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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 == | ||
| + | *[[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