<div>{{DISPLAYTITLE: Serialization Plugin}}<br />
__TOC__<br />
=Purpose=<br />
Since the release of OptFlux 3.3.0 the workspace of previous version became deprecated and are not loaded by this or recent versions.<br><br />
The '''Serialization Plugin''' was developed for the OptFlux 3.2 version to garantee the backward compatible of pre-3.3.0 workspaces with newer OptFlux versions.<br><br />
This plugin can convert most of the workspace items that OptFlux v3.2 can generate. (Check [[OptFlux3:Serialization:NonBackwardCompatible|not backward compatible items]])<br />
*Backup the workspace before performing the conversion.<br />
<br />
=Installation=<br />
<br />
Before installing the 3.3.0 version, install the 3.2.7 version of OptFlux and perform all updates, the Serialization4OptFlux plugin can be installed through the repository manager operation.<br />
*You can access the '''Repository''' option under the '''Help -> Repository Manager''' menu.<br><br />
*See also [[KnownProblems:RepositoryManager|Problem with Repository Manager in 3.2 versions]]<br />
<br />
[[Image:PluginManager2.jpg|800px]]<br />
<br />
<br />
After the restart check if the plugin is installed by opening the '''Repository Manager'''.<br><br />
<br />
*'''Special Case:''' Sometimes some plugins may be disabled which results in a disabled '''Serialization Plugin'''. If that happens make sure all plugins are enabled.<br />
<br />
[[Image:PluginManager4.png|800px]]<br />
<br />
=How to Use=<br />
<br />
==Convert Workspace==<br />
Clipboard must have at least one project to enable operation.<br><br />
*Projects can be either open or closed.<br />
[[Image:Serialization1.jpg|800px]]<br />
<br />
Select '''File -> Workspace -> Convert Workspace...'''<br />
<br />
<br>The '''Convert Workspace''' window will be present.<br><br />
Select a folder that will be the workspace folder for the '''OptFlux v3.3 or newer'''.<br />
*Folder must be empty.<br />
[[Image:Serialization2.jpg|800px]]<br />
<br />
<br>If everything went as expected the converter will present a successful message similar to the following image.<br />
<br />
[[Image:Serialization3.jpg|550px]]<br />
<br />
==Special cases==<br />
Since there are some items that are [[OptFlux3:Serialization:NonBackwardCompatible|not backward compatible]] the converter will not present the previous successfull message.<br><br />
For that cases a message similar to the following image is present.<br><br />
*In this particular case the TNA items were not successfull converted.<br />
[[Image:SerializationExtra.jpg|800px]]<br />
<br />
==Workspace after conversion==<br />
After a successfull conversion the new workspace will only be loaded by OptFlux v3.3 or newer and it will be similar to the original workspace.<br />
*The following image represents the converted workspace loaded by the '''OptFlux 3.3.0''' version.<br />
[[Image:SerializationFinal.jpg|800px]]</div>Adminhttp://www.optflux.org/wiki/index.php?title=OptFlux3:Serialization&diff=2086OptFlux3:Serialization2016-06-01T09:00:16Z<p>Admin: /* Installation */</p>
<hr />
<div>{{DISPLAYTITLE: Serialization Plugin}}<br />
__TOC__<br />
=Purpose=<br />
Since the release of OptFlux 3.3.0 the workspace of previous version became deprecated and are not loaded by this or recent versions.<br><br />
The '''Serialization Plugin''' was developed for the OptFlux 3.2 version to garantee the backward compatible of pre-3.3.0 workspaces with newer OptFlux versions.<br><br />
This plugin can convert most of the workspace items that OptFlux v3.2 can generate. (Check [[OptFlux3:Serialization:NonBackwardCompatible|not backward compatible items]])<br />
*Backup the workspace before performing the conversion.<br />
<br />
=Installation=<br />
<br />
After install the 3.2.7 version of OptFlux and perform all updates, the Serialization4OptFlux plugin can be installed through the repository manager operation.<br />
*You can access the '''Repository''' option under the '''Help -> Repository Manager''' menu.<br><br />
*See also [[KnownProblems:RepositoryManager|Problem with Repository Manager in 3.2 versions]]<br />
<br />
[[Image:PluginManager2.jpg|800px]]<br />
<br />
<br />
After the restart check if the plugin is installed by opening the '''Repository Manager'''.<br><br />
<br />
*'''Special Case:''' Sometimes some plugins may be disabled which results in a disabled '''Serialization Plugin'''. If that happens make sure all plugins are enabled.<br />
<br />
[[Image:PluginManager4.png|800px]]<br />
<br />
=How to Use=<br />
<br />
==Convert Workspace==<br />
Clipboard must have at least one project to enable operation.<br><br />
*Projects can be either open or closed.<br />
[[Image:Serialization1.jpg|800px]]<br />
<br />
Select '''File -> Workspace -> Convert Workspace...'''<br />
<br />
<br>The '''Convert Workspace''' window will be present.<br><br />
Select a folder that will be the workspace folder for the '''OptFlux v3.3 or newer'''.<br />
*Folder must be empty.<br />
[[Image:Serialization2.jpg|800px]]<br />
<br />
<br>If everything went as expected the converter will present a successful message similar to the following image.<br />
<br />
[[Image:Serialization3.jpg|550px]]<br />
<br />
==Special cases==<br />
Since there are some items that are [[OptFlux3:Serialization:NonBackwardCompatible|not backward compatible]] the converter will not present the previous successfull message.<br><br />
For that cases a message similar to the following image is present.<br><br />
*In this particular case the TNA items were not successfull converted.<br />
[[Image:SerializationExtra.jpg|800px]]<br />
<br />
==Workspace after conversion==<br />
After a successfull conversion the new workspace will only be loaded by OptFlux v3.3 or newer and it will be similar to the original workspace.<br />
*The following image represents the converted workspace loaded by the '''OptFlux 3.3.0''' version.<br />
[[Image:SerializationFinal.jpg|800px]]</div>Adminhttp://www.optflux.org/wiki/index.php?title=OptFlux3:Serialization&diff=2085OptFlux3:Serialization2016-06-01T08:55:16Z<p>Admin: /* Installation */</p>
<hr />
<div>{{DISPLAYTITLE: Serialization Plugin}}<br />
__TOC__<br />
=Purpose=<br />
Since the release of OptFlux 3.3.0 the workspace of previous version became deprecated and are not loaded by this or recent versions.<br><br />
The '''Serialization Plugin''' was developed for the OptFlux 3.2 version to garantee the backward compatible of pre-3.3.0 workspaces with newer OptFlux versions.<br><br />
