Index

_

__prepare_context() (in module gemtract.views) _create_dir() (modules.gemtractor.utils.Utils static method) _extract_genes_from_sbml_notes() (modules.gemtractor.gemtractor.GEMtractor method) _GEMtractor__find_genes() (modules.gemtractor.gemtractor.GEMtractor method) _GEMtractor__get_expression_parser() (modules.gemtractor.gemtractor.GEMtractor method) _get_bigg_model_base_path() (modules.gemtractor.utils.Utils static method) _get_biomodel_base_path() (modules.gemtractor.utils.Utils static method) _get_genes() (modules.gemtractor.gemtractor.GEMtractor method) _implode_genes() (modules.gemtractor.gemtractor.GEMtractor method)

_Network__create_sbml_gene() (modules.gemtractor.network.network.Network method) _Network__create_sbml_gene_complex() (modules.gemtractor.network.network.Network method) _Network__create_sbml_reaction_species() (modules.gemtractor.network.network.Network method) _overwrite_genes_in_sbml_notes() (modules.gemtractor.gemtractor.GEMtractor method) _parse_expression() (modules.gemtractor.gemtractor.GEMtractor method) _set_genes_in_sbml() (modules.gemtractor.gemtractor.GEMtractor method) _unfold_complex_expression() (modules.gemtractor.gemtractor.GEMtractor method) _Utils__cleanup() (modules.gemtractor.utils.Utils static method) _Utils__collect_stats() (modules.gemtractor.utils.Utils static method) _Utils__logger (modules.gemtractor.utils.Utils attribute)

A

add_gene() (modules.gemtractor.network.genecomplex.GeneComplex method) (modules.gemtractor.network.network.Network method) add_genes() (modules.gemtractor.network.genecomplex.GeneComplex method) (modules.gemtractor.network.network.Network method) add_input() (modules.gemtractor.network.reaction.Reaction method)

add_model_note() (modules.gemtractor.utils.Utils static method) add_output() (modules.gemtractor.network.reaction.Reaction method) add_reaction() (modules.gemtractor.network.network.Network method) add_species() (modules.gemtractor.network.network.Network method) addclass() (in module gemtract.templatetags.template_tags) api.views (module)

B

base_fields (gemtract.forms.ExportForm attribute)

BreakLoops

C

calc_genenet() (modules.gemtractor.network.network.Network method) calc_id() (modules.gemtractor.network.genecomplex.GeneComplex method) calc_reaction_net() (modules.gemtractor.network.network.Network method) clean() (gemtract.forms.ExportForm method) cleanup() (modules.gemtractor.utils.Utils static method) clear_data() (in module api.views) collect_stats() (modules.gemtractor.utils.Utils static method) Constants (class in modules.gemtractor.constants)

contains_one_of() (modules.gemtractor.network.gene.Gene method) (modules.gemtractor.network.genecomplex.GeneComplex method) create_generated_file_web() (modules.gemtractor.utils.Utils static method) create_gml_edge() (modules.gemtractor.network.network.Network static method) create_gml_node() (modules.gemtractor.network.network.Network static method) create_gml_prefix() (modules.gemtractor.network.network.Network static method) create_graphml_node() (modules.gemtractor.network.network.Network static method) create_graphml_prefix() (modules.gemtractor.network.network.Network static method) create_sbml_reaction() (modules.gemtractor.network.network.Network static method)

D

declared_fields (gemtract.forms.ExportForm attribute)

del_session_key() (modules.gemtractor.utils.Utils static method)

E

execute() (in module api.views) export() (in module api.views) (in module gemtract.views) export_en_csv() (modules.gemtractor.network.network.Network method) export_en_dot() (modules.gemtractor.network.network.Network method) export_en_gml() (modules.gemtractor.network.network.Network method) export_en_graphml() (modules.gemtractor.network.network.Network method) export_en_sbml() (modules.gemtractor.network.network.Network method) export_mn_csv() (modules.gemtractor.network.network.Network method)

export_mn_dot() (modules.gemtractor.network.network.Network method) export_mn_gml() (modules.gemtractor.network.network.Network method) export_mn_graphml() (modules.gemtractor.network.network.Network method) export_rn_csv() (modules.gemtractor.network.network.Network method) export_rn_dot() (modules.gemtractor.network.network.Network method) export_rn_gml() (modules.gemtractor.network.network.Network method) export_rn_graphml() (modules.gemtractor.network.network.Network method) export_rn_sbml() (modules.gemtractor.network.network.Network method) ExportForm (class in gemtract.forms) extract_network_from_sbml() (modules.gemtractor.gemtractor.GEMtractor method)

