http://www.optflux.org/wiki/api.php?action=feedcontributions&user=Simao.soares&feedformat=atomOptflux - User contributions [en]2024-03-28T09:57:38ZUser contributionsMediaWiki 1.28.0http://www.optflux.org/wiki/index.php?title=Main_Page&diff=1943Main Page2014-10-21T14:31:56Z<p>Simao.soares: /* CEB */</p>
<hr />
<div><center><br />
[[Image:Optflux splash 20141020.png]]<br />
</center><br />
<br />
__NOTOC__<br />
<br />
<br />
{|<br />
|-<br />
|[[Image:1258649492 label new red.png]] <br />
||<br />
*'''New Optflux3 available! Download it here -> [http://sourceforge.net/projects/optflux/files/latest/download (Multi-platform)] <br><br />
A major new release of OptFlux is now available, with several important improvements and new features.<br><br />
Please visit also the new OptFlux website at [http://www.optflux.org www.optflux.org].<br><br />
'''A new tutorial is available in the section [[BeginnersTutorial]].'''<br />
|}<br />
<br />
'''SOURCEFORGE NOW AVAILABLE:''' - All the code is now available at sourceforge.<br />
<br />
* Go to the [http://sourceforge.net/projects/optflux/ OptFlux Sourceforge Project].<br />
* You can also subscribe the [http://sourceforge.net/export/rss2_keepsake.php?group_id=327485 RSS Feed] to keep track of all the changes, releases and news !<br />
<br />
<br />
'''OptFlux is published, Please cite using:'''<br />
<br />
*Isabel Rocha , Paulo Maia , Pedro Evangelista , Paulo Vilaça , Simão Soares , José P Pinto , Jens Nielsen , Kiran R Patil , Eugénio C Ferreira and Miguel Rocha.<br />
[http://www.biomedcentral.com/1752-0509/4/45 OptFlux: an open-source software platform for in silico metabolic engineering].<br />
''BMC Systems Biology'' 2010, '''4''':45<br />
<br />
*Miguel Rocha , Paulo Maia , Rui Mendes , José P Pinto , Eugénio C Ferreira , Jens Nielsen , Kiran Raosaheb Patil and Isabel Rocha. <br />
[http://www.biomedcentral.com/1471-2105/9/499/ Natural computation meta-heuristics for the in silico optimization of microbial strains].<br />
''BMC Bioinformatics'' 2008, '''9''':499<br />
<br />
*Kiran Raosaheb Patil , Isabel Rocha , Jochen Förster and Jens Nielsen. <br />
[http://www.biomedcentral.com/1471-2105/6/308/ Evolutionary programming as a platform for in silico metabolic engineering].<br />
''BMC Bioinformatics'' 2005, '''6''':308<br />
<br />
{|<br />
|-<br />
||<br />
'''Older versions:<br />
*'''OptFlux 2.4 with Add Reactions plug-in ''' Check the [[Plugins|plugins section]] for the download link and the documentation. <br><br />
*'''OptFlux 2.3 with Over and Under Expression plug-in ''' Check the [[Plugins|plugins section]] for the download link and the documentation. <br><br />
*'''Regulatory Tool''' Check the [[Downloads|downloads section]] and the [[Plugins|plugins documentation]]. <br />
|}<br />
<br />
Problems with SBML? Validate your sbml model [http://sbml.org/Facilities/Validator here]!<br />
<br />
== Introduction ==<br />
<br />
'''The OptFlux application includes a number of tools to support <font color="#FF7800">''in silico'' metabolic engineering</font>. The application allows the user to load a genome-scale model of a given organism. This will serve as the basis to simulate the <font color="#FF7800">wild type and mutants</font> (original strain with a set of selected gene deletions).'''<br />
<br />
<br />
<br />
'''The simulation of these strains will be conducted using a number of approaches (e.g. <font color="#FF7800">Flux-Balance Analysis, Minimization of Metabolic Adjustment or Regulatory On/Off Minimization of metabolic fluxes</font>) that allow the set of fluxes in the organism's metabolism to be determined, given a set of environmental constraints. The software also includes a number of optimization methods (e.g. <font color="#FF7800">Evolutionary Algorithms or Simulated Annealing</font>) to reach the best set of gene deletions given an objective function, typically related with a given industrial goal. It also integrates visualization tools from the BioVisualizer application.'''<br />
<br />
<br />
'''The OptFlux application is being developed taking as a basis the <font color="#FF7800">AIBench framework</font>. This is an environment for the development of Data Mining/ Bioinformatics tools, using the Java programming language. The details of this project, a collaboration between the universities of Minho (Portugal) and Vigo (Spain), as well as updated documentation can be found at the web site.''' <br />
<br />
<br />
== Institutions ==<br />
<br />
=== University of Minho ===<br />
'''[http://www.uminho.pt University of Minho]'''<br />
<br />
[[Image:Uminho.gif]] <br />
<br />
=== CEB ===<br />
<br />
'''[http://ceb.uminho.pt/ Centre of Biological Engineering]'''<br />
<br />
[[Image:Logoceb.png]]<br />
<br />
=== SilicoLife ===<br />
<br />
'''[http://www.silicolife.com SilicoLife]'''<br />
<br />
[[Image:Silicolife_logo_w.png]]<br />
<br />
== Powered By ==<br />
<br />
[[Image:Aibenchlogo.png]] [http://www.aibench.org www.aibench.org]<br />
<br />
[[Image:Sbml.jpg]] [http://www.sbml.org www.sbml.org]<br />
<br />
<br />
<br />
<br />
== License ==<br />
<br />
<br><font color="#FF7800"><b>Copyright 2009-2014<br><br />
[http://www.ceb.uminho.pt/ CEB - Centre of Biological Engineering]<br><br />
[http://www.uminho.pt/ University of Minho]<br><br />
[http://www.silicolife.com/ SilicoLife Lda.]<br />
<br><br />
<br>This is free software: you can redistribute it and/or modify<br />
<br>it under the terms of the GNU Public License as published by<br />
<br>the Free Software Foundation, either version 3 of the License, or<br />
<br>(at your option) any later version.<br />
<br><br />
<br>This code is distributed in the hope that it will be useful,<br />
<br>but WITHOUT ANY WARRANTY; without even the implied warranty of<br />
<br>MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the<br />
<br>GNU Public License for more details.<br />
<br><br />
<br>You should have received a copy of the GNU Public License<br />
<br>along with this code. If not, see [http://www.gnu.org/licenses/ http://www.gnu.org/licenses/]<br />
<br><br />
<br><font color="#FF7800">Created inside the SysBio Research Group [http://sysbio.di.uminho.pt/ (http://sysbio.di.uminho.pt)]<br />
</font><br />
<br><font color="#FF7800">Supported by SilicoLife Lda. [http://www.silicolife.com/ (http://www.silicolife.com)]<br />
</font><br />
<br />
<br />
[[Image:Gpl.png]]<br />
[http://www.gnu.org/licenses/gpl-3.0.html http://www.gnu.org/licenses/gpl-3.0.html]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=File:Logoceb.png&diff=1942File:Logoceb.png2014-10-21T14:31:33Z<p>Simao.soares: </p>
<hr />
<div></div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Main_Page&diff=1941Main Page2014-10-21T14:28:11Z<p>Simao.soares: /* License */</p>
<hr />
<div><center><br />
[[Image:Optflux splash 20141020.png]]<br />
</center><br />
<br />
__NOTOC__<br />
<br />
<br />
{|<br />
|-<br />
|[[Image:1258649492 label new red.png]] <br />
||<br />
*'''New Optflux3 available! Download it here -> [http://sourceforge.net/projects/optflux/files/latest/download (Multi-platform)] <br><br />
A major new release of OptFlux is now available, with several important improvements and new features.<br><br />
Please visit also the new OptFlux website at [http://www.optflux.org www.optflux.org].<br><br />
'''A new tutorial is available in the section [[BeginnersTutorial]].'''<br />
|}<br />
<br />
'''SOURCEFORGE NOW AVAILABLE:''' - All the code is now available at sourceforge.<br />
<br />
* Go to the [http://sourceforge.net/projects/optflux/ OptFlux Sourceforge Project].<br />
* You can also subscribe the [http://sourceforge.net/export/rss2_keepsake.php?group_id=327485 RSS Feed] to keep track of all the changes, releases and news !<br />
<br />
<br />
'''OptFlux is published, Please cite using:'''<br />
<br />
*Isabel Rocha , Paulo Maia , Pedro Evangelista , Paulo Vilaça , Simão Soares , José P Pinto , Jens Nielsen , Kiran R Patil , Eugénio C Ferreira and Miguel Rocha.<br />
[http://www.biomedcentral.com/1752-0509/4/45 OptFlux: an open-source software platform for in silico metabolic engineering].<br />
''BMC Systems Biology'' 2010, '''4''':45<br />
<br />
*Miguel Rocha , Paulo Maia , Rui Mendes , José P Pinto , Eugénio C Ferreira , Jens Nielsen , Kiran Raosaheb Patil and Isabel Rocha. <br />
[http://www.biomedcentral.com/1471-2105/9/499/ Natural computation meta-heuristics for the in silico optimization of microbial strains].<br />
''BMC Bioinformatics'' 2008, '''9''':499<br />
<br />
*Kiran Raosaheb Patil , Isabel Rocha , Jochen Förster and Jens Nielsen. <br />
[http://www.biomedcentral.com/1471-2105/6/308/ Evolutionary programming as a platform for in silico metabolic engineering].<br />
''BMC Bioinformatics'' 2005, '''6''':308<br />
<br />
{|<br />
|-<br />
||<br />
'''Older versions:<br />
*'''OptFlux 2.4 with Add Reactions plug-in ''' Check the [[Plugins|plugins section]] for the download link and the documentation. <br><br />
*'''OptFlux 2.3 with Over and Under Expression plug-in ''' Check the [[Plugins|plugins section]] for the download link and the documentation. <br><br />
*'''Regulatory Tool''' Check the [[Downloads|downloads section]] and the [[Plugins|plugins documentation]]. <br />
|}<br />
<br />
Problems with SBML? Validate your sbml model [http://sbml.org/Facilities/Validator here]!<br />
<br />
== Introduction ==<br />
<br />
'''The OptFlux application includes a number of tools to support <font color="#FF7800">''in silico'' metabolic engineering</font>. The application allows the user to load a genome-scale model of a given organism. This will serve as the basis to simulate the <font color="#FF7800">wild type and mutants</font> (original strain with a set of selected gene deletions).'''<br />
<br />
<br />
<br />
