CycSim : simulating with constraint-based models of metabolism

Features:
  design of in silico gene knock-out experiments,
  prediction of growth phenotypes for single and multiple, gene deletion mutants on selected environmental conditions,
  comparison of predictions with experimental results,
  visualization of both predictions and experimental results on metabolic maps.

Methods:
  Metabolite Producibility analysis : prediction of growth phenotype with essential biomass precursors,
  Flux Balance Analysis Phenotype : prediction of growth phenotype by maximizing the biomass production flux,
  Flux Balance Analysis Distribution : prediction of a flux distribution maximizing the flux of a chosen reaction using flux balance analysis.

Parameters:
  a metabolic model, for a given organism,
  a set of genetic perturbation (knock-outs),
  a set of medium.