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{{DISPLAYTITLE:How Tos for Optflux 3}}
 
{{DISPLAYTITLE:How Tos for Optflux 3}}
  
== Project ==
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== Project And Model Handling==
 
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*[[OptFlux3:CORE:NewProject|New project]]
*[[NewProjectOptflux3|New project]]
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**[[CORE:Readers:Drains | Drains Definition]]
**[[Drains Definition]]
 
 
**[[OptFlux Readers]]
 
**[[OptFlux Readers]]
 
***[[SBML Reader]]
 
***[[SBML Reader]]
***[[OptFlux Repository]]
 
 
***[[Flat Files Reader]]
 
***[[Flat Files Reader]]
 +
***[[Metatool]]
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***[[OptFlux3:MR | OptFlux Repository]]
 
***[[Table format Reader]]
 
***[[Table format Reader]]
 
***[[Cell Designer Reader]]
 
***[[Cell Designer Reader]]
*Import Project
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*[[OptFlux3:CORE:ImportProject | Import Project]]
*Model Simplification
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*[[OptFlux3:SMP |Model Simplification]]
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=== Model Handling ===
 +
 
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*[[Create Environmental conditions]]
  
 
== Simulation ==
 
== Simulation ==
*[[How to simulate a Wild type | Wild Type]]
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*[[OptFlux3:SIM:WildType | Wild Type]]
*[[How to do a mutant simulation in Optflux3 | Knockouts]]
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*[[OptFlux3:SIM:Knockouts | Knockouts]]
*[[Hot to do an Under and Over Expression Simulation in OptFlux3 | Under-Over Expression]]
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*[[OptFlux3:SIM:UnderOverExpression | Under-Over Expression]]
  
 
== Analysis ==
 
== Analysis ==
*Critial Genes/Reactions
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*[[OptFlux3:OPT:Critical | Critical Genes/Reactions]]
*Balance Checker
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*[[OptFlux3:BC:balancechecker | Balance Checker]]
 
*Flux Variability Analysis
 
*Flux Variability Analysis
**Zero-flux values
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**[[OptFlux3:SIM:ZeroFluxFVA | Zero-flux values]]
**Flux-variation plot
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**[[OptFlux3:SIM:VarPlot | Flux-variation plot]]
**Flux limits
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**[[OptFlux3:SIM:FluxLim | Flux limits]]
 
*Structural Analysis
 
*Structural Analysis
**Zero-flux values
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**[[OptFlux3:SIM:ZeroFluxStruc | Zero-flux values]]
**Equivalent-flux values
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**[[OptFlux3:SIM:EquivalentFluxes | Equivalent-flux values]]
  
 
== Optimization ==
 
== Optimization ==
*Evolutionary
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*[[OptFlux3:Evolutionary | Evolutionary]]
*[[OptFlux3:Opt:Optknock | Optknock]]
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*[[OptFlux3:OPK | Optknock]]
  
 
== Help ==
 
== Help ==
 
*Repository Manager
 
*Repository Manager
 +
**[[KnownProblems:RepositoryManager | Known Problems]]
 
*Updates
 
*Updates
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*Preferences
 +
**[[Cplex Configuration:Preferences | Cplex Configuration]]
 +
 +
== Plugins ==
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*[[OptFlux3:CORE|Core]]
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*[[OptFlux3:MR  | Model Repository]]
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*[[OptFlux3:SIM | Simulation]]
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*[[OptFlux3:Evolutionary | Optimization]]
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*[[OptFlux3:SMP | Simplification]]
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*[[OptFlux3:BC:balancechecker:hgfhgf | Mass Balance Validator]]
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*[[OptFlux3:OPK | OptKnock]]
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*[[OptFlux3:TNA | Network Topology Analysis (TNA)]]
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*[[OptFlux3:EFM | Elementary Flux Modes]]
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*[[OptFlux3:RT | Reg4OptFlux - Regulatory plugin]]
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*[[OptFlux3:METAVIZ | Metabolic Network Visualization Plugin]]
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*[[OptFlux3:MFA | Metabolic Flux Analysis]]
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*[[OptFlux3:COBRA | Cobra4OptFlux - Cobra plugin]]
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*[[OptFlux3:Serialization | Serialization plugin]]

Latest revision as of 10:16, 21 December 2016


Project And Model Handling[edit]

Model Handling[edit]

Simulation[edit]

Analysis[edit]

Optimization[edit]

Help[edit]

Plugins[edit]