Difference between revisions of "HowTos"

Latest revision as of 11:31, 29 July 2011

HowTos for OptFlux 2[edit]

• How to create a new model/project from SBML

• How to create a new model/project from text files

• How to save and load projects

• How to export models to SBML

• How to export models to Flat Files

• Interaction with Cell Designer

           *How to load a CD model for visualization
           *How to export a model to CD SBML (with results)
           *How to do a simulation overlap with a CD model

• How to do a wild type simulation

• How to do a mutant simulation

           *Reaction deletion
           *Gene knockout

• Environmental conditions

• Flux Variability Analysis

           *How to Calculate Flux Limits
           *How to generate a Flux Variability Graph

• Essential genes/reactions

          *Determining essential genes/reactions
          *Loading from file

• How to calculate a Simplified Model

• How to optimize the knockout set

           *Reaction deletions
           *Gene knockouts

Formats specifications

           *Flat files format specifications
           *SBML

Plugins

             *EFM4OptFlux
             *MFA4OptFlux
             *OptKnock4OptFlux
             *TNA4OptFlux
             *RegulatoryTool
             *OverUnder4OptFlux