diff --git a/syn_elong/model_changes.py b/syn_elong/model_changes.py index fb5ade4..3d74b75 100644 --- a/syn_elong/model_changes.py +++ b/syn_elong/model_changes.py @@ -14,8 +14,7 @@ import os import logging -from concerto.utils.biolog_help import add_biolog_exchanges - +from concerto.utils.biolog_help import add_biolog_exchanges, universal_model log = logging.getLogger() @@ -40,10 +39,30 @@ def update_1(model): model = add_biolog_exchanges(model) return model +def update_2(model): + # Add the sucrose transporter SUCRt2 and associated gene + log.info("Adding Sucrose Transporter") + + # Copy sucrose transport from universal model + sucr_transport = universal_model.reactions.SUCRt2.copy() + + # Set the lower bounds for the sucrose reactions + sucr_transport.lower_bound = -1000.0 + model.reactions.EX_sucr_e.lower_bound = 0.011 + # Add the transport reaction to the model + model.add_reactions([sucr_transport]) + + # Add the gene name of the sucrose transporter to the model + gene_add = cobra.core.Gene(id='cscB',name='cscB',functional=True) + model.reactions.SUCRt2.gene_reaction_rule = '( cscB )' + + return model + def process_model_steps(): # Fix compartments model = update_1(starting_model) + model = update_2(model) write_model(model) diff --git a/syn_elong/syn_elong.xml b/syn_elong/syn_elong.xml index ddcff89..f1db34c 100644 --- a/syn_elong/syn_elong.xml +++ b/syn_elong/syn_elong.xml @@ -19731,122 +19731,3939 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + +

original_bigg_ids: ['tre', 'tre[e]', 'tre_e']

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original_bigg_ids: ['man', 'man[e]', 'man_e']

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original_bigg_ids: ['galt', 'galt[e]', 'galt_e']

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original_bigg_ids: ['arab-L[e]', 'arab_DASH_L_e', 'arab_L[e]', 'arab_L_e', 'arab__L', 'arab__L_e']

+ + + + + + + + + + + + + + + + + + + + + + + + +

original_bigg_ids: ['acgam', 'acgam[e]', 'acgam_e']

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original_bigg_ids: ['glcr', 'glcr[e]', 'glcr_e']

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original_bigg_ids: ['succ', 'succ[e]', 'succ_e']

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original_bigg_ids: ['gal', 'gal[e]', 'gal_e']

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original_bigg_ids: ['asp-L[e]', 'asp_DASH_L_e', 'asp_L[e]', 'asp_L_e', 'asp__L', 'asp__L_e']

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

original_bigg_ids: ['pro-L[e]', 'pro_DASH_L_e', 'pro_L[e]', 'pro_L_e', 'pro__L', 'pro__L_e']

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original_bigg_ids: ['ala-D[e]', 'ala_DASH_D_e', 'ala_D[e]', 'ala_D_e', 'ala__D', 'ala__D_e']

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original_bigg_ids: ['ser-D[e]', 'ser_DASH_D_e', 'ser_D[e]', 'ser_D_e', 'ser__D', 'ser__D_e']

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original_bigg_ids: ['for', 'for[e]', 'for_e']

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original_bigg_ids: ['mnl', 'mnl_e']

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original_bigg_ids: ['glu-L[e]', 'glu_DASH_L_e', 'glu_L[e]', 'glu_L_e', 'glu__L', 'glu__L_e']

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original_bigg_ids: ['sbt_DASH_D_e', 'sbt_D[e]', 'sbt_D_e', 'sbt__D', 'sbt__D_e']

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original_bigg_ids: ['glyc', 'glyc[e]', 'glyc_e']

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original_bigg_ids: ['fuc_DASH_L_e', 'fuc_L[e]', 'fuc_L_e', 'fuc__L', 'fuc__L_e']

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original_bigg_ids: ['glcur', 'glcur[e]', 'glcur_e']

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original_bigg_ids: ['glcn', 'glcn[e]', 'glcn_e']

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original_bigg_ids: ['glyc3p', 'glyc3p[e]', 'glyc3p_e']

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original_bigg_ids: ['xyl-D[e]', 'xyl_DASH_D_e', 'xyl_D[e]', 'xyl_D_e', 'xyl__D', 'xyl__D_e']

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original_bigg_ids: ['lac-L[e]', 'lac_DASH_L_e', 'lac_L[e]', 'lac_L_e', 'lac__L', 'lac__L_e']

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original_bigg_ids: ['g6p', 'g6p_e']

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original_bigg_ids: ['malt', 'malt[e]', 'malt_e']

