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{{DISPLAYTITLE:How Tos for Optflux 3}} | {{DISPLAYTITLE:How Tos for Optflux 3}} | ||
− | == Project == | + | == Project And Model Handling== |
− | + | *[[OptFlux3:CORE:NewProject|New project]] | |
− | *[[ | + | **[[CORE:Readers:Drains | Drains Definition]] |
− | **[[Drains Definition]] | ||
**[[OptFlux Readers]] | **[[OptFlux Readers]] | ||
***[[SBML Reader]] | ***[[SBML Reader]] | ||
− | |||
***[[Flat Files Reader]] | ***[[Flat Files Reader]] | ||
+ | ***[[Metatool]] | ||
+ | ***[[OptFlux3:MR | OptFlux Repository]] | ||
***[[Table format Reader]] | ***[[Table format Reader]] | ||
***[[Cell Designer Reader]] | ***[[Cell Designer Reader]] | ||
− | *Import Project | + | *[[OptFlux3:CORE:ImportProject | Import Project]] |
− | *Model Simplification | + | *[[OptFlux3:SMP |Model Simplification]] |
+ | |||
+ | === Model Handling === | ||
+ | |||
+ | *[[Create Environmental conditions]] | ||
== Simulation == | == Simulation == | ||
− | *[[ | + | *[[OptFlux3:SIM:WildType | Wild Type]] |
− | *[[ | + | *[[OptFlux3:SIM:Knockouts | Knockouts]] |
− | *[[ | + | *[[OptFlux3:SIM:UnderOverExpression | Under-Over Expression]] |
== Analysis == | == Analysis == | ||
− | * | + | *[[OptFlux3:OPT:Critical | Critical Genes/Reactions]] |
− | *Balance Checker | + | *[[OptFlux3:BC:balancechecker | Balance Checker]] |
*Flux Variability Analysis | *Flux Variability Analysis | ||
− | **Zero-flux values | + | **[[OptFlux3:SIM:ZeroFluxFVA | Zero-flux values]] |
− | **Flux-variation plot | + | **[[OptFlux3:SIM:VarPlot | Flux-variation plot]] |
− | **Flux limits | + | **[[OptFlux3:SIM:FluxLim | Flux limits]] |
*Structural Analysis | *Structural Analysis | ||
− | **Zero-flux values | + | **[[OptFlux3:SIM:ZeroFluxStruc | Zero-flux values]] |
− | **Equivalent-flux values | + | **[[OptFlux3:SIM:EquivalentFluxes | Equivalent-flux values]] |
== Optimization == | == Optimization == | ||
− | *Evolutionary | + | *[[OptFlux3:Evolutionary | Evolutionary]] |
− | *[[OptFlux3: | + | *[[OptFlux3:OPK | Optknock]] |
== Help == | == Help == | ||
*Repository Manager | *Repository Manager | ||
+ | **[[KnownProblems:RepositoryManager | Known Problems]] | ||
*Updates | *Updates | ||
+ | *Preferences | ||
+ | **[[Cplex Configuration:Preferences | Cplex Configuration]] | ||
+ | |||
+ | == Plugins == | ||
+ | *[[OptFlux3:CORE|Core]] | ||
+ | *[[OptFlux3:MR | Model Repository]] | ||
+ | *[[OptFlux3:SIM | Simulation]] | ||
+ | *[[OptFlux3:Evolutionary | Optimization]] | ||
+ | *[[OptFlux3:SMP | Simplification]] | ||
+ | *[[OptFlux3:BC:balancechecker:hgfhgf | Mass Balance Validator]] | ||
+ | *[[OptFlux3:OPK | OptKnock]] | ||
+ | *[[OptFlux3:TNA | Network Topology Analysis (TNA)]] | ||
+ | *[[OptFlux3:EFM | Elementary Flux Modes]] | ||
+ | *[[OptFlux3:RT | Reg4OptFlux - Regulatory plugin]] | ||
+ | *[[OptFlux3:METAVIZ | Metabolic Network Visualization Plugin]] | ||
+ | *[[OptFlux3:MFA | Metabolic Flux Analysis]] | ||
+ | *[[OptFlux3:COBRA | Cobra4OptFlux - Cobra plugin]] | ||
+ | *[[OptFlux3:Serialization | Serialization plugin]] |
Latest revision as of 10:16, 21 December 2016
Contents
Project And Model Handling[edit]
Model Handling[edit]
Simulation[edit]
Analysis[edit]
- Critical Genes/Reactions
- Balance Checker
- Flux Variability Analysis
- Structural Analysis
Optimization[edit]
Help[edit]
- Repository Manager
- Updates
- Preferences