'''The simulation of these strains will be conducted using a number of approaches (e.g. <font color="#FF7800">Flux-Balance Analysis, Minimization of Metabolic Adjustment or Regulatory On/Off Minimization of metabolic fluxes</font>) that allow the set of fluxes in the organism's metabolism to be determined, given a set of environmental constraints. The software also includes a number of optimization methods (e.g. <font color="#FF7800">Evolutionary Algorithms or Simulated Annealing</font>) to reach the best set of gene deletions given an objective function, typically related with a given industrial goal. It also integrates visualization tools from the BioVisualizer application.'''<br />
<br />
<br />
'''The OptFlux application is being developed taking as a basis the <font color="#FF7800">AIBench framework</font>. This is an environment for the development of Data Mining/ Bioinformatics tools, using the Java programming language. The details of this project, a collaboration between the universities of Minho (Portugal) and Vigo (Spain), as well as updated documentation can be found at the web site.''' <br />
<br />
<br />
== Institutions ==<br />
<br />
=== University of Minho ===<br />
'''[http://www.uminho.pt University of Minho]'''<br />
<br />
[[Image:Uminho.gif]] <br />
<br />
=== CEB ===<br />
<br />
'''[http://ceb.uminho.pt/ Centre of Biological Engineering]'''<br />
<br />
[[Image:Logo_ibb.png]] <br />
<br />
<br />
=== SilicoLife ===<br />
<br />
'''[http://www.silicolife.com SilicoLife]'''<br />
<br />
[[Image:Silicolife_logo_w.png]]<br />
<br />
== Powered By ==<br />
<br />
[[Image:Aibenchlogo.png]] [http://www.aibench.org www.aibench.org]<br />
<br />
[[Image:Sbml.jpg]] [http://www.sbml.org www.sbml.org]<br />
<br />
<br />
<br />
<br />
== License ==<br />
<br />
<br><font color="#FF7800"><b>Copyright 2009-2014<br><br />
[http://www.ceb.uminho.pt/ CEB - Centre of Biological Engineering]<br><br />
[http://www.uminho.pt/ University of Minho]<br><br />
[http://www.silicolife.com/ SilicoLife Lda.]<br />
<br><br />
<br>This is free software: you can redistribute it and/or modify<br />
<br>it under the terms of the GNU Public License as published by<br />
<br>the Free Software Foundation, either version 3 of the License, or<br />
<br>(at your option) any later version.<br />
<br><br />
<br>This code is distributed in the hope that it will be useful,<br />
<br>but WITHOUT ANY WARRANTY; without even the implied warranty of<br />
<br>MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the<br />
<br>GNU Public License for more details.<br />
<br><br />
<br>You should have received a copy of the GNU Public License<br />
<br>along with this code. If not, see [http://www.gnu.org/licenses/ http://www.gnu.org/licenses/]<br />
<br><br />
<br><font color="#FF7800">Created inside the SysBio Research Group [http://sysbio.di.uminho.pt/ (http://sysbio.di.uminho.pt)]<br />
</font><br />
<br><font color="#FF7800">Supported by SilicoLife Lda. [http://www.silicolife.com/ (http://www.silicolife.com)]<br />
</font><br />
<br />
<br />
[[Image:Gpl.png]]<br />
[http://www.gnu.org/licenses/gpl-3.0.html http://www.gnu.org/licenses/gpl-3.0.html]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Main_Page&diff=1940Main Page2014-10-21T14:27:52Z<p>Simao.soares: /* License */</p>
<hr />
<div><center><br />
[[Image:Optflux splash 20141020.png]]<br />
</center><br />
<br />
__NOTOC__<br />
<br />
<br />
{|<br />
|-<br />
|[[Image:1258649492 label new red.png]] <br />
||<br />
*'''New Optflux3 available! Download it here -> [http://sourceforge.net/projects/optflux/files/latest/download (Multi-platform)] <br><br />
A major new release of OptFlux is now available, with several important improvements and new features.<br><br />
Please visit also the new OptFlux website at [http://www.optflux.org www.optflux.org].<br><br />
'''A new tutorial is available in the section [[BeginnersTutorial]].'''<br />
|}<br />
<br />
'''SOURCEFORGE NOW AVAILABLE:''' - All the code is now available at sourceforge.<br />
<br />
* Go to the [http://sourceforge.net/projects/optflux/ OptFlux Sourceforge Project].<br />
* You can also subscribe the [http://sourceforge.net/export/rss2_keepsake.php?group_id=327485 RSS Feed] to keep track of all the changes, releases and news !<br />
<br />
<br />
'''OptFlux is published, Please cite using:'''<br />
<br />
*Isabel Rocha , Paulo Maia , Pedro Evangelista , Paulo Vilaça , Simão Soares , José P Pinto , Jens Nielsen , Kiran R Patil , Eugénio C Ferreira and Miguel Rocha.<br />
[http://www.biomedcentral.com/1752-0509/4/45 OptFlux: an open-source software platform for in silico metabolic engineering].<br />
''BMC Systems Biology'' 2010, '''4''':45<br />
<br />
*Miguel Rocha , Paulo Maia , Rui Mendes , José P Pinto , Eugénio C Ferreira , Jens Nielsen , Kiran Raosaheb Patil and Isabel Rocha. <br />
[http://www.biomedcentral.com/1471-2105/9/499/ Natural computation meta-heuristics for the in silico optimization of microbial strains].<br />
''BMC Bioinformatics'' 2008, '''9''':499<br />
<br />
*Kiran Raosaheb Patil , Isabel Rocha , Jochen Förster and Jens Nielsen. <br />
[http://www.biomedcentral.com/1471-2105/6/308/ Evolutionary programming as a platform for in silico metabolic engineering].<br />
''BMC Bioinformatics'' 2005, '''6''':308<br />
<br />
{|<br />
|-<br />
||<br />
'''Older versions:<br />
*'''OptFlux 2.4 with Add Reactions plug-in ''' Check the [[Plugins|plugins section]] for the download link and the documentation. <br><br />
*'''OptFlux 2.3 with Over and Under Expression plug-in ''' Check the [[Plugins|plugins section]] for the download link and the documentation. <br><br />
*'''Regulatory Tool''' Check the [[Downloads|downloads section]] and the [[Plugins|plugins documentation]]. <br />
|}<br />
<br />
Problems with SBML? Validate your sbml model [http://sbml.org/Facilities/Validator here]!<br />
<br />
== Introduction ==<br />
<br />
'''The OptFlux application includes a number of tools to support <font color="#FF7800">''in silico'' metabolic engineering</font>. The application allows the user to load a genome-scale model of a given organism. This will serve as the basis to simulate the <font color="#FF7800">wild type and mutants</font> (original strain with a set of selected gene deletions).'''<br />
<br />
<br />
<br />
'''The simulation of these strains will be conducted using a number of approaches (e.g. <font color="#FF7800">Flux-Balance Analysis, Minimization of Metabolic Adjustment or Regulatory On/Off Minimization of metabolic fluxes</font>) that allow the set of fluxes in the organism's metabolism to be determined, given a set of environmental constraints. The software also includes a number of optimization methods (e.g. <font color="#FF7800">Evolutionary Algorithms or Simulated Annealing</font>) to reach the best set of gene deletions given an objective function, typically related with a given industrial goal. It also integrates visualization tools from the BioVisualizer application.'''<br />
<br />
<br />
'''The OptFlux application is being developed taking as a basis the <font color="#FF7800">AIBench framework</font>. This is an environment for the development of Data Mining/ Bioinformatics tools, using the Java programming language. The details of this project, a collaboration between the universities of Minho (Portugal) and Vigo (Spain), as well as updated documentation can be found at the web site.''' <br />
<br />
<br />
== Institutions ==<br />
<br />
=== University of Minho ===<br />
'''[http://www.uminho.pt University of Minho]'''<br />
<br />
[[Image:Uminho.gif]] <br />
<br />
=== CEB ===<br />
<br />
'''[http://ceb.uminho.pt/ Centre of Biological Engineering]'''<br />
<br />
[[Image:Logo_ibb.png]] <br />
<br />
<br />
=== SilicoLife ===<br />
<br />
'''[http://www.silicolife.com SilicoLife]'''<br />
<br />
[[Image:Silicolife_logo_w.png]]<br />
<br />
== Powered By ==<br />
<br />
[[Image:Aibenchlogo.png]] [http://www.aibench.org www.aibench.org]<br />
<br />
[[Image:Sbml.jpg]] [http://www.sbml.org www.sbml.org]<br />
<br />
<br />
<br />
<br />
== License ==<br />
<br />
<br><font color="#FF7800"><b>Copyright 2009-2014<br><br />
[http://www.ceb.uminho.pt/ CEB - Centre of Biological Engineering]<br><br />
[http://www.uminho.pt/ University of Minho]<br />
[http://www.silicolife.com/ SilicoLife Lda.]<br />
<br><br />
<br>This is free software: you can redistribute it and/or modify<br />
<br>it under the terms of the GNU Public License as published by<br />
<br>the Free Software Foundation, either version 3 of the License, or<br />
<br>(at your option) any later version.<br />
<br><br />
<br>This code is distributed in the hope that it will be useful,<br />
<br>but WITHOUT ANY WARRANTY; without even the implied warranty of<br />
<br>MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the<br />
<br>GNU Public License for more details.<br />
<br><br />
<br>You should have received a copy of the GNU Public License<br />
<br>along with this code. If not, see [http://www.gnu.org/licenses/ http://www.gnu.org/licenses/]<br />
<br><br />
<br><font color="#FF7800">Created inside the SysBio Research Group [http://sysbio.di.uminho.pt/ (http://sysbio.di.uminho.pt)]<br />
</font><br />
<br><font color="#FF7800">Supported by SilicoLife Lda. [http://www.silicolife.com/ (http://www.silicolife.com)]<br />
</font><br />
<br />
<br />
[[Image:Gpl.png]]<br />
[http://www.gnu.org/licenses/gpl-3.0.html http://www.gnu.org/licenses/gpl-3.0.html]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Main_Page&diff=1939Main Page2014-10-21T14:27:21Z<p>Simao.soares: </p>
<hr />
<div><center><br />
[[Image:Optflux splash 20141020.png]]<br />
</center><br />
<br />
__NOTOC__<br />
<br />
<br />
{|<br />
|-<br />
|[[Image:1258649492 label new red.png]] <br />
||<br />
*'''New Optflux3 available! Download it here -> [http://sourceforge.net/projects/optflux/files/latest/download (Multi-platform)] <br><br />
A major new release of OptFlux is now available, with several important improvements and new features.<br><br />
