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− | + | {{DISPLAYTITLE:How Tos for Optflux 3}} | |
+ | == Project And Model Handling== | ||
+ | *[[OptFlux3:CORE:NewProject|New project]] | ||
+ | **[[CORE:Readers:Drains | Drains Definition]] | ||
+ | **[[OptFlux Readers]] | ||
+ | ***[[SBML Reader]] | ||
+ | ***[[Flat Files Reader]] | ||
+ | ***[[Metatool]] | ||
+ | ***[[OptFlux3:MR | OptFlux Repository]] | ||
+ | ***[[Table format Reader]] | ||
+ | ***[[Cell Designer Reader]] | ||
+ | *[[OptFlux3:CORE:ImportProject | Import Project]] | ||
+ | *[[OptFlux3:SMP |Model Simplification]] | ||
− | *[[ | + | === Model Handling === |
− | + | ||
− | + | *[[Create Environmental conditions]] | |
− | *[[ | + | |
− | *[[ | + | == Simulation == |
− | *[[ | + | *[[OptFlux3:SIM:WildType | Wild Type]] |
− | + | *[[OptFlux3:SIM:Knockouts | Knockouts]] | |
− | + | *[[OptFlux3:SIM:UnderOverExpression | Under-Over Expression]] | |
+ | |||
+ | == Analysis == | ||
+ | *[[OptFlux3:OPT:Critical | Critical Genes/Reactions]] | ||
+ | *[[OptFlux3:BC:balancechecker | Balance Checker]] | ||
+ | *Flux Variability Analysis | ||
+ | **[[OptFlux3:SIM:ZeroFluxFVA | Zero-flux values]] | ||
+ | **[[OptFlux3:SIM:VarPlot | Flux-variation plot]] | ||
+ | **[[OptFlux3:SIM:FluxLim | Flux limits]] | ||
+ | *Structural Analysis | ||
+ | **[[OptFlux3:SIM:ZeroFluxStruc | Zero-flux values]] | ||
+ | **[[OptFlux3:SIM:EquivalentFluxes | Equivalent-flux values]] | ||
+ | |||
+ | == Optimization == | ||
+ | *[[OptFlux3:Evolutionary | Evolutionary]] | ||
+ | *[[OptFlux3:OPK | Optknock]] | ||
+ | |||
+ | == Help == | ||
+ | *Repository Manager | ||
+ | **[[KnownProblems:RepositoryManager | Known Problems]] | ||
+ | *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