F

filter() (in module gemtract.views)

G

gemtract.forms (module) gemtract.templatetags.template_tags (module) gemtract.views (module) GEMtractor (class in modules.gemtractor.gemtractor) Gene (class in modules.gemtractor.network.gene) GeneComplex (class in modules.gemtractor.network.genecomplex) get_bigg_model() (modules.gemtractor.utils.Utils static method) get_bigg_models() (in module api.views) (modules.gemtractor.utils.Utils static method) get_biomodel() (modules.gemtractor.utils.Utils static method)

get_biomodels() (in module api.views) (modules.gemtractor.utils.Utils static method) get_gene_product_annotations() (modules.gemtractor.gemtractor.GEMtractor method) get_id() (modules.gemtractor.network.genecomplex.GeneComplex method) get_model_path() (modules.gemtractor.utils.Utils static method) get_network() (in module api.views) get_reaction_annotations() (modules.gemtractor.gemtractor.GEMtractor method) get_sbml() (modules.gemtractor.gemtractor.GEMtractor method) get_session_data() (in module api.views) get_upload_path() (modules.gemtractor.utils.Utils static method)

H

human_readable_bytes() (modules.gemtractor.utils.Utils static method)

I

index() (in module gemtract.views) InvalidBiggId

InvalidBiomodelsId InvalidGeneComplexExpression InvalidGeneExpression

M

media (gemtract.forms.ExportForm attribute) model_exists() (in module gemtract.views) modules.gemtractor.constants (module) modules.gemtractor.exceptions (module) modules.gemtractor.gemtractor (module)

modules.gemtractor.network.gene (module) modules.gemtractor.network.genecomplex (module) modules.gemtractor.network.network (module) modules.gemtractor.network.reaction (module) modules.gemtractor.network.species (module) modules.gemtractor.utils (module)

N

Network (class in modules.gemtractor.network.network)

NotYetImplemented

P

parse_json_body() (in module api.views)

prepare_filter() (in module api.views)

R

Reaction (class in modules.gemtractor.network.reaction)

rm_cached_bigg_model() (modules.gemtractor.utils.Utils static method) rm_cached_biomodel() (modules.gemtractor.utils.Utils static method)

S

select_bigg_model() (in module api.views) select_biomodel() (in module api.views) serialize() (modules.gemtractor.network.gene.Gene method) (modules.gemtractor.network.genecomplex.GeneComplex method) (modules.gemtractor.network.network.Network method) (modules.gemtractor.network.reaction.Reaction method) (modules.gemtractor.network.species.Species method) serve_file() (in module api.views) (modules.gemtractor.utils.Utils static method) SESSION_FILTER_ENZYME_COMPLEXES (modules.gemtractor.constants.Constants attribute) SESSION_FILTER_ENZYMES (modules.gemtractor.constants.Constants attribute) SESSION_FILTER_REACTION (modules.gemtractor.constants.Constants attribute) SESSION_FILTER_SPECIES (modules.gemtractor.constants.Constants attribute) SESSION_HAS_SESSION (modules.gemtractor.constants.Constants attribute)

SESSION_HAS_SESSION_VALUE (modules.gemtractor.constants.Constants attribute) SESSION_MODEL_ID (modules.gemtractor.constants.Constants attribute) SESSION_MODEL_NAME (modules.gemtractor.constants.Constants attribute) SESSION_MODEL_TYPE (modules.gemtractor.constants.Constants attribute) SESSION_MODEL_TYPE_BIGG (modules.gemtractor.constants.Constants attribute) SESSION_MODEL_TYPE_BIOMODELS (modules.gemtractor.constants.Constants attribute) SESSION_MODEL_TYPE_UPLOAD (modules.gemtractor.constants.Constants attribute) sort_gene_complexes() (in module api.views) Species (class in modules.gemtractor.network.species) status() (in module api.views) STORAGE_BIGG_DIR (modules.gemtractor.constants.Constants attribute) STORAGE_BIOMODELS_DIR (modules.gemtractor.constants.Constants attribute) STORAGE_GENERATED_DIR (modules.gemtractor.constants.Constants attribute) STORAGE_UPLOAD_DIR (modules.gemtractor.constants.Constants attribute) store_filter() (in module api.views)

T

to_sbml_string() (modules.gemtractor.network.gene.Gene method) (modules.gemtractor.network.genecomplex.GeneComplex method)

to_string() (modules.gemtractor.network.gene.Gene method) (modules.gemtractor.network.genecomplex.GeneComplex method) TooBigForBrowser

U

UnableToRetrieveBiomodel

Utils (class in modules.gemtractor.utils)