Please visit also the new OptFlux website at [http://www.optflux.org www.optflux.org].<br><br />
'''A new tutorial is available in the section [[BeginnersTutorial]].'''<br />
|}<br />
<br />
'''SOURCEFORGE NOW AVAILABLE:''' - All the code is now available at sourceforge.<br />
<br />
* Go to the [http://sourceforge.net/projects/optflux/ OptFlux Sourceforge Project].<br />
* You can also subscribe the [http://sourceforge.net/export/rss2_keepsake.php?group_id=327485 RSS Feed] to keep track of all the changes, releases and news !<br />
<br />
<br />
'''OptFlux is published, Please cite using:'''<br />
<br />
*Isabel Rocha , Paulo Maia , Pedro Evangelista , Paulo Vilaça , Simão Soares , José P Pinto , Jens Nielsen , Kiran R Patil , Eugénio C Ferreira and Miguel Rocha.<br />
[http://www.biomedcentral.com/1752-0509/4/45 OptFlux: an open-source software platform for in silico metabolic engineering].<br />
''BMC Systems Biology'' 2010, '''4''':45<br />
<br />
*Miguel Rocha , Paulo Maia , Rui Mendes , José P Pinto , Eugénio C Ferreira , Jens Nielsen , Kiran Raosaheb Patil and Isabel Rocha. <br />
[http://www.biomedcentral.com/1471-2105/9/499/ Natural computation meta-heuristics for the in silico optimization of microbial strains].<br />
''BMC Bioinformatics'' 2008, '''9''':499<br />
<br />
*Kiran Raosaheb Patil , Isabel Rocha , Jochen Förster and Jens Nielsen. <br />
[http://www.biomedcentral.com/1471-2105/6/308/ Evolutionary programming as a platform for in silico metabolic engineering].<br />
''BMC Bioinformatics'' 2005, '''6''':308<br />
<br />
{|<br />
|-<br />
||<br />
'''Older versions:<br />
*'''OptFlux 2.4 with Add Reactions plug-in ''' Check the [[Plugins|plugins section]] for the download link and the documentation. <br><br />
*'''OptFlux 2.3 with Over and Under Expression plug-in ''' Check the [[Plugins|plugins section]] for the download link and the documentation. <br><br />
*'''Regulatory Tool''' Check the [[Downloads|downloads section]] and the [[Plugins|plugins documentation]]. <br />
|}<br />
<br />
Problems with SBML? Validate your sbml model [http://sbml.org/Facilities/Validator here]!<br />
<br />
== Introduction ==<br />
<br />
'''The OptFlux application includes a number of tools to support <font color="#FF7800">''in silico'' metabolic engineering</font>. The application allows the user to load a genome-scale model of a given organism. This will serve as the basis to simulate the <font color="#FF7800">wild type and mutants</font> (original strain with a set of selected gene deletions).'''<br />
<br />
<br />
<br />
'''The simulation of these strains will be conducted using a number of approaches (e.g. <font color="#FF7800">Flux-Balance Analysis, Minimization of Metabolic Adjustment or Regulatory On/Off Minimization of metabolic fluxes</font>) that allow the set of fluxes in the organism's metabolism to be determined, given a set of environmental constraints. The software also includes a number of optimization methods (e.g. <font color="#FF7800">Evolutionary Algorithms or Simulated Annealing</font>) to reach the best set of gene deletions given an objective function, typically related with a given industrial goal. It also integrates visualization tools from the BioVisualizer application.'''<br />
<br />
<br />
'''The OptFlux application is being developed taking as a basis the <font color="#FF7800">AIBench framework</font>. This is an environment for the development of Data Mining/ Bioinformatics tools, using the Java programming language. The details of this project, a collaboration between the universities of Minho (Portugal) and Vigo (Spain), as well as updated documentation can be found at the web site.''' <br />
<br />
<br />
== Institutions ==<br />
<br />
=== University of Minho ===<br />
'''[http://www.uminho.pt University of Minho]'''<br />
<br />
[[Image:Uminho.gif]] <br />
<br />
=== CEB ===<br />
<br />
'''[http://ceb.uminho.pt/ Centre of Biological Engineering]'''<br />
<br />
[[Image:Logo_ibb.png]] <br />
<br />
<br />
=== SilicoLife ===<br />
<br />
'''[http://www.silicolife.com SilicoLife]'''<br />
<br />
[[Image:Silicolife_logo_w.png]]<br />
<br />
== Powered By ==<br />
<br />
[[Image:Aibenchlogo.png]] [http://www.aibench.org www.aibench.org]<br />
<br />
[[Image:Sbml.jpg]] [http://www.sbml.org www.sbml.org]<br />
<br />
<br />
<br />
<br />
== License ==<br />
<br />
<br><font color="#FF7800"><b>Copyright 2009<br><br />
[http://cctc.uminho.pt CCTC - Computer Science and Technology Center]<br><br />
[http://www.ceb.uminho.pt/ IBB-CEB - Institute for Biotechnology and Bioengineering - Centre of Biological Engineering]<br><br />
[http://www.uminho.pt/ University of Minho]<br />
[http://www.silicolife.com/ SilicoLife Lda.]<br />
<br><br />
<br>This is free software: you can redistribute it and/or modify<br />
<br>it under the terms of the GNU Public License as published by<br />
<br>the Free Software Foundation, either version 3 of the License, or<br />
<br>(at your option) any later version.<br />
<br><br />
<br>This code is distributed in the hope that it will be useful,<br />
<br>but WITHOUT ANY WARRANTY; without even the implied warranty of<br />
<br>MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the<br />
<br>GNU Public License for more details.<br />
<br><br />
<br>You should have received a copy of the GNU Public License<br />
<br>along with this code. If not, see [http://www.gnu.org/licenses/ http://www.gnu.org/licenses/]<br />
<br><br />
<br><font color="#FF7800">Created inside the SysBio Research Group [http://sysbio.di.uminho.pt/ (http://sysbio.di.uminho.pt)]<br />
</font><br />
<br><font color="#FF7800">Supported by SilicoLife Lda. [http://www.silicolife.com/ (http://www.silicolife.com)]<br />
</font><br />
<br />
<br />
[[Image:Gpl.png]]<br />
[http://www.gnu.org/licenses/gpl-3.0.html http://www.gnu.org/licenses/gpl-3.0.html]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Optflux:About&diff=1938Optflux:About2014-10-21T14:26:43Z<p>Simao.soares: </p>
<hr />
<div>CEB - Centre of Biological Engineering<br />
University of Minho<br />
<br />
SilicoLife - Computational Solutions for the Life Sciences<br />
<br />
Contact & Support: [mailto:support@optflux.org support@optflux.org]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Main_Page&diff=1937Main Page2014-10-21T14:25:23Z<p>Simao.soares: </p>
<hr />
<div><center><br />
[[Image:Optflux splash 20141020.png]]<br />
</center><br />
<br />
__NOTOC__<br />
<br />
<br />
{|<br />
|-<br />
|[[Image:1258649492 label new red.png]] <br />
||<br />
*'''New Optflux3 available! Download it here -> [http://sourceforge.net/projects/optflux/files/latest/download (Multi-platform)] <br><br />
A major new release of OptFlux is now available, with several important improvements and new features.<br><br />
Please visit also the new OptFlux website at [http://www.optflux.org www.optflux.org].<br><br />
'''A new tutorial is available in the section [[BeginnersTutorial]].'''<br />
|}<br />
<br />
'''SOURCEFORGE NOW AVAILABLE:''' - All the code is now available at sourceforge.<br />
<br />
* Go to the [http://sourceforge.net/projects/optflux/ OptFlux Sourceforge Project].<br />
* You can also subscribe the [http://sourceforge.net/export/rss2_keepsake.php?group_id=327485 RSS Feed] to keep track of all the changes, releases and news !<br />
<br />
<br />
'''OptFlux is published, Please cite using:'''<br />
<br />
*Isabel Rocha , Paulo Maia , Pedro Evangelista , Paulo Vilaça , Simão Soares , José P Pinto , Jens Nielsen , Kiran R Patil , Eugénio C Ferreira and Miguel Rocha.<br />
[http://www.biomedcentral.com/1752-0509/4/45 OptFlux: an open-source software platform for in silico metabolic engineering].<br />
''BMC Systems Biology'' 2010, '''4''':45<br />
<br />
*Miguel Rocha , Paulo Maia , Rui Mendes , José P Pinto , Eugénio C Ferreira , Jens Nielsen , Kiran Raosaheb Patil and Isabel Rocha. <br />
[http://www.biomedcentral.com/1471-2105/9/499/ Natural computation meta-heuristics for the in silico optimization of microbial strains].<br />
''BMC Bioinformatics'' 2008, '''9''':499<br />
<br />
*Kiran Raosaheb Patil , Isabel Rocha , Jochen Förster and Jens Nielsen. <br />
[http://www.biomedcentral.com/1471-2105/6/308/ Evolutionary programming as a platform for in silico metabolic engineering].<br />
''BMC Bioinformatics'' 2005, '''6''':308<br />
<br />
{|<br />
|-<br />
||<br />
'''Older versions:<br />
*'''OptFlux 2.4 with Add Reactions plug-in ''' Check the [[Plugins|plugins section]] for the download link and the documentation. <br><br />
*'''OptFlux 2.3 with Over and Under Expression plug-in ''' Check the [[Plugins|plugins section]] for the download link and the documentation. <br><br />
*'''Regulatory Tool''' Check the [[Downloads|downloads section]] and the [[Plugins|plugins documentation]]. <br />
|}<br />
<br />
Problems with SBML? Validate your sbml model [http://sbml.org/Facilities/Validator here]!<br />
<br />
== Introduction ==<br />
<br />
'''The OptFlux application includes a number of tools to support <font color="#FF7800">''in silico'' metabolic engineering</font>. The application allows the user to load a genome-scale model of a given organism. This will serve as the basis to simulate the <font color="#FF7800">wild type and mutants</font> (original strain with a set of selected gene deletions).'''<br />
<br />
<br />
<br />
'''The simulation of these strains will be conducted using a number of approaches (e.g. <font color="#FF7800">Flux-Balance Analysis, Minimization of Metabolic Adjustment or Regulatory On/Off Minimization of metabolic fluxes</font>) that allow the set of fluxes in the organism's metabolism to be determined, given a set of environmental constraints. The software also includes a number of optimization methods (e.g. <font color="#FF7800">Evolutionary Algorithms or Simulated Annealing</font>) to reach the best set of gene deletions given an objective function, typically related with a given industrial goal. It also integrates visualization tools from the BioVisualizer application.'''<br />
