alternative pathways | BYPASS_REACTIONS_SUBSTRATE, to find the influx and efflux reactions available to a particular metabolite/substrate |

BFD_Processor | BFD_Processor, a Bi-Flux-Del-Processor function |

bypass reactions for metabolites | BYPASS_REACTIONS_SUBSTRATE, to find the influx and efflux reactions available to a particular metabolite/substrate |

BYPASS_REACTIONS_SUBSTRATE | BYPASS_REACTIONS_SUBSTRATE, to find the influx and efflux reactions available to a particular metabolite/substrate |

change objective | CHANGE_OBJ_FUNCTION, a function to change the objective for optimization |

Change Reaction Bounds | CHANGE_RXN_BOUNDS, Change Reaction Bounds |

CHANGE_OBJ_FUNCTION | CHANGE_OBJ_FUNCTION, a function to change the objective for optimization |

CHANGE_RXN_BOUNDS | CHANGE_RXN_BOUNDS, Change Reaction Bounds |

comparison of single deletion flux distributions | SINGLE_DEL_FLUXOME, a function to generate comparative fluxome graphs |

degree-measure | DEGREE_MEASURE, measures the in-degree and out-degree of the metabolites in the network. |

DEGREE_MEASURE | DEGREE_MEASURE, measures the in-degree and out-degree of the metabolites in the network. |

double knockout | Exhaustive_double_deletion, a function for computing synthetic double knockouts. |

double knockout result processor | BFD_Processor, a Bi-Flux-Del-Processor function |

double synthetic lethality | Exhaustive_double_deletion, a function for computing synthetic double knockouts. |

Ecoli_core | E.coli core model 72 reactions and 95 metabolites |

Ec_iAF1260_flux1 | E.coli model 1260 ORF's |

Ec_iAF1260_flux2 | E.coli model 1260 ORF's |

Ec_iJR904 | E.coli model 904 ORF's |

Exhaustive_double_deletion | Exhaustive_double_deletion, a function for computing synthetic double knockouts. |

Exhaustive_single_deletion | Exhaustive_single_deletion, a function that deletes each reaction in the network one at a time and returns results describing reaction lethality |

FBA_solve | FBA_solve, a function to solve CBM problems |

flux distribution comparisons | flux_difference_plotter, a function to plot two pre-existing flux distributions obtained using FBA_solve |

Flux Variability Analysis | FLUX_VAR_ANALYSIS, a function to perform a flux variability analysis. |

fluxome graphs | SINGLE_DEL_FLUXOME, a function to generate comparative fluxome graphs |

flux_difference_plotter | flux_difference_plotter, a function to plot two pre-existing flux distributions obtained using FBA_solve |

Flux_Ranger | Flux_Ranger - a function to create a flux ramp. |

FLUX_VAR_ANALYSIS | FLUX_VAR_ANALYSIS, a function to perform a flux variability analysis. |

FVA_robustness | FVA_robustness, a function to determine the change in robustness of the network caused by a mutation. |

gene deletion | Gene_del, a function to create Gene Deletion mutants |

genetic mutants | Gene_del, a function to create Gene Deletion mutants |

Gene_del | Gene_del, a function to create Gene Deletion mutants |

H_pylori_iIT341 | Helicobacter pylori by Ines Thiele |

H_sapien_Recon1 | H. sapien Recon1, human metabolic network reconstruction |

in-degree | DEGREE_MEASURE, measures the in-degree and out-degree of the metabolites in the network. |

M_barkeri_iAF629 | Genome scale metabolic model for the archaeal methanogen M. Barkeri |

M_tb_iNJ661 | M. tuberculosis model iNJ661 |

Objective function | View_objective, a function that shows the components of the objective function. |

objective function | CHANGE_OBJ_FUNCTION, a function to change the objective for optimization |

out-degree | DEGREE_MEASURE, measures the in-degree and out-degree of the metabolites in the network. |

parallel multi-core simulation | Exhaustive_double_deletion, a function for computing synthetic double knockouts. |

PERTURBATION_analysis | PERTURBATION_analysis, a function for robustness analysis. |

phenotypic phase plane analysis | PHPP, phenotypic phase plane analysis |

PHPP | PHPP, phenotypic phase plane analysis |

ramp-down | PERTURBATION_analysis, a function for robustness analysis. |

ramp-up | PERTURBATION_analysis, a function for robustness analysis. |

robustness analysis | PERTURBATION_analysis, a function for robustness analysis. |

Robustness analysis using FVA | FVA_robustness, a function to determine the change in robustness of the network caused by a mutation. |

SBML | Sybil_2_FBA_obj, a function to convert a model generated by Sybil into the one used by abcdeFBA. |

Search-metabolite | SEARCH_metabolite, a function to search for metabolites in a model using a simple text query |

Search-reaction | SEARCH_reaction, a function to search for reactions in a model using a simple text query |

SEARCH_metabolite | SEARCH_metabolite, a function to search for metabolites in a model using a simple text query |

SEARCH_reaction | SEARCH_reaction, a function to search for reactions in a model using a simple text query |

single knockouts | Exhaustive_single_deletion, a function that deletes each reaction in the network one at a time and returns results describing reaction lethality |

SINGLE_DEL_FLUXOME | SINGLE_DEL_FLUXOME, a function to generate comparative fluxome graphs |

solve FBA problem | FBA_solve, a function to solve CBM problems |

Sybil_2_FBA_obj | Sybil_2_FBA_obj, a function to convert a model generated by Sybil into the one used by abcdeFBA. |

Sybil_S4_object | Sybil_2_FBA_obj, a function to convert a model generated by Sybil into the one used by abcdeFBA. |

S_aureus_iSB619 | Staphylococcus aureus model iSB619 by S.Becker |

S_cerevisiae_IND750 | Saccharomyces Cerevisiae iND750 |

View_objective | View_objective, a function that shows the components of the objective function. |