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original_bigg_ids: ['melib', 'melib[e]', 'melib_e']

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original_bigg_ids: ['thymd', 'thymd[e]', 'thymd_e']

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original_bigg_ids: ['galctn-D[e]', 'galctn_DASH_D_e', 'galctn_D_e', 'galctn__D', 'galctn__D_e']

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original_bigg_ids: ['rib-D[e]', 'rib_DASH_D_e', 'rib_D[e]', 'rib_D_e', 'rib__D', 'rib__D_e']

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original_bigg_ids: ['rmn', 'rmn[e]', 'rmn_e']

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original_bigg_ids: ['fru', 'fru[e]', 'fru_e']

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original_bigg_ids: ['ac', 'ac[e]', 'ac_e']

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original_bigg_ids: ['glc-D[e]', 'glc_DASH_D_e', 'glc_D[e]', 'glc_D_e', 'glc__D', 'glc__D_e']

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

original_bigg_ids: ['asn-L[e]', 'asn_DASH_L_e', 'asn_L[e]', 'asn_L_e', 'asn__L', 'asn__L_e']

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original_bigg_ids: ['sucr', 'sucr[e]', 'sucr_e']

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original_bigg_ids: ['uri', 'uri[e]', 'uri_e']

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original_bigg_ids: ['12ppd_DASH_S_e', '12ppd_S_e', '12ppd__S', '12ppd__S_e']

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original_bigg_ids: ['akg', 'akg[e]', 'akg_e']

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original_bigg_ids: ['lcts', 'lcts[e]', 'lcts_e']

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original_bigg_ids: ['malttr', 'malttr[e]', 'malttr_e']

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original_bigg_ids: ['dad_2', 'dad_2[e]', 'dad_2_e', 'dad_DASH_2_e', 'dad__2_e']

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original_bigg_ids: ['adn', 'adn[e]', 'adn_e']

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original_bigg_ids: ['g1p', 'g1p[e]', 'g1p_e']

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original_bigg_ids: ['f6p', 'f6p_e']

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original_bigg_ids: ['ins', 'ins[e]', 'ins_e']

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original_bigg_ids: ['cit', 'cit[e]', 'cit_e']

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original_bigg_ids: ['inost', 'inost[e]', 'inost_e']

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original_bigg_ids: ['fum', 'fum[e]', 'fum_e']

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original_bigg_ids: ['ppa', 'ppa[e]', 'ppa_e']

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original_bigg_ids: ['galct_DASH_D_e', 'galct_D_e', 'galct__D', 'galct__D_e']

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original_bigg_ids: ['glyclt', 'glyclt[e]', 'glyclt_e']

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original_bigg_ids: ['mal_DASH_D_e', 'mal_D_e', 'mal__D', 'mal__D_e']

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original_bigg_ids: ['mal_DASH_L_e', 'mal_L[e]', 'mal_L_e', 'mal__L', 'mal__L_e']

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

original_bigg_ids: ['ser-L[e]', 'ser_DASH_L_e', 'ser_L[e]', 'ser_L_e', 'ser__L', 'ser__L_e']

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original_bigg_ids: ['thr_DASH_L_e', 'thr_L[e]', 'thr_L_e', 'thr__L', 'thr__L_e']

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

original_bigg_ids: ['ala_DASH_L_e', 'ala_L[e]', 'ala_L_e', 'ala__L', 'ala__L_e']

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original_bigg_ids: ['acac', 'acac[e]', 'acac_e']

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original_bigg_ids: ['acmana', 'acmana[e]', 'acmana_e']

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original_bigg_ids: ['galur', 'galur[e]', 'galur_e']

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original_bigg_ids: ['peamn', 'peamn_e']

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original_bigg_ids: ['etha', 'etha[e]', 'etha_e']

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original_bigg_ids: ['tym', 'tym[e]', 'tym_e']

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original_bigg_ids: ['lyx_DASH_L_e', 'lyx_L_e', 'lyx__L', 'lyx__L_e']

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original_bigg_ids: ['pyr', 'pyr[e]', 'pyr_e']

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original_bigg_ids: ['galctn_DASH_L_e', 'galctn_L_e', 'galctn__L', 'galctn__L_e']

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original_bigg_ids: ['acnam', 'acnam[e]', 'acnam_e']

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original_bigg_ids: ['all_DASH_D_e', 'all_D_e', 'all__D', 'all__D_e']

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original_bigg_ids: ['4abut', '4abut[e]', '4abut_e']

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original_bigg_ids: ['but', 'but[e]', 'but_e']

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original_bigg_ids: ['dca', 'dca[e]', 'dca_e']