<br />
<br />
'''The OptFlux application is being developed taking as a basis the <font color="#FF7800">AIBench framework</font>. This is an environment for the development of Data Mining/ Bioinformatics tools, using the Java programming language. The details of this project, a collaboration between the universities of Minho (Portugal) and Vigo (Spain), as well as updated documentation can be found at the web site.''' <br />
<br />
<br />
== Institutions ==<br />
<br />
=== University of Minho ===<br />
'''[http://www.uminho.pt University of Minho]'''<br />
<br />
[[Image:Uminho.gif]] <br />
<br />
=== IBB-CEB ===<br />
<br />
'''[http://www.ibb.pt/ IBB - Institute for Biotechnology and Bioengineering]'''<br />
<br />
'''[http://ceb.uminho.pt/ Centre of Biological Engineering]'''<br />
<br />
[[Image:Logo_ibb.png]] <br />
<br />
=== CCTC ===<br />
<br />
'''[http://cctc.di.uminho.pt CCTC - Computer Science and Technology Center]'''<br />
<br />
[[Image:Logo_cctc.png]]<br />
<br />
=== SilicoLife ===<br />
<br />
'''[http://www.silicolife.com SilicoLife]'''<br />
<br />
[[Image:Silicolife_logo_w.png]]<br />
<br />
== Powered By ==<br />
<br />
[[Image:Aibenchlogo.png]] [http://www.aibench.org www.aibench.org]<br />
<br />
[[Image:Sbml.jpg]] [http://www.sbml.org www.sbml.org]<br />
<br />
<br />
<br />
<br />
== License ==<br />
<br />
<br><font color="#FF7800"><b>Copyright 2009<br><br />
[http://cctc.uminho.pt CCTC - Computer Science and Technology Center]<br><br />
[http://www.ceb.uminho.pt/ IBB-CEB - Institute for Biotechnology and Bioengineering - Centre of Biological Engineering]<br><br />
[http://www.uminho.pt/ University of Minho]<br />
[http://www.silicolife.com/ SilicoLife Lda.]<br />
<br><br />
<br>This is free software: you can redistribute it and/or modify<br />
<br>it under the terms of the GNU Public License as published by<br />
<br>the Free Software Foundation, either version 3 of the License, or<br />
<br>(at your option) any later version.<br />
<br><br />
<br>This code is distributed in the hope that it will be useful,<br />
<br>but WITHOUT ANY WARRANTY; without even the implied warranty of<br />
<br>MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the<br />
<br>GNU Public License for more details.<br />
<br><br />
<br>You should have received a copy of the GNU Public License<br />
<br>along with this code. If not, see [http://www.gnu.org/licenses/ http://www.gnu.org/licenses/]<br />
<br><br />
<br><font color="#FF7800">Created inside the SysBio Research Group [http://sysbio.di.uminho.pt/ (http://sysbio.di.uminho.pt)]<br />
</font><br />
<br><font color="#FF7800">Supported by SilicoLife Lda. [http://www.silicolife.com/ (http://www.silicolife.com)]<br />
</font><br />
<br />
<br />
[[Image:Gpl.png]]<br />
[http://www.gnu.org/licenses/gpl-3.0.html http://www.gnu.org/licenses/gpl-3.0.html]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=File:Optflux_splash_20141020.png&diff=1936File:Optflux splash 20141020.png2014-10-21T14:24:44Z<p>Simao.soares: </p>
<hr />
<div></div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Optflux:Acknowledgements&diff=1800Optflux:Acknowledgements2013-11-13T16:46:01Z<p>Simao.soares: /* Acknowledgements */</p>
<hr />
<div>== Acknowledgements ==<br />
<br />
<br />
This work has been developed with the support of the following Institutions:<br />
<br />
*European Comission under the scope of the project [http://sysbio.di.uminho.pt/sysinbio.php SYSINBIO - Systems Biology as a Driver for Industrial Biotechnology] - Coordination and support action (call FP7-KBBE-2007-1)<br />
<br />
*Dupont under the scope of the project [http://www.deb.uminho.pt/News/Dupont-EN.aspx Development of a user-friendly software platform for the rational design of improved microbial strains] - Dupont European University Support Program<br />
<br />
*Portuguese Science and Technology Foundation under the scope of the MIT-Portugal framework project [http://biopseg.deb.uminho.pt/MIT-Project/default.html Bridging Systems and Synthetic Biology for the development of Improved Microbial Cell Factories]<br />
<br />
*[http://www.silicolife.com SilicoLife] - Computational Biology Solutions for the Life Sciences<br />
<br />
*[http://www.silicolife.com/pem PEM – Platform for Metabolic Engineering], developed by SilicoLife Lda. and University of Minho, co-funded by the European Regional Development Fund (ERDF) under the Operational Programme for Competitiveness Factors (COMPETE).</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Optflux:Acknowledgements&diff=1799Optflux:Acknowledgements2013-11-13T16:45:42Z<p>Simao.soares: /* Acknowledgements */</p>
<hr />
<div>== Acknowledgements ==<br />
<br />
<br />
This work has been developed with the support of the following Institutions:<br />
<br />
*European Comission under the scope of the project [http://sysbio.di.uminho.pt/sysinbio.php SYSINBIO - Systems Biology as a Driver for Industrial Biotechnology] - Coordination and support action (call FP7-KBBE-2007-1)<br />
<br />
*Dupont under the scope of the project [http://www.deb.uminho.pt/News/Dupont-EN.aspx Development of a user-friendly software platform for the rational design of improved microbial strains] - Dupont European University Support Program<br />
<br />
*Portuguese Science and Technology Foundation under the scope of the MIT-Portugal framework project [http://biopseg.deb.uminho.pt/MIT-Project/default.html Bridging Systems and Synthetic Biology for the development of Improved Microbial Cell Factories]<br />
<br />
*[http://www.silicolife.com SilicoLife] - Computational Biology Solutions for the Life Sciences<br />
<br />
*[http://www.silicolife.com/pem PEM – Platform for Metabolic Engineering], developed by SilicoLife Lda. and University of Minho, co-funded by the European Regional Development Fund (ERDF) under the Operational Programme for Competitiveness Factors (COMPETE) and contracted with ADI (Nº23060).</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-import&diff=1642Ms-import2013-03-25T18:34:40Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: import}}<br />
<br />
[[File:Operations-import.png]]<br />
<br />
The Model-seed works in two levels, a local server and The seed server, it is possible to import to the local model-seed: <br />
*biochemistry data<br />
*genome annotations<br />
*mappings <br />
And use these data elements in local operations.<br />
<br />
== Import biochemistry ==<br />
To import a biochemistry select the option Plugin Builder > MSeed > Import > Biochemistry and choose a name for the local data element. OptFlux will then ask Model-seed to retrieve the latest biochemistry version from The Seed and to create local of version with the selected name.<br /> <br />
[[File:Import-biochem.png]]<br />
<br />
== Import mappings ==<br />
To import a mapping select the option Plugin Builder > MSeed > Import > Mappings and choose a name for the local data element and the local biochemistry to be associated to the new mapping. OptFlux will then ask Model-seed to retrieve the mapping from The Seed and to create a local of version with the inserted name and connected to the selected local biochemistry.<br /> <br />
<br />
[[File:Import-mappings.png]]<br />
<br />
== Import genome ==<br />
To import a genome select the option Plugin Builder > MSeed > Import > Mappings:<br />
*choose one of the available genomes in The Seed<br />
*a name for the local annotation<br />
*the mapping available locally to be used. <br />
A new genome annotation will be created in the local model-seed with the inserted name.<br /><br />
[[File:Import-genome.png]]<br />
<br />
<br /><br />
<br />[[MS-howto|''Return to the Model-seed How-to Index'']]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Merge-biochems&diff=1641Merge-biochems2013-03-25T18:34:16Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: merge}}<br />
<br />
[[File:Operations.png]]<br />
<br />
== Merge biochemistries ==<br />
To merge two local biochemistries select the option Plugin Builder > MSeed > Operations > Merge biochemistry... and select the source biochemistry and the destination biochemistry, the destination biochemistry will be updated with the information from the source biochemistry. This operation only works with local elements.<br /> <br />
[[File:Merge-biochem.png]]<br />
<br />
<br /><br />
<br />[[MS-howto|''Return to the Model-seed How-to Index'']]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-commit&diff=1640Ms-commit2013-03-25T18:34:03Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: commit (from OptFlux to MSeed)}}<br />
The import operations of elements from OptFlux to the local model-seed are grouped in the menu Plugin Builder > MSeed > Commit.<br /><br />
[[File:Ms-commit.png]]<br />
<br />
<br />
==Commit model==<br />
To import a model from OptFlux to the local model-seed go to Plugin Builder > MSeed > Commit > Model. The user has to select the OptFlux project and insert a name for the new model, the model from the selected project will be created in the local model-seed with the inserted name.<br /><br />
[[File:Commit-model.png]]<br />
<br />
==Commit media==<br />
To import a Media/Environmental condition from OptFlux to the local model-seed go to Plugin Builder > MSeed > Commit > Media. The user has to select: <br />
*the local model-seed biochemistry <br />
*the OptFlux project containing the Environmental Condition<br />
*the Environmental condition name. <br />
A new Media will be created in the local model-seed from the selected Environmental Condition.<br /><br />
[[File:Commit-media.png]]<br />
<br />
<br /><br />
<br />[[MS-howto|''Return to the Model-seed How-to Index'']]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-pull&diff=1639Ms-pull2013-03-25T18:33:45Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: pull}}<br />
