Tutorials

The following tutorials are based on Jupyter notebooks that are also available as live code at try.cameo.bio. Furthermore, course materials are available for a 2-day course in cell factory engineering.

• Import models
  • Import models from files
  • Import models from the internet
• Simulate models
  • Primer: Constraint-Based Modeling
  • Flux Balance Analysis
  • Parsimonious Flux Balance Analysis
  • Setp 2: Simulate knockouts phenotypes
• Analyzing models
  • Flux Variability Analysis
  • Phenotpic Phase Plane
  • Flux Balance Impact Degree
• Predict gene knockout strategies
  • OptGene
  • OptKnock
  • References
• Predict expression modulation targets
  • Flux Scanning based on Enforced Objective Flux
  • Differential flux variability analysis
• Predict heterologous pathways
• High-level interface for users
  • IPython notebook
• Vanillin production
• Genome-scale metabolic model
• Heterologous pathway
• Using meta-heuristics to search for knockout strategies.
  • Load model
  • Setup optimization strategy for gene knockouts
  • Run optimization for gene knockouts with single objective
  • Load model
  • Define objective function for search (multiple objectives)
  • Setup optimization strategy for gene knockouts
  • Run optimization for gene knockouts with multiple objective
  • Select model and define objective function for reaction knockout search (single objective)
  • Setup the optimization - ATP maintenance reaction is removed from targets
  • Run reaction knockout optimization
  • Define objectives for reaction knockout search
  • Setup the optimization
  • Run reaction knockout optimization