From Optflux
Jump to: navigation, search

Warning: You are not logged in. Your IP address will be publicly visible if you make any edits. If you log in or create an account, your edits will be attributed to your username, along with other benefits.

The edit can be undone. Please check the comparison below to verify that this is what you want to do, and then save the changes below to finish undoing the edit.
Latest revision Your text
Line 1: Line 1:
== HowTos for OptFlux 2 ==
+
[[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]]
+
[[How to save and load projects]]
  
*[[How to create a new model/project from text files]]
+
[[How to export models to SBML]]
  
*[[How to save and load projects]]
+
[[How to export models to Flat Files]]
  
*[[How to export models to SBML]]
+
[[Interaction with Cell Designer]]
  
*[[How to export models to Flat Files]]
+
            [[How to load a CD model for visualization]]
 +
            [[How to export a model to CD SBML (with results)]]
 +
            [[How to do a simulation overlap with a CD model]]
  
*[[Interaction with Cell Designer]]
 
  
            *[[How to load a CD model for visualization]]
+
[[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]]
 
  
 +
[[How to do a mutant simulation]]
  
*[[How to do a wild type simulation]]
+
            [[Reaction deletion]]
 +
            [[Gene knockout]]
  
*[[How to do a mutant simulation]]
+
[[Environmental conditions]]
  
            *[[Reaction deletion]]
+
Flux Variability Analysis
            *[[Gene knockout]]
 
  
*[[Environmental conditions]]
+
            [[How to Calculate Flux Limits]]
 +
            [[How to generate a Flux Variability Graph]]
  
*Flux Variability Analysis
+
Essential genes/reactions
  
            *[[How to Calculate Flux Limits]]
+
          [[Determining essential genes/reactions]]
            *[[How to generate a Flux Variability Graph]]
+
          [[Loading from file]]
  
*Essential genes/reactions
+
[[How to calculate a Simplified Model]]
 
 
          *[[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]]
+
[[How to optimize the knockout set]]
  
             *[[Reaction deletions]]
+
             [[Reaction deletions]]
             *[[Gene knockouts]]
+
             [[Gene knockouts]]
  
Formats specifications
+
[[File format specifications]]
 
 
            *[[Flat files format specifications]]
 
            *[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]]
 

Please note that all contributions to Optflux may be edited, altered, or removed by other contributors. If you do not want your writing to be edited mercilessly, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource (see Optflux:Copyrights for details). Do not submit copyrighted work without permission!

Cancel | Editing help (opens in new window)