The import operations of elements from local model-seed to OptFlux are grouped in the menu Plugin Builder > MSeed > Pull.<br /><br />
[[File:Operations-pull.png]]<br />
<br />
<br />
==Pull model==<br />
To import a model from the local model-seed go to Plugin Builder > MSeed > Pull > Model. The user has to select the id of the local model to be imported and to identify the external compartment. A new project with the selected model will be created in the OptFlux workspace.<br /><br />
[[File:Pull-model.png]]<br />
<br />
==Pull media==<br />
To import a Media/Environmental condition from the local model-seed go to Plugin Builder > MSeed > Pull > Media. The user has to select: <br />
*the local model-seed biochemistry <br />
*the OptFlux project where the media will be added<br />
*the Media to be pulled (that is retrieved directly from The Seed). <br />
A new Environmental condition will be created in the selected OptFlux project.<br /><br />
[[File:Pull-media.png]]<br />
<br />
<br /><br />
<br />[[MS-howto|''Return to the Model-seed How-to Index'']]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-loginout&diff=1638Ms-loginout2013-03-25T18:33:26Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: login/logout}}<br />
<br />
[[File:logout.png]]<br />
== Login ==<br />
To login into your Model-seed account select Plugin Builder > MSeed > Login.<br /> <br />
[[File:login.png]]<br /> <br />
Insert your user name and password and press OK to complete the login operation.<br /> <br />
If you need a new account go to http://seed-viewer.theseed.org/.<br />
== Logout ==<br />
To logout from the account that is currently active just select Plugin Builder > MSeed > Logout.<br />
<br />
<br /><br />
<br />[[MS-howto|''Return to the Model-seed How-to Index'']]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-fba&diff=1637Ms-fba2013-03-25T18:33:05Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: Model FBA}}<br />
<br />
[[File:Operations-model-fba.png]]<br /><br />
The operations to perform FBA simulations in model-seed with local model-seed models are grouped in the menu Plugin Builder > MSeed > Operations > Model > FBA.<br />
<br />
==Wild-type FBA ==<br />
To do a Wild-type simulation go to Plugin Builder > MSeed > Operations > Model > FBA > Wild Type and select the local model-seed to use and the biochemistry and media to be used in the simulation.<br /><br />
A simulation result will be created in the OptFlux workspace.<br /><br />
[[File:Model-fba-wt.png]]<br />
<br />
==Reaction KO FBA==<br />
To perform a reaction knock-out simulation go to Plugin Builder > MSeed > Operations > Model > FBA > Reaction KO and select:<br />
*the local model-seed<br />
*the biochemisty<br />
*media <br />
*reactions to be turned off in the simulation.<br /><br />
A simulation result will be created in the OptFlux workspace.<br /><br />
[[File:Model-fba-reactions.png]]<br />
<br />
==Gene KO FBA==<br />
N/A<br />
<br />
<br /><br />
<br />[[MS-howto|''Return to the Model-seed How-to Index'']]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-model&diff=1636Ms-model2013-03-25T18:32:31Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: model}}<br />
[[File:Operations-model.png]]<br /><br />
The operations to create a new model and to perform FBA simulations using Model-seed and the local model-seed data are grouped in the menu Plugin Builder > MSeed > Operations > Model.<br />
==Build a model==<br />
To build a model from an annotation in the local model-seed go to the menu Plugin Builder > MSeed > Operations > Model > build. The user needs to select the annotation (from local model-seed) to be used in the model reconstruction process and the name for the new model. A new model will be added to the local model-seed with the defined name. <br /><br />
[[File:Model-build.png]]<br />
==[[Ms-fba | Model FBA]]==<br />
[[Ms-fba | Quick how-to to perform Wild-type and Reaction KO simulations.]]<br />
<br />
<br /><br />
<br />[[MS-howto|''Return to the Model-seed How-to Index'']]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-loginout&diff=1635Ms-loginout2013-03-25T18:28:08Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: login/logout}}<br />
<br />
[[File:logout.png]]<br />
== Login ==<br />
To login into your Model-seed account select MSeed>Login.<br /> <br />
[[File:login.png]]<br /> <br />
Insert your user name and password and press OK to complete the login operation.<br /> <br />
If you need a new account go to http://seed-viewer.theseed.org/.<br />
== Logout ==<br />
To logout from the account that is currently active just select MSeed>Logout.<br />
<br />
<br /><br />
<br />[[MS-howto|''Return to the Model-seed How-to Index'']]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-pull&diff=1634Ms-pull2013-03-25T18:27:57Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: pull}}<br />
The import operations of elements from local model-seed to OptFlux are grouped in the menu MSeed > Pull.<br /><br />
[[File:Operations-pull.png]]<br />
<br />
<br />
==Pull model==<br />
To import a model from the local model-seed go to MSeed > Pull > Model. The user has to select the id of the local model to be imported and to identify the external compartment. A new project with the selected model will be created in the OptFlux workspace.<br /><br />
[[File:Pull-model.png]]<br />
<br />
==Pull media==<br />
To import a Media/Environmental condition from the local model-seed go to MSeed > Pull > Media. The user has to select: <br />
*the local model-seed biochemistry <br />
*the OptFlux project where the media will be added<br />
*the Media to be pulled (that is retrieved directly from The Seed). <br />
A new Environmental condition will be created in the selected OptFlux project.<br /><br />
[[File:Pull-media.png]]<br />
<br />
<br /><br />
<br />[[MS-howto|''Return to the Model-seed How-to Index'']]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-commit&diff=1633Ms-commit2013-03-25T18:27:50Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: commit (from OptFlux to MSeed)}}<br />
The import operations of elements from OptFlux to the local model-seed are grouped in the menu MSeed > Commit.<br /><br />
[[File:Ms-commit.png]]<br />
<br />
<br />
==Commit model==<br />
To import a model from OptFlux to the local model-seed go to MSeed > Commit > Model. The user has to select the OptFlux project and insert a name for the new model, the model from the selected project will be created in the local model-seed with the inserted name.<br /><br />
[[File:Commit-model.png]]<br />
<br />
==Commit media==<br />
To import a Media/Environmental condition from OptFlux to the local model-seed go to MSeed > Commit > Media. The user has to select: <br />
*the local model-seed biochemistry <br />
*the OptFlux project containing the Environmental Condition<br />
*the Environmental condition name. <br />
A new Media will be created in the local model-seed from the selected Environmental Condition.<br /><br />
[[File:Commit-media.png]]<br />
<br />
<br /><br />
<br />[[MS-howto|''Return to the Model-seed How-to Index'']]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Merge-biochems&diff=1632Merge-biochems2013-03-25T18:27:43Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: merge}}<br />
<br />
[[File:Operations.png]]<br />
<br />
== Merge biochemistries ==<br />
To merge two local biochemistries select the option MSeed > Operations > Merge biochemistry... and select the source biochemistry and the destination biochemistry, the destination biochemistry will be updated with the information from the source biochemistry. This operation only works with local elements.<br /> <br />
[[File:Merge-biochem.png]]<br />
<br />
<br /><br />
<br />[[MS-howto|''Return to the Model-seed How-to Index'']]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-import&diff=1631Ms-import2013-03-25T18:27:35Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: import}}<br />
<br />
[[File:Operations-import.png]]<br />
<br />
The Model-seed works in two levels, a local server and The seed server, it is possible to import to the local model-seed: <br />
*biochemistry data<br />
*genome annotations<br />
*mappings <br />
And use these data elements in local operations.<br />
<br />
== Import biochemistry ==<br />
To import a biochemistry select the option MSeed > Import > Biochemistry and choose a name for the local data element. OptFlux will then ask Model-seed to retrieve the latest biochemistry version from The Seed and to create local of version with the selected name.<br /> <br />
[[File:Import-biochem.png]]<br />
<br />
== Import mappings ==<br />
To import a mapping select the option MSeed > Import > Mappings and choose a name for the local data element and the local biochemistry to be associated to the new mapping. OptFlux will then ask Model-seed to retrieve the mapping from The Seed and to create a local of version with the inserted name and connected to the selected local biochemistry.<br /> <br />
<br />
[[File:Import-mappings.png]]<br />
<br />
== Import genome ==<br />
To import a genome select the option MSeed > Import > Mappings:<br />
*choose one of the available genomes in The Seed<br />
*a name for the local annotation<br />
*the mapping available locally to be used. <br />
A new genome annotation will be created in the local model-seed with the inserted name.<br /><br />
[[File:Import-genome.png]]<br />
<br />
<br /><br />
<br />[[MS-howto|''Return to the Model-seed How-to Index'']]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-fba&diff=1630Ms-fba2013-03-25T18:27:25Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: Model FBA}}<br />
<br />
[[File:Operations-model-fba.png]]<br /><br />
The operations to perform FBA simulations in model-seed with local model-seed models are grouped in the menu MSeed > Operations > Model > FBA.<br />