This plugin can convert most of the workspace items that OptFlux v3.2 can generate. (Check [[OptFlux3:Serialization:NonBackwardCompatible|not backward compatible items]])<br />
*Backup the workspace before performing the conversion.<br />
<br />
=Installation=<br />
<br />
After install the 3.2.7 version of OptFlux and perform all updates, the Serialization4OptFlux plugin can be installed through the repository manager operation.<br />
*You can access the '''Repository''' option under the '''Help -> Repository Manager''' menu.<br><br />
<br />
[[Image:PluginManager2.jpg|800px]]<br />
<br />
<br />
After the restart check if the plugin is installed by opening the '''Repository Manager'''.<br><br />
<br />
*'''Special Case:''' Sometimes some plugins may be disabled which results in a disabled '''Serialization Plugin'''. If that happens make sure all plugins are enabled.<br />
<br />
[[Image:PluginManager4.png|800px]]<br />
<br />
=How to Use=<br />
<br />
==Convert Workspace==<br />
Clipboard must have at least one project to enable operation.<br><br />
*Projects can be either open or closed.<br />
[[Image:Serialization1.jpg|800px]]<br />
<br />
Select '''File -> Workspace -> Convert Workspace...'''<br />
<br />
<br>The '''Convert Workspace''' window will be present.<br><br />
Select a folder that will be the workspace folder for the '''OptFlux v3.3 or newer'''.<br />
*Folder must be empty.<br />
[[Image:Serialization2.jpg|800px]]<br />
<br />
<br>If everything went as expected the converter will present a successful message similar to the following image.<br />
<br />
[[Image:Serialization3.jpg|550px]]<br />
<br />
==Special cases==<br />
Since there are some items that are [[OptFlux3:Serialization:NonBackwardCompatible|not backward compatible]] the converter will not present the previous successfull message.<br><br />
For that cases a message similar to the following image is present.<br><br />
*In this particular case the TNA items were not successfull converted.<br />
[[Image:SerializationExtra.jpg|800px]]<br />
<br />
==Workspace after conversion==<br />
After a successfull conversion the new workspace will only be loaded by OptFlux v3.3 or newer and it will be similar to the original workspace.<br />
*The following image represents the converted workspace loaded by the '''OptFlux 3.3.0''' version.<br />
[[Image:SerializationFinal.jpg|800px]]</div>Adminhttp://www.optflux.org/wiki/index.php?title=OptFlux3:Serialization&diff=2084OptFlux3:Serialization2016-06-01T08:54:45Z<p>Admin: /* Installation */</p>
<hr />
<div>{{DISPLAYTITLE: Serialization Plugin}}<br />
__TOC__<br />
=Purpose=<br />
Since the release of OptFlux 3.3.0 the workspace of previous version became deprecated and are not loaded by this or recent versions.<br><br />
The '''Serialization Plugin''' was developed for the OptFlux 3.2 version to garantee the backward compatible of pre-3.3.0 workspaces with newer OptFlux versions.<br><br />
This plugin can convert most of the workspace items that OptFlux v3.2 can generate. (Check [[OptFlux3:Serialization:NonBackwardCompatible|not backward compatible items]])<br />
*Backup the workspace before performing the conversion.<br />
<br />
=Installation=<br />
<br />
After install the 3.2.7 version of OptFlux and perform all updates, the Serialization4OptFlux plugin can be installed through the repository manager present in OptFlux.<br />
*You can access the '''Repository''' option under the '''Help -> Repository Manager''' menu.<br><br />
<br />
[[Image:PluginManager2.jpg|800px]]<br />
<br />
<br />
After the restart check if the plugin is installed by opening the '''Repository Manager'''.<br><br />
<br />
*'''Special Case:''' Sometimes some plugins may be disabled which results in a disabled '''Serialization Plugin'''. If that happens make sure all plugins are enabled.<br />
<br />
[[Image:PluginManager4.png|800px]]<br />
<br />
=How to Use=<br />
<br />
==Convert Workspace==<br />
Clipboard must have at least one project to enable operation.<br><br />
*Projects can be either open or closed.<br />
[[Image:Serialization1.jpg|800px]]<br />
<br />
Select '''File -> Workspace -> Convert Workspace...'''<br />
<br />
<br>The '''Convert Workspace''' window will be present.<br><br />
Select a folder that will be the workspace folder for the '''OptFlux v3.3 or newer'''.<br />
*Folder must be empty.<br />
[[Image:Serialization2.jpg|800px]]<br />
<br />
<br>If everything went as expected the converter will present a successful message similar to the following image.<br />
<br />
[[Image:Serialization3.jpg|550px]]<br />
<br />
==Special cases==<br />
Since there are some items that are [[OptFlux3:Serialization:NonBackwardCompatible|not backward compatible]] the converter will not present the previous successfull message.<br><br />
For that cases a message similar to the following image is present.<br><br />
*In this particular case the TNA items were not successfull converted.<br />
[[Image:SerializationExtra.jpg|800px]]<br />
<br />
==Workspace after conversion==<br />
After a successfull conversion the new workspace will only be loaded by OptFlux v3.3 or newer and it will be similar to the original workspace.<br />
*The following image represents the converted workspace loaded by the '''OptFlux 3.3.0''' version.<br />
[[Image:SerializationFinal.jpg|800px]]</div>Adminhttp://www.optflux.org/wiki/index.php?title=OptFlux3:OPK&diff=2083OptFlux3:OPK2016-06-01T08:39:51Z<p>Admin: </p>
<hr />
<div>{{DISPLAYTITLE:OptKnock}}<br />
<br />
__TOC__<br />
<br />
'''Note:''' This plugin has been discontinued in current versions of OptFlux.<br />
<br />
=Example file=<br />
<br />
You can download it here -> [[Media:OptKnock_toy.zip| OptKnock_toy.zip]]<br />
<br />
An illustrative image of this model can be found below.<br />
<br />
[[Image:OptKnock_toy_image.png]]<br />
<br />
The simple network is constituted of seven reactions. The reactions: Desired, Biomass and substrate represents the production of the biological coumpound of interest, the formation of biomass and the uptake of metabolite M1 from surrounding media, respectively.<br />
<br />
The coefficient of reaction <b>R2</b> (M1->M3) are such that two molecules of M1 create one molecule of M3, while the stoichiometric coefficients of all other reactions reflect a one-to-one relationship between molecule quantities.<br />
<br />
<br />
