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== HowTos for OptFlux 2 ==
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[[How to create a new model/project from SBML]]
  
 +
[[How to create a new model/project from text files]]
  
*[[How to create a new model/project from SBML]]
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[[How to save and load projects]]
  
*[[How to create a new model/project from text files]]
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[[How to export models to SBML]]
  
*[[How to save and load projects]]
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[[Interaction with Cell Designer]]
  
*[[How to export models to SBML]]
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            [[How to load a CD model for visualization]]
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            [[How to export a model to CD SBML (with results)]]
  
*[[How to export models to Flat Files]]
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[[How to do a wild type simulation]]
  
*[[Interaction with Cell Designer]]
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[[How to do a mutant simulation]]
  
             *[[How to load a CD model for visualization]]
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             [[Reaction delection]]
             *[[How to export a model to CD SBML (with results)]]
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             [[Gene knockout]]
            *[[How to do a simulation overlap with a CD model]]
 
  
 +
[[Environmental conditions]]
  
*[[How to do a wild type simulation]]
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Flux Variability Analysis
  
*[[How to do a mutant simulation]]
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            [[How to Calculate Flux Limits]]
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            [[How to generate a Flux Variability Graph]]
  
            *[[Reaction deletion]]
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Essential genes/reactions
            *[[Gene knockout]]
 
  
*[[Environmental conditions]]
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          [[Determining essential genes/reactions]]
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          [[Loading from file]]
  
*Flux Variability Analysis
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[[How to calculate a Simplified Model]]
  
            *[[How to Calculate Flux Limits]]
 
            *[[How to generate a Flux Variability Graph]]
 
 
*Essential genes/reactions
 
 
          *[[Determining essential genes/reactions]]
 
          *[[Loading from file]]
 
 
*[[How to calculate a Simplified Model]]
 
 
<!--
 
 
           [[How to calculate critical genes/reactions]]
 
           [[How to calculate critical genes/reactions]]
-->
 
*[[How to optimize the knockout set]]
 
  
            *[[Reaction deletions]]
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[[How to optimize the knockout set]]
            *[[Gene knockouts]]
 
  
Formats specifications
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            [[Reaction deletions]]
 +
            [[Gene knockouts]]
  
            *[[Flat files format specifications]]
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Graph overlap!
            *[http://sbml.org/Documents/Specifications SBML]
 
  
 
<!--
 
<!--
 
[[How to use Multiobjective strain optimization]]
 
[[How to use Multiobjective strain optimization]]
 
-->
 
-->
 
[[Plugins]]
 
 
              *[[EFM4OptFlux]]
 
              *[[MFA4OptFlux]]
 
              *[[OptKnock4OptFlux]]
 
              *[[TNA4OptFlux]]
 
              *[[RegulatoryTool]]
 
              *[[OverUnder4OptFlux]]
 

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