<br />
==Wild-type FBA ==<br />
To do a Wild-type simulation go to MSeed > Operations > Model > FBA > Wild Type and select the local model-seed to use and the biochemisty and media to be used in the simulation.<br /><br />
A simulation result will be created in the OptFlux workspace.<br /><br />
[[File:Model-fba-wt.png]]<br />
<br />
==Reaction KO FBA==<br />
To perform a reaction knock-out simulation go to MSeed > Operations > Model > FBA > Reaction KO and select:<br />
*the local model-seed<br />
*the biochemisty<br />
*media <br />
*reactions to be turned off in the simulation.<br /><br />
A simulation result will be created in the OptFlux workspace.<br /><br />
[[File:Model-fba-reactions.png]]<br />
<br />
==Gene KO FBA==<br />
N/A<br />
<br />
<br /><br />
<br />[[MS-howto|''Return to the Model-seed How-to Index'']]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-model&diff=1629Ms-model2013-03-25T18:26:54Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: model}}<br />
[[File:Operations-model.png]]<br /><br />
The operations to create a new model and to perform FBA simulations using Model-seed and the local model-seed data are grouped in the menu MSeed > Operations > Model.<br />
==Build a model==<br />
To build a model from an annotation in the local model-seed go to the menu MSeed > Operations > Model > build. The user needs to select the annotation (from local model-seed) to be used in the model reconstruction process and the name for the new model. A new model will be added to the local model-seed with the defined name. <br /><br />
[[File:Model-build.png]]<br />
==[[Ms-fba | Model FBA]]==<br />
[[Ms-fba | Quick how-to to perform Wild-type and Reaction KO simulations.]]<br />
<br />
<br /><br />
<br />[[MS-howto|''Return to the Model-seed How-to Index'']]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-model&diff=1628Ms-model2013-03-25T18:25:30Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: model}}<br />
[[File:Operations-model.png]]<br /><br />
The operations to create a new model and to perform FBA simulations using Model-seed and the local model-seed data are grouped in the menu MSeed > Operations > Model.<br />
==Build a model==<br />
To build a model from an annotation in the local model-seed go to the menu MSeed > Operations > Model > build. The user needs to select the annotation (from local model-seed) to be used in the model reconstruction process and the name for the new model. A new model will be added to the local model-seed with the defined name. <br /><br />
[[File:Model-build.png]]<br />
==[[Ms-fba | Model FBA]]==<br />
[[Ms-fba | Quick how-to to perform Wild-type and Reaction KO simulations.]]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-model&diff=1627Ms-model2013-03-25T18:25:16Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: model}}<br />
[[File:Operations-model.png]]<br />
The operations to create a new model and to perform FBA simulations using Model-seed and the local model-seed data are grouped in the menu MSeed > Operations > Model.<br />
==Build a model==<br />
To build a model from an annotation in the local model-seed go to the menu MSeed > Operations > Model > build. The user needs to select the annotation (from local model-seed) to be used in the model reconstruction process and the name for the new model. A new model will be added to the local model-seed with the defined name. <br /><br />
[[File:Model-build.png]]<br />
==[[Ms-fba | Model FBA]]==<br />
[[Ms-fba | Quick how-to to perform Wild-type and Reaction KO simulations.]]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-model&diff=1626Ms-model2013-03-25T18:21:09Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: model}}<br />
[[File:Operations-model.png]]<br />
==Build a model==<br />
[[File:Model-build.png]]<br />
==[[Ms-fba | Model FBA]]==<br />
[[Ms-fba | Quick how-to to perform Wild-type and Reaction KO simulations.]]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=File:Model-build.png&diff=1625File:Model-build.png2013-03-25T18:20:31Z<p>Simao.soares: </p>
<hr />
<div></div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=File:Operations-model.png&diff=1624File:Operations-model.png2013-03-25T18:20:02Z<p>Simao.soares: </p>
<hr />
<div></div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-model&diff=1623Ms-model2013-03-25T18:19:34Z<p>Simao.soares: /* Model FBA */</p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: model}}<br />
<br />
==Build a model==<br />
<br />
==[[Ms-fba | Model FBA]]==<br />
Quick how-to to perform Wild-type and Reaction KO simulations.</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-model&diff=1622Ms-model2013-03-25T18:19:10Z<p>Simao.soares: Created page with "{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: model}} ==Build a model== == Model FBA=="</p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: model}}<br />
<br />
==Build a model==<br />
<br />
==[[Ms-fba | Model FBA]]==</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=MS-howto&diff=1621MS-howto2013-03-25T18:18:44Z<p>Simao.soares: /* Model-seed plug-in operations */</p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3}}<br />
<br />
The Model-seed operations are located in the menu Plug-in Builder -> MSeed.<br /> <br />
If the MS plug-in is not yet loaded in OptFlux, just go to to Plug-in Builder -> Create... and select the MS XML file, OptFlux will then automatically build the new plug-in.<br /><br />
In the log window (bottom of the OptFlux window) it is possible to see the communication between OptFlux and Model-seed and the commands that are being executed.<br />
<br />
== Model-seed plug-in operations ==<br />
[[File:Menu-ms.png]]<br />
*[[ms-loginout | Login: operation to login in the local model-seed]]<br />
*[[ms-loginout | Logout: operation to logout]]<br />
*[[ms-pull | Pull (from MSeed to OptFlux):]]<br />
**[[ms-pull#Pull_model | Model: import a model from model-seed to OptFlux]]<br />
**[[ms-pull#Pull_media | Media: import a media from model-seed to OptFlux]]<br />
* [[ms-commit | Commit (from OptFlux to MSeed):]]<br />
**[[ms-commit#Commit_model |Model: send a model from OptFlux to model-seed]]<br />
**[[ms-commit#Commit_media |Media: send a media from OptFlux to model-seed]]<br />
*[[merge-biochems | Merge Biochemistry: merge two biochemistries in local model-seed]]<br />
*[[ms-import | Import from server to local model-seed:]]<br />
**[[ms-import#Import_biochemistry | Biochemistry: import biochemistry]]<br />
**[[ms-import#Import_mappings | Mappings: import mappings ]]<br />
**[[ms-import#Import_genome | Genome: import annotation]]<br />
*[[ms-model | Model]]<br />
**[[ms-model | Build: build a model in local model-seed]]<br />
**[[ms-fba | FBA]]<br />
***[[ms-fba#Wild-type_FBA | Wild Type]]<br />
***[[ms-fba#Reaction_KO_FBA | Reaction KO]]<br />
***[[ms-fba#Gene_KO_FBA | Gene KO]]<br />
<br />
== Technical documentation for developers ==<br />
*[[Create a new plugin using the plugin builder (pdf)]]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=MS-howto&diff=1620MS-howto2013-03-25T18:18:26Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3}}<br />
<br />
The Model-seed operations are located in the menu Plug-in Builder -> MSeed.<br /> <br />
If the MS plug-in is not yet loaded in OptFlux, just go to to Plug-in Builder -> Create... and select the MS XML file, OptFlux will then automatically build the new plug-in.<br /><br />
In the log window (bottom of the OptFlux window) it is possible to see the communication between OptFlux and Model-seed and the commands that are being executed.<br />
<br />
== Model-seed plug-in operations ==<br />
[[File:Menu-ms.png]]<br />
*[[ms-loginout | Login: operation to login in the local model-seed]]<br />
*[[ms-loginout | Logout: operation to logout]]<br />
*[[ms-pull | Pull (from MSeed to OptFlux):]]<br />
**[[ms-pull#Pull_model | Model: import a model from model-seed to OptFlux]]<br />
**[[ms-pull#Pull_media | Media: import a media from model-seed to OptFlux]]<br />
* [[ms-commit | Commit (from OptFlux to MSeed):]]<br />
**[[ms-commit#Commit_model |Model: send a model from OptFlux to model-seed]]<br />
**[[ms-commit#Commit_media |Media: send a media from OptFlux to model-seed]]<br />
*[[merge-biochems | Merge Biochemistry: merge two biochemistries in local model-seed]]<br />
*[[ms-import | Import from server to local model-seed:]]<br />
**[[ms-import#Import_biochemistry | Biochemistry: import biochemistry]]<br />
**[[ms-import#Import_mappings | Mappings: import mappings ]]<br />
**[[ms-import#Import_genome | Genome: import annotation]]<br />
*[[ms-model | Model]]<br />
**[[ms-model | Build: build a model in local model-seed]]<br />
**[[ms-fba | FBA]]<br />
***[[ms-fba#Wild-type | Wild Type]]<br />
***[[ms-fba#Reaction_KO_FBA | Reaction KO]]<br />
***[[ms-fba#Gene_KO_FBA | Gene KO]]<br />
<br />
== Technical documentation for developers ==<br />
*[[Create a new plugin using the plugin builder (pdf)]]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=MS-howto&diff=1619MS-howto2013-03-25T18:16:40Z<p>Simao.soares: /* Model-seed plug-in operations */</p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3}}<br />
<br />
The Model-seed operations are located in the menu Plug-in Builder -> MSeed.<br /> <br />
If the MS plug-in is not yet loaded in OptFlux, just go to to Plug-in Builder -> Create... and select the MS XML file, OptFlux will then automatically build the new plug-in.<br /><br />
In the log window (bottom of the OptFlux window) it is possible to see the communication between OptFlux and Model-seed and the commands that are being executed.<br />
<br />
== Model-seed plug-in operations ==<br />
[[File:Menu-ms.png]]<br />
*[[ms-loginout | Login: operation to login in the local model-seed]]<br />
*[[ms-loginout | Logout: operation to logout]]<br />
*[[ms-pull | Pull (from MSeed to OptFlux):]]<br />