=Brief tutorial=<br />
<br />
This brief tutorial will help you to begin working with OptKnock4OptFlux.<br />
<br />
*To start, you will need load a model in OptFlux(see how to [[HowTos| here]]). You must pay attention to select a correct biomass flux.<br />
<br />
==Run OptKnock==<br />
<br />
* 1 - Start by accessing the menu '''Plugins->OptKnock->OptKnock Optimization'''.<br />
<br />
[[Image:OptKnock_menu.png]]<br />
<br />
<br><br />
<br><br />
<br />
* 2 - The following dialog will be displayed.<br />
<br />
[[Image:OptKnock_dialog.png]]<br />
<br />
<br><br />
<b><i>Select Project and Model</i></b><br><br />
You can select the model/project to work.<br />
<br><br><br />
<b><i>Substrate Definition</i></b><br><br />
You can select the substrate flux and its uptake value.<br />
<br><br><br />
<b><i>Biomass Minimum Value</i></b><br><br />
You can define the minimum value for the biomass (in %).<br />
<br><br><br />
<b><i>Desired Flux Definition</i></b><br><br />
You can select the reaction representing the production of the desired compound.<br />
<br><br><br />
<b><i>Knockouts Definition</i></b><br><br />
You can define de maximum numbers of knockouts.<br />
<br><br><br />
<b><i>Selected Environmental Conditions</i></b><br><br />
You can define the environmental conditions if you have created any.<br />
<br><br />
<br><br />
<br />
* 3 - After execution, a new datatype will be placed in the clipboard, under the '''Optimizations Results -> OptKnock Optimizations'''. <br />
[[Image:OptKnock_datatype.png]]<br />
<br />
<br><br />
Pressing it will launch three viewers.<br />
<br />
<b>1. <i>OptKnockView</i></b><br />
<br />
[[Image:OptKnock_view.png]]<br />
<br />
<br><br />
<b>2. <i>Drain Fluxes</i></b><br />
<br />
[[Image:OptKnock_DrainsFluxes.png]]<br />
<br />
<br><br />
<b>3. <i>Internal Fluxes</i></b><br />
<br />
[[Image:OptKnock_InterFluxes.png]]<br />
<br></div>Adminhttp://www.optflux.org/wiki/index.php?title=KnownProblems:LowMemory&diff=2082KnownProblems:LowMemory2016-04-04T10:54:16Z<p>Admin: </p>
<hr />
<div>{{DISPLAYTITLE: OptFlux is too slow}}<br />
=Problem=<br />
Sometimes OptFlux performance may slow down after several operations, e.g optimizations.<br><br />
This slow down can be avoided by changing a parameter in the OptFlux configuration and allowing the application to use more resources from the machine.<br />
<br />
*Currently OptFlux is using 1Gb of your machine memory. You can increase to 2Gb by replacing a single file by this one -> [http://darwin.di.uminho.pt/optfluxwiki/images/1/17/morememoryfix.zip MoreMemoryFix.zip].<br />
<br />
*'''If you have a 32bit machine we do not advise this procedure.'''<br />
<br />
<gallery mode="packed" widths=700px heights=450px ><br />
File:MoreMemory01.jpg|Extract the '''main.conf''' file and copy it.<br />
File:MoreMemory02.jpg|Go to the OptFlux folder in your machine and paste this '''main.conf''' file to the '''conf''' folder.<br>The system will ask to replace the file.<br />
</gallery><br />
<br />
=Manual change=<br />
You can also manually change how much memory you want to allow OptFlux to use.<br><br />
This can be done by changing a property in the '''main.conf''' file.<br><br />
<br />
[[File:MoreMemory03.jpg]]<br><br />
*Open the '''main.conf''' file with NotePad or another text editor.<br />
<br><br />
<br />
<br />
[[File:MoreMemory04.jpg]]<br><br />
*Find the '''-Xmx''' text and replace 1024m by the desired value.<br><br />
<br />
<br>Possible values:<br />
*2048m (2 Gigabytes)<br />
*2g (2 Gigabytes)<br />
*3g (3 Gigabytes)<br />
*4g (4 Gigabytes)</div>Adminhttp://www.optflux.org/wiki/index.php?title=KnownProblems:LowMemory&diff=2081KnownProblems:LowMemory2016-04-04T10:41:45Z<p>Admin: /* Manual change */</p>
<hr />
<div>{{DISPLAYTITLE: OptFlux is too slow}}<br />
=Problem=<br />
Sometimes OptFlux performance may slow down after several operations, e.g optimizations.<br><br />
This slow down can be avoided by changing a parameter in the OptFlux configuration and allowing the application to use more resources from the machine.<br />
<br />
*Currently OptFlux is using 1Gb of your machine memory. You can increase to 2Gb by replacing a single file by this one -> [http://darwin.di.uminho.pt/optfluxwiki/images/1/17/morememoryfix.zip MoreMemoryFix.zip].<br />
<br />
<gallery mode="packed" widths=700px heights=450px ><br />
File:MoreMemory01.jpg|Extract the '''main.conf''' file and copy it.<br />
File:MoreMemory02.jpg|Go to the OptFlux folder in your machine and paste this '''main.conf''' file to the '''conf''' folder.<br>The system will ask to replace the file.<br />
</gallery><br />
<br />
=Manual change=<br />
You can also manually change how much memory you want to allow OptFlux to use.<br><br />
This can be done by changing a property in the '''main.conf''' file.<br><br />
<br />
[[File:MoreMemory03.jpg]]<br><br />
*Open the '''main.conf''' file with NotePad or another text editor.<br />
<br><br />
<br />
<br />
[[File:MoreMemory04.jpg]]<br><br />
*Find the '''-Xmx''' text and replace 1024m by the desired value.<br><br />
<br />
<br>Possible values:<br />
*2048m (2 Gigabytes)<br />
*2g (2 Gigabytes)<br />
*3g (3 Gigabytes)<br />
*4g (4 Gigabytes)</div>Adminhttp://www.optflux.org/wiki/index.php?title=KnownProblems:LowMemory&diff=2080KnownProblems:LowMemory2016-04-04T10:41:30Z<p>Admin: /* Manual change */</p>
<hr />
<div>{{DISPLAYTITLE: OptFlux is too slow}}<br />
=Problem=<br />
Sometimes OptFlux performance may slow down after several operations, e.g optimizations.<br><br />
This slow down can be avoided by changing a parameter in the OptFlux configuration and allowing the application to use more resources from the machine.<br />
<br />
*Currently OptFlux is using 1Gb of your machine memory. You can increase to 2Gb by replacing a single file by this one -> [http://darwin.di.uminho.pt/optfluxwiki/images/1/17/morememoryfix.zip MoreMemoryFix.zip].<br />
<br />
<gallery mode="packed" widths=700px heights=450px ><br />
File:MoreMemory01.jpg|Extract the '''main.conf''' file and copy it.<br />
File:MoreMemory02.jpg|Go to the OptFlux folder in your machine and paste this '''main.conf''' file to the '''conf''' folder.<br>The system will ask to replace the file.<br />
</gallery><br />
<br />
=Manual change=<br />
You can also manually change how much memory you want to allow OptFlux to use.<br><br />
This can be done by changing a property in the '''main.conf''' file.<br><br />
<br />
