API documentation

Here you can find the API documentation for all functions.

Analysis functions

• Analysis functions
  • Metabolic Control Analysis
  • Metabolic Control and Response Analysis
  • Test ensemble stability
  • Plot metabolic control analysis results
  • Plot metabolic control and response analysis results
  • Simulate the model ensemble

Ensemble functions

• Ensemble functions
  • Add kinetic functions to path
  • Build ensemble
  • Check stability
  • Compute Gibbs free energy ranges
  • Compute robust fluxes
  • Export model to SBML
  • Extract prior
  • Find issues with TMFA
  • Fix variable names
  • General Hit-and-Run sampler
  • Initial sampler
  • Initialize ensemble
  • Load ensemble structure
  • Pool constraint function
  • Sample allostery
  • Sample enzyme abundances
  • Sample fluxes and Gibbs free energies for each model
  • Sample general reversibilities
  • Sample modifier elementary fluxes

Pattern functions

• Pattern functions
  • Algebra
  • Build allosteric
  • Build diffusion
  • Build fixed exchange
  • Build free exchange
  • Build kinetic function
  • Build mass action
  • Build ODE function
  • Build reaction
  • Calculate extreme pathways
  • Calculate kinetic parameters
  • Column vector
  • Compute branched reversibilities
  • Cycled paths
  • Get expression
  • Get link
  • Get weight
  • Reaction pattern
  • Read input

Simulations visualization

• Simulation visualization
  • Check simulations
  • Import simulation data
  • Process thermodynamic data
  • Visualize MCA
  • Visualize simulations
  • Visualize simulations, interactively