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original_bigg_ids: ['5dglcn', '5dglcn_e']

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original_bigg_ids: ['hxa', 'hxa[e]', 'hxa_e']

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original_bigg_ids: ['tartr_DASH_L_e', 'tartr_L_e', 'tartr__L', 'tartr__L_e']

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original_bigg_ids: ['lys-L[e]', 'lys_DASH_L_e', 'lys_L[e]', 'lys_L_e', 'lys__L', 'lys__L_e']

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original_bigg_ids: ['met-L[e]', 'met_DASH_L_e', 'met_L[e]', 'met_L_e', 'met__L', 'met__L_e']

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original_bigg_ids: ['gly', 'gly[e]', 'gly_e']

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original_bigg_ids: ['hom_DASH_L_e', 'hom_L[e]', 'hom_L_e', 'hom__L', 'hom__L_e']

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +

original_bigg_ids: ['ile-L[e]', 'ile_DASH_L_e', 'ile_L[e]', 'ile_L_e', 'ile__L', 'ile__L_e']

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original_bigg_ids: ['orn', 'orn[e]', 'orn_e']

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original_bigg_ids: ['phe_DASH_L_e', 'phe_L[e]', 'phe_L_e', 'phe__L', 'phe__L_e']

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original_bigg_ids: ['val-L[e]', 'val_DASH_L_e', 'val_L[e]', 'val_L_e', 'val__L', 'val__L_e']

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original_bigg_ids: ['dha', 'dha[e]', 'dha_e']

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original_bigg_ids: ['cys-L[e]', 'cys_DASH_L_e', 'cys_L[e]', 'cys_L_e', 'cys__L', 'cys__L_e']

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original_bigg_ids: ['urea', 'urea[e]', 'urea_e']

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original_bigg_ids: ['trp-L[e]', 'trp_DASH_L_e', 'trp_L[e]', 'trp_L_e', 'trp__L', 'trp__L_e']

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original_bigg_ids: ['tyr_DASH_L_e', 'tyr_L[e]', 'tyr_L_e', 'tyr__L', 'tyr__L_e']

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original_bigg_ids: ['agm', 'agm[e]', 'agm_e']

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original_bigg_ids: ['acgal', 'acgal[e]', 'acgal_e']

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original_bigg_ids: ['gam', 'gam[e]', 'gam_e']

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original_bigg_ids: ['ura', 'ura[e]', 'ura_e']

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original_bigg_ids: ['ade', 'ade[e]', 'ade_e']

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original_bigg_ids: ['cytd', 'cytd[e]', 'cytd_e']

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original_bigg_ids: ['csn', 'csn[e]', 'csn_e']

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original_bigg_ids: ['gua', 'gua[e]', 'gua_e']

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original_bigg_ids: ['gsn', 'gsn[e]', 'gsn_e']

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original_bigg_ids: ['thym', 'thym[e]', 'thym_e']

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original_bigg_ids: ['xan', 'xan[e]', 'xan_e']

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original_bigg_ids: ['xtsn', 'xtsn[e]', 'xtsn_e']

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original_bigg_ids: ['alltn', 'alltn[e]', 'alltn_e']

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original_bigg_ids: ['23camp', '23camp_e']

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original_bigg_ids: ['3amp', '3amp_e']

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original_bigg_ids: ['gmp', 'gmp[e]', 'gmp_e']

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original_bigg_ids: ['23cgmp', '23cgmp_e']

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original_bigg_ids: ['3gmp', '3gmp_e']

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original_bigg_ids: ['cmp', 'cmp[e]', 'cmp_e']

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original_bigg_ids: ['23ccmp', '23ccmp_e']

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original_bigg_ids: ['gam6p', 'gam6p_e']

+ + + + + + + + + + + + + + + + + + + + + + + + +

original_bigg_ids: ['3cmp', '3cmp_e']

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original_bigg_ids: ['ump', 'ump[e]', 'ump_e']

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original_bigg_ids: ['23cump', '23cump[e]', '23cump_e']

+ + + + + + + + + + + + + + + + + + + + + + + + + + +

original_bigg_ids: ['man6p', 'man6p_e']

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original_bigg_ids: ['pser_DASH_L_e', 'pser_L[e]', 'pser_L_e', 'pser__L', 'pser__L_e']

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original_bigg_ids: ['thrp', 'thrp_e']

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original_bigg_ids: ['3ump', '3ump[e]', '3ump_e']

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original_bigg_ids: ['tyrp', 'tyrp_e']

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original_bigg_ids: ['minohp', 'minohp_e']

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original_bigg_ids: ['SUCRt2']

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