**[[ms-pull#Pull_model | Model: import a model from model-seed to OptFlux]]<br />
**[[ms-pull#Pull_media | Media: import a media from model-seed to OptFlux]]<br />
* [[ms-commit | Commit (from OptFlux to MSeed):]]<br />
**[[ms-commit#Commit_model |Model: send a model from OptFlux to model-seed]]<br />
**[[ms-commit#Commit_media |Media: send a media from OptFlux to model-seed]]<br />
*[[merge-biochems | Merge Biochemistry: merge two biochemistries in local model-seed]]<br />
*[[ms-import | Import from server to local model-seed:]]<br />
**[[ms-import#Import_biochemistry | Biochemistry: import biochemistry]]<br />
**[[ms-import#Import_mappings | Mappings: import mappings ]]<br />
**[[ms-import#Import_genome | Genome: import annotation]]<br />
*[[ms-model | Model]]<br />
**[[ms-model | Build: build a model in local model-seed]]<br />
**[[ms-fba#Wild-type_FBA | FBA]]<br />
***[[ms-fba | Wild Type]]<br />
***[[ms-fba#Reaction_KO_FBA | Reaction KO]]<br />
***[[ms-fba#Gene_KO_FBA | Gene KO]]<br />
<br />
== Technical documentation for developers ==<br />
*[[Create a new plugin using the plugin builder (pdf)]]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=MS-howto&diff=1618MS-howto2013-03-25T18:15:00Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3}}<br />
<br />
The Model-seed operations are located in the menu Plug-in Builder -> MSeed.<br /> <br />
If the MS plug-in is not yet loaded in OptFlux, just go to to Plug-in Builder -> Create... and select the MS XML file, OptFlux will then automatically build the new plug-in.<br /><br />
In the log window (bottom of the OptFlux window) it is possible to see the communication between OptFlux and Model-seed and the commands that are being executed.<br />
<br />
== Model-seed plug-in operations ==<br />
[[File:Menu-ms.png]]<br />
*[[ms-loginout | Login: operation to login in the local model-seed]]<br />
*[[ms-loginout | Logout: operation to logout]]<br />
*[[ms-pull | Pull (from MSeed to OptFlux):]]<br />
**[[ms-pull#Pull_model | Model: import a model from model-seed to OptFlux]]<br />
**[[ms-pull#Pull_media | Media: import a media from model-seed to OptFlux]]<br />
* [[ms-commit | Commit (from OptFlux to MSeed):]]<br />
**[[ms-commit#Commit_model |Model: send a model from OptFlux to model-seed]]<br />
**[[ms-commit#Commit_media |Media: send a media from OptFlux to model-seed]]<br />
*[[merge-biochems | Merge Biochemistry: merge two biochemistries in local model-seed]]<br />
*[[ms-import | Import from server to local model-seed:]]<br />
**[[ms-import#Import_biochemistry | Biochemistry: import biochemistry]]<br />
**[[ms-import#Import_mappings | Mappings: import mappings ]]<br />
**[[ms-import#Import_genome | Genome: import annotation]]<br />
*Model<br />
**Build: build a model in local model-seed<br />
**[[ms-fba#Wild-type_FBA | FBA]]<br />
***[[ms-fba | Wild Type]]<br />
***[[ms-fba#Reaction_KO_FBA | Reaction KO]]<br />
***[[ms-fba#Gene_KO_FBA | Gene KO]]<br />
<br />
== Technical documentation for developers ==<br />
*[[Create a new plugin using the plugin builder (pdf)]]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=MS-howto&diff=1617MS-howto2013-03-25T18:13:20Z<p>Simao.soares: /* Model-seed plug-in operations */</p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3}}<br />
<br />
The Model-seed operations are located in the menu Plug-in Builder -> MSeed.<br /> <br />
If the MS plug-in is not yet loaded in OptFlux, just go to to Plug-in Builder -> Create... and select the MS XML file, OptFlux will then automatically build the new plug-in.<br />
<br />
== Model-seed plug-in operations ==<br />
[[File:Menu-ms.png]]<br />
*[[ms-loginout | Login: operation to login in the local model-seed]]<br />
*[[ms-loginout | Logout: operation to logout]]<br />
*[[ms-pull | Pull (from MSeed to OptFlux):]]<br />
**[[ms-pull#Pull_model | Model: import a model from model-seed to OptFlux]]<br />
**[[ms-pull#Pull_media | Media: import a media from model-seed to OptFlux]]<br />
* [[ms-commit | Commit (from OptFlux to MSeed):]]<br />
**[[ms-commit#Commit_model |Model: send a model from OptFlux to model-seed]]<br />
**[[ms-commit#Commit_media |Media: send a media from OptFlux to model-seed]]<br />
*[[merge-biochems | Merge Biochemistry: merge two biochemistries in local model-seed]]<br />
*[[ms-import | Import from server to local model-seed:]]<br />
**[[ms-import#Import_biochemistry | Biochemistry: import biochemistry]]<br />
**[[ms-import#Import_mappings | Mappings: import mappings ]]<br />
**[[ms-import#Import_genome | Genome: import annotation]]<br />
*Model<br />
**Build: build a model in local model-seed<br />
**[[ms-fba#Wild-type_FBA | FBA]]<br />
***[[ms-fba | Wild Type]]<br />
***[[ms-fba#Reaction_KO_FBA | Reaction KO]]<br />
***[[ms-fba#Gene_KO_FBA | Gene KO]]<br />
<br />
== Technical documentation for developers ==<br />
*[[Create a new plugin using the plugin builder (pdf)]]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=MS-howto&diff=1616MS-howto2013-03-25T18:12:44Z<p>Simao.soares: /* Model-seed plug-in operations */</p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3}}<br />
<br />
The Model-seed operations are located in the menu Plug-in Builder -> MSeed.<br /> <br />
If the MS plug-in is not yet loaded in OptFlux, just go to to Plug-in Builder -> Create... and select the MS XML file, OptFlux will then automatically build the new plug-in.<br />
<br />
== Model-seed plug-in operations ==<br />
[[File:Menu-ms.png]]<br />
*[[ms-loginout | Login: operation to login in the local model-seed]]<br />
*[[ms-loginout | Logout: operation to logout]]<br />
*[[ms-pull | Pull (from MSeed to OptFlux):]]<br />
**[[ms-pull#Pull_model | Model: import a model from model-seed to OptFlux]]<br />
**[[ms-pull#Pull_media | Media: import a media from model-seed to OptFlux]]<br />
* [[ms-commit | Commit (from OptFlux to MSeed):]]<br />
**[[ms-commit |Model: send a model from OptFlux to model-seed]]<br />
**[[ms-commit |Media: send a media from OptFlux to model-seed]]<br />
*[[merge-biochems | Merge Biochemistry: merge two biochemistries in local model-seed]]<br />
*[[ms-import | Import from server to local model-seed:]]<br />
**[[ms-import#Import_biochemistry | Biochemistry: import biochemistry]]<br />
**[[ms-import#Import_mappings | Mappings: import mappings ]]<br />
**[[ms-import#Import_genome | Genome: import annotation]]<br />
*Model<br />
**Build: build a model in local model-seed<br />
**[[ms-fba#Wild-type_FBA | FBA]]<br />
***[[ms-fba | Wild Type]]<br />
***[[ms-fba#Reaction_KO_FBA | Reaction KO]]<br />
***[[ms-fba#Gene_KO_FBA | Gene KO]]<br />
<br />
== Technical documentation for developers ==<br />
*[[Create a new plugin using the plugin builder (pdf)]]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=MS-howto&diff=1615MS-howto2013-03-25T18:12:27Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3}}<br />
<br />
The Model-seed operations are located in the menu Plug-in Builder -> MSeed.<br /> <br />
If the MS plug-in is not yet loaded in OptFlux, just go to to Plug-in Builder -> Create... and select the MS XML file, OptFlux will then automatically build the new plug-in.<br />
<br />
== Model-seed plug-in operations ==<br />
[[File:Menu-ms.png]]<br />
*[[ms-loginout | Login: operation to login in the local model-seed]]<br />
*[[ms-loginout | Logout: operation to logout]]<br />
*[[ms-pull | Pull (from MSeed to OptFlux):]]<br />
**[[ms-pull#Pull_model | Model: import a model from model-seed to OptFlux]]<br />
**[[ms-pullPull_media | Media: import a media from model-seed to OptFlux]]<br />
* [[ms-commit | Commit (from OptFlux to MSeed):]]<br />
**[[ms-commit |Model: send a model from OptFlux to model-seed]]<br />
**[[ms-commit |Media: send a media from OptFlux to model-seed]]<br />
*[[merge-biochems | Merge Biochemistry: merge two biochemistries in local model-seed]]<br />
*[[ms-import | Import from server to local model-seed:]]<br />
**[[ms-import#Import_biochemistry | Biochemistry: import biochemistry]]<br />
**[[ms-import#Import_mappings | Mappings: import mappings ]]<br />
**[[ms-import#Import_genome | Genome: import annotation]]<br />
*Model<br />
**Build: build a model in local model-seed<br />
**[[ms-fba#Wild-type_FBA | FBA]]<br />
***[[ms-fba | Wild Type]]<br />
***[[ms-fba#Reaction_KO_FBA | Reaction KO]]<br />
***[[ms-fba#Gene_KO_FBA | Gene KO]]<br />
<br />
== Technical documentation for developers ==<br />
*[[Create a new plugin using the plugin builder (pdf)]]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=MS-howto&diff=1614MS-howto2013-03-25T18:11:32Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3}}<br />
<br />
The Model-seed operations are located in the menu Plug-in Builder -> MSeed.<br /> <br />
If the MS plug-in is not yet loaded in OptFlux, just go to to Plug-in Builder -> Create... and select the MS XML file, OptFlux will then automatically build the new plug-in.<br />
<br />
== Model-seed plug-in operations ==<br />
[[File:Menu-ms.png]]<br />
*[[ms-loginout | Login: operation to login in the local model-seed]]<br />
*[[ms-loginout | Logout: operation to logout]]<br />
*[[ms-pull | Pull (from MSeed to OptFlux):]]<br />
**[[ms-pull | Model: import a model from model-seed to OptFlux]]<br />
**[[ms-pull | Media: import a media from model-seed to OptFlux]]<br />
* [[ms-commit | Commit (from OptFlux to MSeed):]]<br />
**[[ms-commit |Model: send a model from OptFlux to model-seed]]<br />
**[[ms-commit |Media: send a media from OptFlux to model-seed]]<br />
*[[merge-biochems | Merge Biochemistry: merge two biochemistries in local model-seed]]<br />
*[[ms-import | Import from server to local model-seed:]]<br />
**[[ms-import#Import_biochemistry | Biochemistry: import biochemistry]]<br />
**[[ms-import#Import_mappings | Mappings: import mappings ]]<br />
**[[ms-import#Import_genome | Genome: import annotation]]<br />
*Model<br />
