- Load a model and simulate it
- Obtain a model from a database for a host organism you're interested in
- Understand the basic data structures of models
- Learn how to query models
- Setting objectives and optimizing models
- Manipulating flux bounds for defining media conditions and knocking out reactions
- Importing models from different file formats
- ModelSEED
- Defining reactions and adding pathways to models (add some pathway to e_coli_core)
- Visualizing data in escher
- Importing a model into escher and drawing a pathway map
- Determine gene essentiality
- Flux variablity analysis
- Phenotyptic phase plane
- Fluxomics
- Metabolomics
- Production envelope (fluxes, yields, c-mol yields)
- Knock-out strategies, growth-coupled designs
- Algorithms for computing knock-out strategies
- Comparing flux ranges of WT and production strain
- Differential FVA
- Swapping co-factors in a reaction
- Using OptSwap to find optimal co-factors to swap
Muconic acid, adipic acid