Documentation for ETFBA

ETFBA is a Python package that extends metabolic flux balance analysis (FBA) by incorporating constraints on enzyme protein allocation and thermodynamics. ETFBA is capabable of:

• Growth simulation and metabolic flux estimation

• Variability analysis of flux, enzyme allocation and reaction energetics

with the above constraints separately or together.

Contents:

• 1. Installation
  • 1.1. Using PIP
  • 1.2. Solver Installation
• 2. Building a Model
  • 2.1. Building form Metabolite and Reaction
  • 2.2. Translating from COBRA Model
  • 2.3. Saving and Loading a Model
• 3. Constraints-based Flux analysis
  • 3.1. Basic Mass Balance-constrained Analysis (FBA)
  • 3.2. Constrained by Both Enzyme Protein Allocation and Mass Balance (EFBA)
  • 3.3. Constrained by Both Thermodynamics and Mass Balance (TFBA)
  • 3.4. Constrained by Enzyme Protein Allocation, Thermodynamics and Mass Balance (ETFBA)
• 4. Variability Analysis
  • 4.1. Flux Variability Analysis
  • 4.2. Enzyme Protein Cost Variability Analysis
  • 4.3. Thermodynamic Variability Analysis
• 5. API
  • 5.1. Subpackages
  • 5.2. Submodules
  • 5.3. Attributes
  • 5.4. Classes
  • 5.5. Package Contents

Indices and tables

• Index

• Module Index

• Search Page