[[File:MoreMemory03.jpg]]<br><br />
*Open the '''main.conf''' file with NotePad or another text editor.<br />
<br><br />
<br />
<br />
<br />
[[File:MoreMemory04.jpg]]<br><br />
*Find the '''-Xmx''' text and replace 1024m by the desired value.<br><br />
<br />
<br>Possible values:<br />
*2048m (2 Gigabytes)<br />
*2g (2 Gigabytes)<br />
*3g (3 Gigabytes)<br />
*4g (4 Gigabytes)</div>Adminhttp://www.optflux.org/wiki/index.php?title=KnownProblems&diff=2079KnownProblems2016-04-01T17:03:12Z<p>Admin: </p>
<hr />
<div>{{DISPLAYTITLE:Known Problems in Optflux 3}}<br />
__TOC__<br />
==Repository Manager Problem==<br />
*[[KnownProblems:RepositoryManager|3.2 version]]<br />
<br />
== OS Problems ==<br />
*[https://sourceforge.net/p/optflux/support-requests/28/ OS X 10.11 (El Capitan)]<br />
<br />
== Usage Problems ==<br />
*[https://sourceforge.net/p/optflux/bugs/124/ Application blocks while loading empty workspace]<br />
*[[KnownProblems:LowMemory|Slow OptFlux]]</div>Adminhttp://www.optflux.org/wiki/index.php?title=KnownProblems:LowMemory&diff=2078KnownProblems:LowMemory2016-04-01T17:02:28Z<p>Admin: </p>
<hr />
<div>{{DISPLAYTITLE: OptFlux is too slow}}<br />
=Problem=<br />
Sometimes OptFlux performance may slow down after several operations, e.g optimizations.<br><br />
This slow down can be avoided by changing a parameter in the OptFlux configuration and allowing the application to use more resources from the machine.<br />
<br />
*Currently OptFlux is using 1Gb of your machine memory. You can increase to 2Gb by replacing a single file by this one -> [http://darwin.di.uminho.pt/optfluxwiki/images/1/17/morememoryfix.zip MoreMemoryFix.zip].<br />
<br />
<gallery mode="packed" widths=700px heights=450px ><br />
File:MoreMemory01.jpg|Extract the '''main.conf''' file and copy it.<br />
File:MoreMemory02.jpg|Go to the OptFlux folder in your machine and paste this '''main.conf''' file to the '''conf''' folder.<br>The system will ask to replace the file.<br />
</gallery><br />
<br />
=Manual change=<br />
You can also manually change how much memory you want to allow OptFlux to use.<br><br />
This can be done by changing a property in the '''main.conf''' file.<br><br />
<br />
[[File:MoreMemory03.jpg]]<br><br />
*Open the '''main.conf''' file with NotePad or another text editor.<br />
<br><br />
<br />
<br />
<br />
[[File:MoreMemory04.jpg]]<br><br />
*Find the '''-Xmx''' text and replace 1024m by the desired value.<br><br />
<br />
<br>Possible values:<br />
*2048m (2 Gigabytes)<br />
*2G (2 Gigabytes)<br />
*2560m (2.5 Gigabytes)<br />
*3G (3 Gigabytes)<br />
*4G (4 Gigabytes)</div>Adminhttp://www.optflux.org/wiki/index.php?title=KnownProblems:LowMemory&diff=2077KnownProblems:LowMemory2016-04-01T17:01:27Z<p>Admin: Created page with "{{DISPLAYTITLE: OptFlux is too slow}} =Problem= Sometimes OptFlux performance may slow down after several operations, e.g optimizations.<br> This slow down can be avoided by c..."</p>
<hr />
<div>{{DISPLAYTITLE: OptFlux is too slow}}<br />
=Problem=<br />
Sometimes OptFlux performance may slow down after several operations, e.g optimizations.<br><br />
This slow down can be avoided by changing a parameter in the OptFlux configuration and allowing the application to use more resources from the machine.<br />
<br />
*Currently OptFlux is using 1Gb of your machine memory. You can increase to 2Gb by replacing a single file by this one -> [http://darwin.di.uminho.pt/optfluxwiki/images/1/17/morememoryfix.zip MoreMemoryFix.zip].<br />
<br />
<gallery mode="packed" widths=700px heights=450px ><br />
File:MoreMemory01.jpg|Extract the '''main.conf''' file and copy it.<br />
File:MoreMemory02.jpg|Go to the OptFlux folder in your machine and paste this '''main.conf''' file to the '''conf''' folder.<br>The system will ask to replace the file.<br />
</gallery><br />
<br />
=Manual change=<br />
You can also manually change how much memory you want to allow OptFlux to use.<br><br />
This can be done by changing a property in the '''main.conf''' file.<br><br />
<br />
[[File:MoreMemory03.jpg]]<br><br />
*Open the '''main.conf''' file with NotePad or another text editor.<br />
<br><br />
<br />
<br />
<br />
[[File:MoreMemory04.jpg]]<br><br />
*Find the '''-Xmx''' text and replace 1024m by the desired value.<br><br />
<br />
<br>Possible values:<br />
*2048m<br />
*2G<br />
*2560m<br />
*3G<br />
*4G</div>Adminhttp://www.optflux.org/wiki/index.php?title=File:MoreMemory04.jpg&diff=2076File:MoreMemory04.jpg2016-04-01T16:50:36Z<p>Admin: </p>
<hr />
<div></div>Adminhttp://www.optflux.org/wiki/index.php?title=KnownProblems&diff=2075KnownProblems2016-04-01T11:34:02Z<p>Admin: /* Usage Problems */</p>
<hr />
<div>{{DISPLAYTITLE:Known Problems in Optflux 3}}<br />
__TOC__<br />
==Repository Manager Problem==<br />
*[[KnownProblems:RepositoryManager|3.2 version]]<br />
<br />
== OS Problems ==<br />
*[https://sourceforge.net/p/optflux/support-requests/28/ OS X 10.11 (El Capitan)]<br />
<br />
== Usage Problems ==<br />
*[https://sourceforge.net/p/optflux/bugs/124/ Application blocks while loading empty workspace]</div>Adminhttp://www.optflux.org/wiki/index.php?title=KnownProblems&diff=2074KnownProblems2016-04-01T11:33:09Z<p>Admin: /* Usage Problems */</p>
<hr />
<div>{{DISPLAYTITLE:Known Problems in Optflux 3}}<br />
__TOC__<br />
==Repository Manager Problem==<br />
*[[KnownProblems:RepositoryManager|3.2 version]]<br />
<br />
== OS Problems ==<br />
*[https://sourceforge.net/p/optflux/support-requests/28/ OS X 10.11 (El Capitan)]<br />
<br />
== Usage Problems ==<br />
*[https://sourceforge.net/p/optflux/bugs/124/ Application blocks loading empty workspace]</div>Adminhttp://www.optflux.org/wiki/index.php?title=File:MoreMemory03.jpg&diff=2072File:MoreMemory03.jpg2016-04-01T11:31:48Z<p>Admin: </p>
<hr />
<div></div>Adminhttp://www.optflux.org/wiki/index.php?title=File:MoreMemory02.jpg&diff=2071File:MoreMemory02.jpg2016-04-01T11:31:37Z<p>Admin: </p>
<hr />
<div></div>Adminhttp://www.optflux.org/wiki/index.php?title=File:MoreMemory01.jpg&diff=2070File:MoreMemory01.jpg2016-04-01T11:31:22Z<p>Admin: </p>
<hr />
<div></div>Adminhttp://www.optflux.org/wiki/index.php?title=KnownProblems&diff=2069KnownProblems2016-04-01T11:11:19Z<p>Admin: </p>
<hr />
<div>{{DISPLAYTITLE:Known Problems in Optflux 3}}<br />
__TOC__<br />
==Repository Manager Problem==<br />
*[[KnownProblems:RepositoryManager|3.2 version]]<br />
<br />
== OS Problems ==<br />
