Notebooks and example workflows
- Loading, converting, and saving models
- Loading models
- Using the generic interface to access model details
- Converting between model types
- Saving and exporting models
- Finding balance and variability of constraint-based models
- Optimization solvers in
COBREXA - Flux balance analysis (FBA)
- Modifications
- Flux variability analysis (FVA)
- Parsimonious flux balance analysis (pFBA)
- Flux balance analysis with molecular crowding (FBAwMC)
- Basic usage of
StandardModel - Loading a model
- Basic analysis
- Inspecting the flux solution:
atom_fluxes - Inspecting the flux solution:
metabolite_fluxes - 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 - Basic usage of
CoreModelandCoreModelCoupled - Loading a
CoreModel - Basic analysis on
CoreModel - Structure of
CoreModel CoreModelCoupledadds coupling constraints toCoreModel- Model construction and modification
- Exploring model variants with
screen - Building and analysing a small community model
- Load the base model
- Load the models and inspect fba solutions
- Build a community model of the cytochrome oxidase knockout and the ATP synthase knockout models
- Set exchange reaction bounds of community model based on the bounds of the individual models
- Add objective function to community model`
- Perform community FBA
- Add the enolase knockout to the community model
- Allow the mutants to rescue each other by sharing pyruvate
- Using a custom model data structure