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