*[https://sourceforge.net/p/optflux/support-requests/28/ OS X 10.11 (El Capitan)]<br />
<br />
== Usage Problems ==<br />
*[https://sourceforge.net/p/optflux/bugs/124/ Blocks loading empty workspace]</div>Adminhttp://www.optflux.org/wiki/index.php?title=HowTos:OptFlux3&diff=2068HowTos:OptFlux32016-04-01T10:15:45Z<p>Admin: </p>
<hr />
<div>{{DISPLAYTITLE:How Tos for Optflux 3}}<br />
<br />
== Project And Model Handling==<br />
*[[OptFlux3:CORE:NewProject|New project]]<br />
**[[CORE:Readers:Drains | Drains Definition]]<br />
**[[OptFlux Readers]]<br />
***[[SBML Reader]]<br />
***[[Flat Files Reader]]<br />
***[[Metatool]]<br />
***[[OptFlux3:MR | OptFlux Repository]]<br />
***[[Table format Reader]]<br />
***[[Cell Designer Reader]]<br />
*[[OptFlux3:CORE:ImportProject | Import Project]]<br />
*[[OptFlux3:SMP |Model Simplification]]<br />
<br />
=== Model Handling ===<br />
<br />
*[[Create Environmental conditions]]<br />
<br />
== Simulation ==<br />
*[[OptFlux3:SIM:WildType | Wild Type]]<br />
*[[OptFlux3:SIM:Knockouts | Knockouts]]<br />
*[[OptFlux3:SIM:UnderOverExpression | Under-Over Expression]]<br />
<br />
== Analysis ==<br />
*[[OptFlux3:OPT:Critical | Critical Genes/Reactions]]<br />
*[[OptFlux3:BC:balancechecker | Balance Checker]]<br />
*Flux Variability Analysis<br />
**[[OptFlux3:SIM:ZeroFluxFVA | Zero-flux values]]<br />
**[[OptFlux3:SIM:VarPlot | Flux-variation plot]]<br />
**[[OptFlux3:SIM:FluxLim | Flux limits]]<br />
*Structural Analysis<br />
**[[OptFlux3:SIM:ZeroFluxStruc | Zero-flux values]]<br />
**[[OptFlux3:SIM:EquivalentFluxes | Equivalent-flux values]]<br />
<br />
== Optimization ==<br />
*[[OptFlux3:Evolutionary | Evolutionary]]<br />
*[[OptFlux3:OPK | Optknock]]<br />
<br />
== Help ==<br />
*Repository Manager<br />
**[[KnownProblems:RepositoryManager | Known Problems]]<br />
*Updates<br />
*Preferences<br />
<br />
== Plugins ==<br />
*[[OptFlux3:CORE|Core]]<br />
*[[OptFlux3:MR | Model Repository]]<br />
*[[OptFlux3:SIM | Simulation]]<br />
*[[OptFlux3:Evolutionary | Optimization]]<br />
*[[OptFlux3:SMP | Simplification]]<br />
*[[OptFlux3:BC:balancechecker:hgfhgf | Mass Balance Validator]]<br />
*[[OptFlux3:OPK | OptKnock]]<br />
*[[OptFlux3:TNA | Network Topology Analysis (TNA)]]<br />
*[[OptFlux3:EFM | Elementary Flux Modes]]<br />
*[[OptFlux3:RT | Reg4OptFlux - Regulatory plugin]]<br />
*[[OptFlux3:METAVIZ | Metabolic Network Visualization Plugin]]<br />
*[[OptFlux3:MFA | Metabolic Flux Analysis]]<br />
*[[OptFlux3:COBRA | Cobra4OptFlux - Cobra plugin]]<br />
*[[OptFlux3:Serialization | Serialization plugin]]</div>Adminhttp://www.optflux.org/wiki/index.php?title=MediaWiki:Sidebar&diff=2067MediaWiki:Sidebar2016-04-01T10:10:20Z<p>Admin: </p>
<hr />
<div>* navigation<br />
** http://www.optflux.org | Optflux site<br />
** Welcome | Optflux wiki<br />
** http://sourceforge.net/projects/optflux/files/latest/download | Downloads<br />
<!--** ** Plugins | Plugins (2.x only) --><br />
<!--** Installation | Installation --><br />
** CaseStudy | Case Study<br />
** OptFlux:About | Support/Contact<br />
** OptFlux:Acknowledgements | Acknowledgements<br />
<br />
* Documentation<br />
** BeginnersTutorial | Beginners Tutorial<br />
<!--** ** Manual | OptFlux Manual --><br />
** HowTos:OptFlux3|HowTos OptFlux 3<br />
<!--** ** HowTos|HowTos OptFlux 2.x --><br />
<br />
* Support<br />
** https://sourceforge.net/p/optflux/bugs/ | Bug tracker<br />
** https://sourceforge.net/p/optflux/support-requests/ | Support tracker<br />
** https://sourceforge.net/p/optflux/feature-requests/ | Feature Requests<br />
** KnownProblems | Known Problems<br />
* TOOLBOX<br />
<!--** recentchanges-url|recentchanges--><br />
<!--** currentevents-url|currentevents--><br />
* LANGUAGES</div>Adminhttp://www.optflux.org/wiki/index.php?title=KnownProblems&diff=2066KnownProblems2016-04-01T10:09:39Z<p>Admin: </p>
<hr />
<div>{{DISPLAYTITLE:Known Problems in Optflux 3}}<br />
__TOC__<br />
==Repository Manager Problem==<br />
*[[KnownProblems:RepositoryManager|3.2 version]]<br />
<br />
== OS Problems ==<br />
*[https://sourceforge.net/p/optflux/support-requests/28/ OS X 10.11 (El Capitan)]</div>Adminhttp://www.optflux.org/wiki/index.php?title=KnownProblems&diff=2065KnownProblems2016-04-01T10:09:32Z<p>Admin: </p>
<hr />
<div>{{DISPLAYTITLE:Known Problems in Optflux 3}}<br />
<br />
__TOC__<br />
==Repository Manager Problem==<br />
*[[KnownProblems:RepositoryManager|3.2 version]]<br />
<br />
== OS Problems ==<br />
*[https://sourceforge.net/p/optflux/support-requests/28/ OS X 10.11 (El Capitan)]</div>Adminhttp://www.optflux.org/wiki/index.php?title=KnownProblems&diff=2064KnownProblems2016-04-01T10:09:23Z<p>Admin: </p>
<hr />
<div>{{DISPLAYTITLE:Known Problems in Optflux 3}}<br />
<br />
__TOC__<br />
<br />
==Repository Manager Problem==<br />
*[[KnownProblems:RepositoryManager|3.2 version]]<br />
<br />
== OS Problems ==<br />
*[https://sourceforge.net/p/optflux/support-requests/28/ OS X 10.11 (El Capitan)]</div>Adminhttp://www.optflux.org/wiki/index.php?title=KnownProblems&diff=2063KnownProblems2016-04-01T10:09:15Z<p>Admin: Created page with "{{DISPLAYTITLE:Known Problems in Optflux 3}} __TOC__ ==Repository Manager Problem== *3.2 version == OS Problems == *[https://sourceforg..."</p>
<hr />
<div>{{DISPLAYTITLE:Known Problems in Optflux 3}}<br />
<br />
__TOC__<br />
<br />
==Repository Manager Problem==<br />
*[[KnownProblems:RepositoryManager|3.2 version]]<br />
<br />
<br />
== OS Problems ==<br />
*[https://sourceforge.net/p/optflux/support-requests/28/ OS X 10.11 (El Capitan)]</div>Adminhttp://www.optflux.org/wiki/index.php?title=MediaWiki:Sidebar&diff=2062MediaWiki:Sidebar2016-04-01T10:00:33Z<p>Admin: </p>
<hr />
<div>* navigation<br />
** http://www.optflux.org | Optflux site<br />
** Welcome | Optflux wiki<br />
** http://sourceforge.net/projects/optflux/files/latest/download | Downloads<br />
<!--** ** Plugins | Plugins (2.x only) --><br />
<!--** Installation | Installation --><br />
** CaseStudy | Case Study<br />
** OptFlux:About | Support/Contact<br />
** OptFlux:Acknowledgements | Acknowledgements<br />
<br />
* Documentation<br />
** BeginnersTutorial | Beginners Tutorial<br />
<!--** ** Manual | OptFlux Manual --><br />
** HowTos:OptFlux3|HowTos OptFlux 3<br />
<!--** ** HowTos|HowTos OptFlux 2.x --><br />
<br />
* Support<br />
