Rough schedule, we will cover as much as we can and leave the rest as homework.
- 5 min Getting started
- Load a model and do FBA
- 30 min Genome scale metabolic models and simulating
- What's in the model, reactions, metabolites, genes
- Expressions and objectives
- Simulating using FBA, changing the objective
- 30 min Manipulating the model
- Adding and emoving reactions, metabolites
- Changing and reverting using the context manager
- 45 min Simulating and analyzing models
- pFBA
- FVA
- Loopless
- Additional constraints
- Production envelope
- Gene and reaction essentiality
- 15 min If there is time: constraints and variables
- Defining own variables and constraints