Welcome to CONTRABASS’s documentation!

• 1. Introduction
  • 1.1. Example
• 2. Installation
• 3. Tool commands
  • 3.1 Flowchart
  • 3.2 Commands and parameters
• 4. Compute vulnerabilities
  • 4.1. Pseudocode
  • 4.2. Command
    • 4.2.1. Spreadsheet data
• 5. Compute growth dependent reactions
  • 5.1. Procedure pseudocode
• 6. Remove Dead-End Metabolites
  • 6.1. Pseudocode
  • 6.2. Command
• 7. Refine model with FVA
  • 7.1. Pseudocode
  • 7.2. Command
• 8. Low Level API
  • Try it with Binder
  • 1. core
    • Import core modules
    • Download example model
    • Read metabolic model
    • Get model info
      • Model info
      • Metabolites
      • Reactions
      • Genes
    • Dead-end metabolites
      • Finding Dead-end metabolites
      • Removing dead-end metabolites
    • Dead reactions
      • Finding Dead reactions
    • Chokepoint reactions
      • Finding chokepoint reactions
    • Flux Balance Analysis
    • Flux Variability Analysis
      • Updating flux of reactions with FVA
    • Essential genes
      • Finding essential genes
    • Essential reactions
      • Finding essential reactions
    • Essential genes reactions
      • Finding essential genes reactions
  • 2. core.Facade core.FacadeUtils
    • Import FacadeUtils modules
    • Generate vulnerabilities summary spreadsheet
    • Generate growth-dependent reactions
• 9. Online Web App
  • 9.1. Usage
    • 9.1.1. Submit model
    • 9.1.2. Run analysis
    • 9.1.3. Download reports
• 10. License