** https://sourceforge.net/p/optflux/bugs/ | Bug tracker<br />
** https://sourceforge.net/p/optflux/support-requests/ | Support tracker<br />
** https://sourceforge.net/p/optflux/feature-requests/ | Feature Requests<br />
** KnownProblems:RepositoryManager | Known Problems<br />
* TOOLBOX<br />
<!--** recentchanges-url|recentchanges--><br />
<!--** currentevents-url|currentevents--><br />
* LANGUAGES</div>Adminhttp://www.optflux.org/wiki/index.php?title=KnownProblems:RepositoryManager&diff=2061KnownProblems:RepositoryManager2016-04-01T10:00:06Z<p>Admin: Created page with "{{DISPLAYTITLE: Repository Manager does not open in 3.2 versions}} =Problem= OptFlux 3.2.* has a problem while opening the repository manager. *The following images show this..."</p>
<hr />
<div>{{DISPLAYTITLE: Repository Manager does not open in 3.2 versions}}<br />
=Problem=<br />
<br />
OptFlux 3.2.* has a problem while opening the repository manager.<br />
*The following images show this problem behavior.<br><br />
<br />
<gallery mode="packed" widths=700px heights=450px ><br />
File:RepositoryProblem1.jpg<br />
File:RepositoryProblem2.jpg<br />
</gallery><br />
<br />
=Fix=<br />
If you are experiencing this problem then please download this file -> [http://darwin.di.uminho.pt/optfluxwiki/images/1/17/repositorymanagerfix.zip RepositoryManagerFix.zip] <br />
<br><br />
*Follow the next steps to solve it. Please perform this steps with your OptFlux closed.<br />
<br />
<gallery mode="packed" widths=700px heights=450px ><br />
File:RepositoryProblem3.jpg|Extract the '''pluginmanager.conf''' file and copy it.<br />
File:RepositoryProblem4.jpg|Go to the OptFlux folder in your machine and paste this '''pluginmanager.conf''' file to the '''conf''' folder.<br>The system will ask to replace the file.<br />
</gallery><br />
<br />
<gallery mode="packed" widths=700px heights=450px ><br />
File:RepositoryProblem5.jpg|Open OptFlux and if everything is alright the Repository Manager will be present as the image shows.<br />
</gallery></div>Adminhttp://www.optflux.org/wiki/index.php?title=MediaWiki:Sidebar&diff=2060MediaWiki:Sidebar2016-04-01T09:50:47Z<p>Admin: </p>
<hr />
<div>* navigation<br />
** http://www.optflux.org | Optflux site<br />
** Welcome | Optflux wiki<br />
** http://sourceforge.net/projects/optflux/files/latest/download | Downloads<br />
<!--** ** Plugins | Plugins (2.x only) --><br />
<!--** Installation | Installation --><br />
** CaseStudy | Case Study<br />
** OptFlux:About | Support/Contact<br />
** OptFlux:Acknowledgements | Acknowledgements<br />
<br />
* Documentation<br />
** BeginnersTutorial | Beginners Tutorial<br />
<!--** ** Manual | OptFlux Manual --><br />
** HowTos:OptFlux3|HowTos OptFlux 3<br />
<!--** ** HowTos|HowTos OptFlux 2.x --><br />
<br />
* Support<br />
** https://sourceforge.net/p/optflux/bugs/ | Bug tracker<br />
** https://sourceforge.net/p/optflux/support-requests/ | Support tracker<br />
** https://sourceforge.net/p/optflux/feature-requests/ | Feature Requests<br />
** Known Problems<br />
* TOOLBOX<br />
<!--** recentchanges-url|recentchanges--><br />
<!--** currentevents-url|currentevents--><br />
* LANGUAGES</div>Adminhttp://www.optflux.org/wiki/index.php?title=MediaWiki:Sidebar&diff=2059MediaWiki:Sidebar2016-04-01T09:50:01Z<p>Admin: </p>
<hr />
<div>* navigation<br />
** http://www.optflux.org | Optflux site<br />
** Welcome | Optflux wiki<br />
** http://sourceforge.net/projects/optflux/files/latest/download | Downloads<br />
<!--** ** Plugins | Plugins (2.x only) --><br />
<!--** Installation | Installation --><br />
** CaseStudy | Case Study<br />
** OptFlux:About | Support/Contact<br />
** OptFlux:Acknowledgements | Acknowledgements<br />
<br />
* Documentation<br />
** BeginnersTutorial | Beginners Tutorial<br />
<!--** ** Manual | OptFlux Manual --><br />
** HowTos:OptFlux3|HowTos OptFlux 3<br />
<!--** ** HowTos|HowTos OptFlux 2.x --><br />
<br />
* Support<br />
** https://sourceforge.net/p/optflux/bugs/ | Bug tracker<br />
** https://sourceforge.net/p/optflux/support-requests/ | Support tracker<br />
** https://sourceforge.net/p/optflux/feature-requests/ | Feature Requests<br />
Known Problems<br />
* TOOLBOX<br />
<!--** recentchanges-url|recentchanges--><br />
<!--** currentevents-url|currentevents--><br />
* LANGUAGES</div>Adminhttp://www.optflux.org/wiki/index.php?title=MediaWiki:Sidebar&diff=2058MediaWiki:Sidebar2016-04-01T09:46:52Z<p>Admin: </p>
<hr />
<div>* navigation<br />
** http://www.optflux.org | Optflux site<br />
** Welcome | Optflux wiki<br />
** http://sourceforge.net/projects/optflux/files/latest/download | Downloads<br />
<!--** ** Plugins | Plugins (2.x only) --><br />
<!--** Installation | Installation --><br />
** CaseStudy | Case Study<br />
** OptFlux:About | Support/Contact<br />
** OptFlux:Acknowledgements | Acknowledgements<br />
<br />
* Documentation<br />
** BeginnersTutorial | Beginners Tutorial<br />
<!--** ** Manual | OptFlux Manual --><br />
** HowTos:OptFlux3|HowTos OptFlux 3<br />
<!--** ** HowTos|HowTos OptFlux 2.x --><br />
* TOOLBOX<br />
<!--** recentchanges-url|recentchanges--><br />
<!--** currentevents-url|currentevents--><br />
* LANGUAGES</div>Adminhttp://www.optflux.org/wiki/index.php?title=OptFlux3:Serialization&diff=2057OptFlux3:Serialization2016-03-23T16:16:48Z<p>Admin: /* Installation */</p>
<hr />
<div>{{DISPLAYTITLE: Serialization Plugin}}<br />
__TOC__<br />
=Purpose=<br />
Since the release of OptFlux 3.3.0 the workspace of previous version became deprecated and are not loaded by this or recent versions.<br><br />
The '''Serialization Plugin''' was developed for the OptFlux 3.2 version to garantee the backward compatible of pre-3.3.0 workspaces with newer OptFlux versions.<br><br />
This plugin can convert most of the workspace items that OptFlux v3.2 can generate. (Check [[OptFlux3:Serialization:NonBackwardCompatible|not backward compatible items]])<br />
*Backup the workspace before performing the conversion.<br />
<br />
=Installation=<br />
<br />
After install the OptFlux, the Serialization4OptFlux plugin can be installed through the repository manager present in OptFlux.<br />
*You can access the '''Repository''' option under the '''Help -> Repository Manager''' menu.<br><br />
<br />
[[Image:PluginManager2.jpg|800px]]<br />
<br />
<br />
After the restart check if the plugin is installed by opening the '''Repository Manager'''.<br><br />
<br />
*'''Special Case:''' Sometimes some plugins may be disabled which results in a disabled '''Serialization Plugin'''. If that happens make sure all plugins are enabled.<br />