**Build: build a model in local model-seed<br />
**[[ms-fba#Wild-type_FBA | FBA]]<br />
***[[ms-fba | Wild Type]]<br />
***[[ms-fba#Reaction_KO_FBA | Reaction KO]]<br />
***[[ms-fba#Gene_KO_FBA | Gene KO]]<br />
<br />
== Technical documentation for developers ==<br />
*[[Create a new plugin using the plugin builder (pdf)]]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=MS-howto&diff=1613MS-howto2013-03-25T18:09:35Z<p>Simao.soares: /* Model-seed plug-in operations */</p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3}}<br />
<br />
The Model-seed operations are located in the menu Plug-in Builder -> MSeed.<br /> <br />
If the MS plug-in is not yet loaded in OptFlux, just go to to Plug-in Builder -> Create... and select the MS XML file, OptFlux will then automatically build the new plug-in.<br />
<br />
== Model-seed plug-in operations ==<br />
[[File:Menu-ms.png]]<br />
*[[ms-loginout | Login: operation to login in the local model-seed]]<br />
*[[ms-loginout | Logout: operation to logout]]<br />
*[[ms-pull | Pull (from MSeed to OptFlux):]]<br />
**[[ms-pull | Model: import a model from model-seed to OptFlux]]<br />
**[[ms-pull | Media: import a media from model-seed to OptFlux]]<br />
* [[ms-commit | Commit (from OptFlux to MSeed):]]<br />
**[[ms-commit |Model: send a model from OptFlux to model-seed]]<br />
**[[ms-commit |Media: send a media from OptFlux to model-seed]]<br />
*[[merge-biochems | Merge Biochemistry: merge two biochemistries in local model-seed]]<br />
*[[ms-import | Import from server to local model-seed:]]<br />
**[[ms-import | Biochemistry: import biochemistry]]<br />
**[[ms-import | Mappings: import mappings ]]<br />
**[[ms-import | Genome: import annotation]]<br />
*Model<br />
**Build: build a model in local model-seed<br />
**[[ms-fba#Wild-type_FBA | FBA]]<br />
***[[ms-fba | Wild Type]]<br />
***[[ms-fba#Reaction_KO_FBA | Reaction KO]]<br />
***[[ms-fba#Gene_KO_FBA | Gene KO]]<br />
<br />
== Technical documentation for developers ==<br />
*[[Create a new plugin using the plugin builder (pdf)]]</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-fba&diff=1612Ms-fba2013-03-25T18:08:29Z<p>Simao.soares: /* Reaction KO FBA */</p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: Model FBA}}<br />
<br />
[[File:Operations-model-fba.png]]<br /><br />
The operations to perform FBA simulations in model-seed with local model-seed models are grouped in the menu MSeed > Operations > Model > FBA.<br />
<br />
==Wild-type FBA ==<br />
To do a Wild-type simulation go to MSeed > Operations > Model > FBA > Wild Type and select the local model-seed to use and the biochemisty and media to be used in the simulation.<br /><br />
A simulation result will be created in the OptFlux workspace.<br /><br />
[[File:Model-fba-wt.png]]<br />
<br />
==Reaction KO FBA==<br />
To perform a reaction knock-out simulation go to MSeed > Operations > Model > FBA > Reaction KO and select:<br />
*the local model-seed<br />
*the biochemisty<br />
*media <br />
*reactions to be turned off in the simulation.<br /><br />
A simulation result will be created in the OptFlux workspace.<br /><br />
[[File:Model-fba-reactions.png]]<br />
<br />
==Gene KO FBA==<br />
N/A</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-fba&diff=1611Ms-fba2013-03-25T18:07:56Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: Model FBA}}<br />
<br />
[[File:Operations-model-fba.png]]<br /><br />
The operations to perform FBA simulations in model-seed with local model-seed models are grouped in the menu MSeed > Operations > Model > FBA.<br />
<br />
==Wild-type FBA ==<br />
To do a Wild-type simulation go to MSeed > Operations > Model > FBA > Wild Type and select the local model-seed to use and the biochemisty and media to be used in the simulation.<br /><br />
A simulation result will be created in the OptFlux workspace.<br /><br />
[[File:Model-fba-wt.png]]<br />
<br />
==Reaction KO FBA==<br />
To perform a reaction knock-out simulation go to MSeed > Operations > Model > FBA > Reaction KO and select:<br />
*the local model-seed<br />
*the biochemisty<br />
*media <br />
*reaction to be turned off in the simulation.<br /><br />
A simulation result will be created in the OptFlux workspace.<br /><br />
[[File:Model-fba-reactions.png]]<br />
<br />
==Gene KO FBA==<br />
N/A</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-fba&diff=1610Ms-fba2013-03-25T18:07:47Z<p>Simao.soares: /* Wild-type FBA */</p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: Model FBA}}<br />
<br />
[[File:Operations-model-fba.png]]<br />
The operations to perform FBA simulations in model-seed with local model-seed models are grouped in the menu MSeed > Operations > Model > FBA.<br />
<br />
==Wild-type FBA ==<br />
To do a Wild-type simulation go to MSeed > Operations > Model > FBA > Wild Type and select the local model-seed to use and the biochemisty and media to be used in the simulation.<br /><br />
A simulation result will be created in the OptFlux workspace.<br /><br />
[[File:Model-fba-wt.png]]<br />
<br />
==Reaction KO FBA==<br />
To perform a reaction knock-out simulation go to MSeed > Operations > Model > FBA > Reaction KO and select:<br />
*the local model-seed<br />
*the biochemisty<br />
*media <br />
*reaction to be turned off in the simulation.<br /><br />
A simulation result will be created in the OptFlux workspace.<br /><br />
[[File:Model-fba-reactions.png]]<br />
<br />
==Gene KO FBA==<br />
N/A</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-fba&diff=1609Ms-fba2013-03-25T18:07:40Z<p>Simao.soares: /* Wild-type FBA */</p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: Model FBA}}<br />
<br />
[[File:Operations-model-fba.png]]<br />
The operations to perform FBA simulations in model-seed with local model-seed models are grouped in the menu MSeed > Operations > Model > FBA.<br />
<br />
==Wild-type FBA ==<br />
To do a Wild-type simulation go to MSeed > Operations > Model > FBA > Wild Type and select the local model-seed to use and the biochemisty and media to be used in the simulation.<br /><br />
A simulation result will be created in the OptFlux workspace.<br />
[[File:Model-fba-wt.png]]<br />
<br />
==Reaction KO FBA==<br />
To perform a reaction knock-out simulation go to MSeed > Operations > Model > FBA > Reaction KO and select:<br />
*the local model-seed<br />
*the biochemisty<br />
*media <br />
*reaction to be turned off in the simulation.<br /><br />
A simulation result will be created in the OptFlux workspace.<br /><br />
[[File:Model-fba-reactions.png]]<br />
<br />
==Gene KO FBA==<br />
N/A</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-fba&diff=1608Ms-fba2013-03-25T18:07:33Z<p>Simao.soares: /* Reaction KO FBA */</p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: Model FBA}}<br />
<br />
[[File:Operations-model-fba.png]]<br />
The operations to perform FBA simulations in model-seed with local model-seed models are grouped in the menu MSeed > Operations > Model > FBA.<br />
<br />
==Wild-type FBA ==<br />
To do a Wild-type simulation go to MSeed > Operations > Model > FBA > Wild Type and select the local model-seed to use and the biochemisty and media to be used in the simulation.<br />
A simulation result will be created in the OptFlux workspace.<br />
[[File:Model-fba-wt.png]]<br />
<br />
==Reaction KO FBA==<br />
To perform a reaction knock-out simulation go to MSeed > Operations > Model > FBA > Reaction KO and select:<br />
*the local model-seed<br />
*the biochemisty<br />
*media <br />
*reaction to be turned off in the simulation.<br /><br />
A simulation result will be created in the OptFlux workspace.<br /><br />
[[File:Model-fba-reactions.png]]<br />
<br />
==Gene KO FBA==<br />
N/A</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-fba&diff=1607Ms-fba2013-03-25T18:07:13Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: Model FBA}}<br />
<br />
[[File:Operations-model-fba.png]]<br />
The operations to perform FBA simulations in model-seed with local model-seed models are grouped in the menu MSeed > Operations > Model > FBA.<br />
<br />
==Wild-type FBA ==<br />
To do a Wild-type simulation go to MSeed > Operations > Model > FBA > Wild Type and select the local model-seed to use and the biochemisty and media to be used in the simulation.<br />
A simulation result will be created in the OptFlux workspace.<br />
[[File:Model-fba-wt.png]]<br />
<br />
==Reaction KO FBA==<br />
To perform a reaction knock-out simulation go to MSeed > Operations > Model > FBA > Reaction KO and select:<br />
*the local model-seed<br />
*the biochemisty<br />
*media <br />
*reaction to be turned off in the simulation.<br /><br />
A simulation result will be created in the OptFlux workspace.<br />
[[File:Model-fba-reactions.png]]<br />
<br />
==Gene KO FBA==<br />
N/A</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-fba&diff=1606Ms-fba2013-03-25T18:02:02Z<p>Simao.soares: /* Wild-type FBA */</p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: Model FBA}}<br />
<br />
[[File:Operations-model-fba.png]]<br />
<br />
==Wild-type FBA ==<br />
[[File:Model-fba-wt.png]]<br />
<br />
==Reaction KO FBA==<br />
[[File:Model-fba-reactions.png]]<br />
<br />
==Gene KO FBA==<br />
N/A</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=Ms-fba&diff=1605Ms-fba2013-03-25T18:01:53Z<p>Simao.soares: </p>
<hr />
<div>{{DISPLAYTITLE:Model-seed plug-in for OptFlux 3: Model FBA}}<br />
<br />
[[File:Operations-model-fba.png]]<br />
<br />
==Wild-type FBA ==<br />
[[File:Model-fba-wt.png]<br />
<br />
<br />
==Reaction KO FBA==<br />
[[File:Model-fba-reactions.png]]<br />
<br />
==Gene KO FBA==<br />
N/A</div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=File:Model-fba-reactions.png&diff=1604File:Model-fba-reactions.png2013-03-25T18:01:31Z<p>Simao.soares: </p>
<hr />
<div></div>Simao.soareshttp://www.optflux.org/wiki/index.php?title=File:Model-fba-wt.png&diff=1603File:Model-fba-wt.png2013-03-25T18:01:20Z<p>Simao.soares: </p>
<hr />
<div></div>Simao.soares