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

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