<br />
[[Image:PluginManager4.png|800px]]<br />
<br />
=How to Use=<br />
<br />
==Convert Workspace==<br />
Clipboard must have at least one project to enable operation.<br><br />
*Projects can be either open or closed.<br />
[[Image:Serialization1.jpg|800px]]<br />
<br />
Select '''File -> Workspace -> Convert Workspace...'''<br />
<br />
<br>The '''Convert Workspace''' window will be present.<br><br />
Select a folder that will be the workspace folder for the '''OptFlux v3.3 or newer'''.<br />
*Folder must be empty.<br />
[[Image:Serialization2.jpg|800px]]<br />
<br />
<br>If everything went as expected the converter will present a successful message similar to the following image.<br />
<br />
[[Image:Serialization3.jpg|550px]]<br />
<br />
==Special cases==<br />
Since there are some items that are [[OptFlux3:Serialization:NonBackwardCompatible|not backward compatible]] the converter will not present the previous successfull message.<br><br />
For that cases a message similar to the following image is present.<br><br />
*In this particular case the TNA items were not successfull converted.<br />
[[Image:SerializationExtra.jpg|800px]]<br />
<br />
==Workspace after conversion==<br />
After a successfull conversion the new workspace will only be loaded by OptFlux v3.3 or newer and it will be similar to the original workspace.<br />
*The following image represents the converted workspace loaded by the '''OptFlux 3.3.0''' version.<br />
[[Image:SerializationFinal.jpg|800px]]</div>Adminhttp://www.optflux.org/wiki/index.php?title=File:PluginManager4.png&diff=2056File:PluginManager4.png2016-03-23T16:15:16Z<p>Admin: </p>
<hr />
<div></div>Adminhttp://www.optflux.org/wiki/index.php?title=File:PluginManager2.jpg&diff=2054File:PluginManager2.jpg2016-03-23T16:13:55Z<p>Admin: </p>
<hr />
<div></div>Adminhttp://www.optflux.org/wiki/index.php?title=OptFlux3:Serialization:NonBackwardCompatible&diff=2050OptFlux3:Serialization:NonBackwardCompatible2016-03-22T14:15:32Z<p>Admin: /* Version 3.2 to 3.3 */</p>
<hr />
<div>{{DISPLAYTITLE: Non Backward Compatible items}}<br />
__TOC__<br />
=Version 3.2 to 3.3=<br />
This list represent the items that are not converted from the OptFlux v3.2 to 3.3.<br><br />
List of items:<br />
*Flux-variation Plot<br />
*All TNA items except the network<br />
<br />
[[Image:SerializationWithProblems.jpg|400px]]<br />
<br>If during the conversion some problems with different items than the ones in the list had occurred feel free to ask for support [https://sourceforge.net/p/optflux/support-requests/29/ here].</div>Adminhttp://www.optflux.org/wiki/index.php?title=OptFlux3:Serialization&diff=2049OptFlux3:Serialization2016-03-22T14:15:08Z<p>Admin: /* Purpose */</p>
<hr />
<div>{{DISPLAYTITLE: Serialization Plugin}}<br />
__TOC__<br />
=Purpose=<br />
Since the release of OptFlux 3.3.0 the workspace of previous version became deprecated and are not loaded by this or recent versions.<br><br />
The '''Serialization Plugin''' was developed for the OptFlux 3.2 version to garantee the backward compatible of pre-3.3.0 workspaces with newer OptFlux versions.<br><br />
This plugin can convert most of the workspace items that OptFlux v3.2 can generate. (Check [[OptFlux3:Serialization:NonBackwardCompatible|not backward compatible items]])<br />
*Backup the workspace before performing the conversion.<br />
<br />
=Installation=<br />
<br />
After install the OptFlux, the Serialization4OptFlux plugin can be installed through the repository manager present in OptFlux.<br />
*You can access the '''Repository''' option under the '''Help -> Repository Manager''' menu.<br><br />
<br />
[[Image:PluginManager1.jpg|800px]]<br />
<br />
<br />
After the restart check if the plugin is installed by opening the '''Repository Manager'''.<br><br />
<br />
*'''Special Case:''' Sometimes some plugins may be disabled which results in a disabled '''Serialization Plugin'''. If that happens make sure all plugins are enabled.<br />
<br />
[[Image:PluginManager2.png|800px]]<br />
<br />
=How to Use=<br />
<br />
==Convert Workspace==<br />
Clipboard must have at least one project to enable operation.<br><br />
*Projects can be either open or closed.<br />
[[Image:Serialization1.jpg|800px]]<br />
<br />
Select '''File -> Workspace -> Convert Workspace...'''<br />
<br />
<br>The '''Convert Workspace''' window will be present.<br><br />
Select a folder that will be the workspace folder for the '''OptFlux v3.3 or newer'''.<br />
*Folder must be empty.<br />
[[Image:Serialization2.jpg|800px]]<br />
<br />
<br>If everything went as expected the converter will present a successful message similar to the following image.<br />
<br />
[[Image:Serialization3.jpg|550px]]<br />
<br />
==Special cases==<br />
Since there are some items that are [[OptFlux3:Serialization:NonBackwardCompatible|not backward compatible]] the converter will not present the previous successfull message.<br><br />
For that cases a message similar to the following image is present.<br><br />
*In this particular case the TNA items were not successfull converted.<br />
[[Image:SerializationExtra.jpg|800px]]<br />
<br />
==Workspace after conversion==<br />
After a successfull conversion the new workspace will only be loaded by OptFlux v3.3 or newer and it will be similar to the original workspace.<br />
*The following image represents the converted workspace loaded by the '''OptFlux 3.3.0''' version.<br />
[[Image:SerializationFinal.jpg|800px]]</div>Adminhttp://www.optflux.org/wiki/index.php?title=OptFlux3:Serialization&diff=2048OptFlux3:Serialization2016-03-22T14:14:55Z<p>Admin: </p>
<hr />
<div>{{DISPLAYTITLE: Serialization Plugin}}<br />
__TOC__<br />
=Purpose=<br />
Since the release of OptFlux 3.3.0 the workspace of previous version became deprecated and are not loaded by this or recent versions.<br><br />
The '''Serialization Plugin''' was developed for the OptFlux 3.2 version to garantee the backward compatible of pre-3.3.0 workspaces with newer OptFlux versions.<br><br />
This plugin can convert most of the workspace items that OptFlux v3.2 can generate. (Check [[OptFlux3:Serialization:NonBackwardCompatible|not backward compatible items]])<br />
*Make sure to backup the workspace before performing the conversion.<br />
<br />
=Installation=<br />
<br />
After install the OptFlux, the Serialization4OptFlux plugin can be installed through the repository manager present in OptFlux.<br />
