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− | {{DISPLAYTITLE:How Tos for Optflux 3}}
| + | == Project Manipulation 3 == |
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− | == Project And Model Handling==
| + | *[[NewProjectOptflux3|New project wizard]] |
− | *[[OptFlux3:CORE:NewProject|New project]] | + | **[[Drains Definition]] |
− | **[[CORE:Readers:Drains | 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]]
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| ***[[Table format Reader]] | | ***[[Table format Reader]] |
| ***[[Cell Designer Reader]] | | ***[[Cell Designer Reader]] |
− | *[[OptFlux3:CORE:ImportProject | Import Project]]
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− | *[[OptFlux3:SMP |Model Simplification]]
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− | === Model Handling === | + | === teste === |
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− | *[[Create Environmental conditions]]
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| == Simulation == | | == Simulation == |
− | *[[OptFlux3:SIM:WildType | Wild Type]] | + | *[[How to simulate a Wild type]] |
− | *[[OptFlux3:SIM:Knockouts | Knockouts]] | + | *[[How to do a mutant simulation in Optflux3]] |
− | *[[OptFlux3:SIM:UnderOverExpression | Under-Over Expression]] | + | *[[Hot to do an Under and Over Expression Simulation in OptFlux3]] |
− | | |
− | == Analysis ==
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− | *[[OptFlux3:OPT:Critical | Critical Genes/Reactions]]
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− | *[[OptFlux3:BC:balancechecker | Balance Checker]]
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− | *Flux Variability Analysis
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− | **[[OptFlux3:SIM:ZeroFluxFVA | Zero-flux values]]
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− | **[[OptFlux3:SIM:VarPlot | Flux-variation plot]]
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− | **[[OptFlux3:SIM:FluxLim | Flux limits]]
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− | *Structural Analysis
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− | **[[OptFlux3:SIM:ZeroFluxStruc | Zero-flux values]]
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− | **[[OptFlux3:SIM:EquivalentFluxes | Equivalent-flux values]]
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− | | |
− | == Optimization ==
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− | *[[OptFlux3:Evolutionary | Evolutionary]]
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− | *[[OptFlux3:OPK | Optknock]]
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− | | |
− | == Help ==
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− | *Repository Manager
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− | **[[KnownProblems:RepositoryManager | Known Problems]]
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− | *Updates
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− | *Preferences
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− | **[[Cplex Configuration:Preferences | Cplex Configuration]]
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| | | |
− | == Plugins == | + | == Simplification == |
− | *[[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]]
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