Elixir-SystemsBiology

Repository holding the contributions of the Systems Biology members of WP5 of ELIXIR 3

Overview

GEM modules

1. gem_extract_exchange: Extracts the exchange reactions of the provided gem as a CSV, which can then be modified and used as an input to modify the environment for the other GEM modules
2. gem_check_memote: Runs memote on provided GEM, returning snapshot report
3. gem_escher_visualization: Runs Escher with specified parameters, giving a modifiable html file with an overview of the metabolic network
4. gem_flux_distribution: Performs FBA to solve the provided model with the provided parameters, returning a flux distribution in the form of a CSV
5. gem_flux_variability_analysis: Performs FVA to return the reachable flux ranges for the proivded model and parameters
6. gem_phenotype_phase_plane: Runs a phenotype phase plane analysis for the provided model and parameters, showing how the model objective scales with the specified reactions
7. gem_knockout: Performs single or double knockout analysis for the provided model and parameters, returning all flux values for WT and KO for every (combination of) gene knockout