Examples
- Loading models
- Converting, modifying and saving models
- Exploring model contents
- Generic accessors
CoreModelusage- Basic usage of
StandardModel - Loading a model in the StandardModel format
- Internals of
StandardModel Genes,Reactions, andMetabolites- Checking the internals of
StandardModels:annotation_index - Checking the internals of
StandardModels:check_duplicate_reaction - Checking the internals of
StandardModels:reaction_mass_balanced - Model construction and modification
- Flux balance analysis (FBA)
- Extending FBA with modifications
- Flux variability analysis (FVA)
- Detailed variability analysis with modifications
- Summarizing the flux variability
- Retrieving details about FVA output
- Gene knockouts
- Deleting a single gene
- Knocking out multiple genes
- Processing all single gene knockouts
- Processing all multiple-gene deletions
- Restricting and disabling individual reactions
- Disabling a reaction
- Restricting a reaction
- Screening for sensitive and critical reactions
- Screening with reaction combinations
- Parsimonious flux balance analysis (pFBA)
- Loopless FBA
- FBA with crowding
- Growth media analysis
- What nutrients does my model need to grow?
- What is the minimal flux of nutrients for my model to grow?
- Maximum-minimum driving force analysis
- Minimization of metabolic adjustment (MOMA)
- sMOMENT
- GECKO
- Hit and run sampling
- Production envelopes