Documentation for FreeFlux

FreeFlux is a Python package for ¹³C metabolic flux analysis (¹³C MFA) of biological systems at isotopic steady state or isotopically nonstationary state (INST) state. Functionally, FreeFlux is capable of:

• Metabolic flux estimation

• Simulation of labeling patterns of metabolite (fragments)

• Constraint-based optimizations, such as flux balance analysis (FBA) and flux variability analysis (FVA)

Contents:

• 1. Installation
  • 1.1. Using PIP
  • 1.2. Solver Installation
  • 1.3. Dependencies and Compatibility
• 2. Quick Start
  • 2.1. Loading a Toy Model
  • 2.2. Setting the Labeling Strategy
  • 2.3. Adding Flux Bounds
  • 2.4. Reading the Measuremnets
  • 2.5. Solving the Fluxes
  • 2.6. Working with the “with” Statement
• 3. MDV
  • 3.1. Creating a MDV
  • 3.2. MDV Convolution
  • 3.3. Correcting for Natural Abundance
  • 3.4. Correcting for Inoculum
  • 3.5. Calculating the MDV of an Unlabeled Fragment
  • 3.6. Calculating the MDV of a Labeled Substrate
• 4. Building a Model
  • 4.1. Building with Metabolite and Reaction
  • 4.2. Reading from File
  • 4.3. Metabolic Network Decomposition
• 5. Simulating MDV at Steady State
• 6. Estimating Fluxes at Steady State
  • 6.1. Solving the Fluxes
  • 6.2. Dilution Parameter
  • 6.3. Solving the Fluxes with Confidence Intervals
• 7. Simulating at INST State
• 8. Estimating Fluxes at INST state
  • 8.1. Solving both the Fluxes and Concentrations
  • 8.2. Dilution Parameter
  • 8.3. Solving the Fluxes with Confidence Intervals
• 9. Flux Balance Analysis
  • 9.1. FBA
  • 9.2. FVA
• 10. API
  • 10.1. Submodules
  • 10.2. Attributes
  • 10.3. Classes
  • 10.4. Functions
  • 10.5. Package Contents

Indices and tables

• Index

• Module Index

• Search Page