*You can access the '''Repository''' option under the '''Help -> Repository Manager''' menu.<br><br />
<br />
[[Image:PluginManager1.jpg|800px]]<br />
<br />
<br />
After the restart check if the plugin is installed by opening the '''Repository Manager'''.<br><br />
<br />
*'''Special Case:''' Sometimes some plugins may be disabled which results in a disabled '''Serialization Plugin'''. If that happens make sure all plugins are enabled.<br />
<br />
[[Image:PluginManager2.png|800px]]<br />
<br />
=How to Use=<br />
<br />
==Convert Workspace==<br />
Clipboard must have at least one project to enable operation.<br><br />
*Projects can be either open or closed.<br />
[[Image:Serialization1.jpg|800px]]<br />
<br />
Select '''File -> Workspace -> Convert Workspace...'''<br />
<br />
<br>The '''Convert Workspace''' window will be present.<br><br />
Select a folder that will be the workspace folder for the '''OptFlux v3.3 or newer'''.<br />
*Folder must be empty.<br />
[[Image:Serialization2.jpg|800px]]<br />
<br />
<br>If everything went as expected the converter will present a successful message similar to the following image.<br />
<br />
[[Image:Serialization3.jpg|550px]]<br />
<br />
==Special cases==<br />
Since there are some items that are [[OptFlux3:Serialization:NonBackwardCompatible|not backward compatible]] the converter will not present the previous successfull message.<br><br />
For that cases a message similar to the following image is present.<br><br />
*In this particular case the TNA items were not successfull converted.<br />
[[Image:SerializationExtra.jpg|800px]]<br />
<br />
==Workspace after conversion==<br />
After a successfull conversion the new workspace will only be loaded by OptFlux v3.3 or newer and it will be similar to the original workspace.<br />
*The following image represents the converted workspace loaded by the '''OptFlux 3.3.0''' version.<br />
[[Image:SerializationFinal.jpg|800px]]</div>Adminhttp://www.optflux.org/wiki/index.php?title=OptFlux3:Serialization:NonBackwardCompatible&diff=2047OptFlux3:Serialization:NonBackwardCompatible2016-03-09T10:44:50Z<p>Admin: </p>
<hr />
<div>{{DISPLAYTITLE: Non Backward Compatible items}}<br />
__TOC__<br />
=Version 3.2 to 3.3=<br />
This list represent the items that are not converted from the OptFlux v3.2 to 3.3.<br><br />
List of items:<br />
*Flux-variation Plot<br />
*All TNA items except the network<br />
*Omics Overlaps<br />
<br />
[[Image:SerializationWithProblems.jpg|400px]]<br />
<br>If during the conversion some problems with different items than the ones in the list had occurred feel free to ask for support [https://sourceforge.net/p/optflux/support-requests/29/ here].</div>Adminhttp://www.optflux.org/wiki/index.php?title=OptFlux3:COBRA:InstallConfig&diff=2046OptFlux3:COBRA:InstallConfig2016-03-04T15:38:02Z<p>Admin: </p>
<hr />
<div>{{DISPLAYTITLE: COBRA Install and Configuration}}<br />
=Installation=<br />
<br />
After install the OptFlux, the COBRA4OptFlux plugin can be installed through the repository manager present in OptFlux.<br />
*You can access the '''Repository''' option under the '''Help -> Repository Manager''' menu.<br><br />
<br />
[[Image:installcobraplugin.png|600px]]<br />
<br />
*After accessing to the '''Repository Manager''' click over the Cobra for OptFlux (version x) and perform the installation by clicking on '''Install - Version x.x.x)'''.<br />
* Click on '''Restart''' button.<br />
<br />
=Configuration=<br />
<br />
<b><i>This plugin only works if the machine has the MATLAB application installed with the COBRA package.</i></b><br><br />
* Follow this link to [https://opencobra.github.io/cobratoolbox/ install COBRA toolbox in MATLAB]<br />
After install the Cobra4OptFlux plugin, some configurations must be performed.<br />
*You can access the '''Preferences''' option under the '''Help -> Preferences''' menu.<br><br />
<br />
[[Image:cobrapreferenceswindow.png|600px]]<br />
<br />
*After accessing the '''Preferences''' click over '''Matlab''' tab. <br />
*Here you must select the '''MATLAB Executable''' path. This path is mandatory to perform the MATLAB operations.<br />
*The '''Gurobi folder''' is optional but most of the available COBRA formulations use this solver thus this preference is highly recommendable.<br />
*The '''Show MATLAB Console Only''' is optional and when disable the MATLAB will be opened as a full application.<br />
* Click on '''Restart''' button if it is enable - Only happens when '''Gurobi Folder''' is added/changed.<br />
<br />
<b><i>And that's all!! You can press OK and if all is well defined the COBRA plugin for OptFlux can be used in full.</i></b><br></div>Adminhttp://www.optflux.org/wiki/index.php?title=OptFlux3:COBRA:InstallConfig&diff=2045OptFlux3:COBRA:InstallConfig2016-03-04T15:31:47Z<p>Admin: /* Installation */</p>
<hr />
<div>{{DISPLAYTITLE: COBRA Install and Configuration}}<br />
=Installation=<br />
<br />
After install the OptFlux, the COBRA4OptFlux plugin can be installed through the repository manager present in OptFlux.<br />
*You can access the '''Repository''' option under the '''Help -> Repository Manager''' menu.<br><br />
<br />
[[Image:installcobraplugin.png|600px]]<br />
<br />
*After accessing to the '''Repository Manager''' click over the Cobra for OptFlux (version x) and perform the installation by clicking on '''Install - Version x.x.x)'''.<br />
* Click on '''Restart''' button.<br />
<br />
=Configuration=<br />
<br />
After install the Cobra4OptFlux plugin, some configurations must be performed.<br />
*You can access the '''Preferences''' option under the '''Help -> Preferences''' menu.<br><br />
<br />
[[Image:cobrapreferenceswindow.png|600px]]<br />
<br />
*After accessing the '''Preferences''' click over '''Matlab''' tab. <br />
*Here you must select the '''MATLAB Executable''' path. This path is mandatory to perform the MATLAB operations.<br />
*The '''Gurobi folder''' is optional but most of the available COBRA formulations use this solver thus this preference is highly recommendable.<br />
*The '''Show MATLAB Console Only''' is optional and when disable the MATLAB will be opened as a full application.<br />
* Click on '''Restart''' button if it is enable - Only happens when '''Gurobi Folder''' is added/changed.<br />
<br />
<b><i>And that's all!! You can press OK and if all is well defined the COBRA plugin for OptFlux can be used in full.</i></b><br></div>Admin