Examples

• Loading and saving models
• • Getting the models reliably from the repositories
  • Loading models
  • Saving models
• Flux balance analysis (FBA)
• • Running a FBA
• Changing optimizer parameters
• Making adjustments to the model
• • Getting the base model
  • Running FBA on modified models
  • Preventing reference-based sharing problems with deepcopy
  • Observing the differences
  • Coupling constraints
• Making adjustments to the constraint system
• • Background: Constraint trees
  • Customizing the model
• Flux variability analysis (FVA)
• • Specifying objective bounds
• Parsimonious flux balance analysis
• • Using different solvers for the problem stages
  • Using linear (L1) parsimonious constraints
• Production envelopes
• Split unidirectional reactions in models
• • Simplifying the system using asymmetric construction
  • Simplifying the system by removing original variables
• Community FBA models
• • Analysing the community
  • Investigating the solution
  • Note: interfaces of constraint systems
  • Connecting the community constraints manually
• Minimization of metabolic adjustment analysis
• • Finding parsimonious solutions
  • Comparing the results
  • Using a custom reference flux
  • Efficient linear-metric MOMA
• Enzyme constrained models
• • Reaction turnover numbers
  • Enzyme molar masses
  • Capacity limitation
  • Running a basic enzyme constrained model
  • Simplified models
  • Variability analysis with enzyme constraints
• Thermodynamic models
• • Thermodynamic data
  • Running basic max min driving force analysis
  • Using a reference solution
  • Solving the MMDF problem
• Loopless flux balance analysis (ll-FBA)
• • Running a loopless FBA (ll-FBA)
• Gene knockouts
• • Single gene knockouts
  • Multiple gene knockouts
• CycleFreeFlux
• • CycleFreeFVA
  • CycleFree sampling
• Gap filling
• • Making the model feasible with a minimal set of reactions
  • Model debugging: which metabolite is missing?
• Flux sampling
• Screening through many model variants
• • Screening in multiple dimensions
  • Screening through non-numeric properties
  • Annotating the results