search

SBRG / bigg_models

The BiGG Models website server
http://bigg.ucsd.edu
Other
80 stars 18 forks source link

Check models loaded by Cobra Toolbox against the database #167

Closed pillmill closed 9 years ago

pillmill commented 9 years ago

Models were loaded using Cobra Toolbox 2.0.5 from .mat files in the latest dump.

It was confirmed that number of genes and metabolites in each model was identical to that returned by corresponding queries using the Web API.

For reactions, differences in the count were reported for 59 of the models:

Model RECON1 Bigg value: 3741 Toolbox value: 3742 Model STM_v1_0 Bigg value: 2545 Toolbox value: 2546 Model iAPECO1_1312 Bigg value: 2733 Toolbox value: 2737 Model iAT_PLT_636 Bigg value: 1007 Toolbox value: 1008 Model iB21_1397 Bigg value: 2739 Toolbox value: 2743 Model iBWG_1329 Bigg value: 2739 Toolbox value: 2743 Model iE2348C_1286 Bigg value: 2701 Toolbox value: 2705 Model iEC042_1314 Bigg value: 2712 Toolbox value: 2716 Model iEC55989_1330 Bigg value: 2754 Toolbox value: 2758 Model iECABU_c1320 Bigg value: 2729 Toolbox value: 2733 Model iECBD_1354 Bigg value: 2746 Toolbox value: 2750 Model iECB_1328 Bigg value: 2746 Toolbox value: 2750 Model iECDH10B_1368 Bigg value: 2740 Toolbox value: 2744 Model iECDH1ME8569_1439 Bigg value: 2755 Toolbox value: 2756 Model iECD_1391 Bigg value: 2739 Toolbox value: 2743 Model iECED1_1282 Bigg value: 2704 Toolbox value: 2708 Model iECH74115_1262 Bigg value: 2693 Toolbox value: 2697 Model iECIAI1_1343 Bigg value: 2765 Toolbox value: 2769 Model iECIAI39_1322 Bigg value: 2719 Toolbox value: 2723 Model iECNA114_1301 Bigg value: 2716 Toolbox value: 2720 Model iECO103_1326 Bigg value: 2756 Toolbox value: 2760 Model iECO111_1330 Bigg value: 2758 Toolbox value: 2762 Model iECO26_1355 Bigg value: 2778 Toolbox value: 2782 Model iECOK1_1307 Bigg value: 2727 Toolbox value: 2731 Model iECP_1309 Bigg value: 2737 Toolbox value: 2741 Model iECS88_1305 Bigg value: 2727 Toolbox value: 2731 Model iECSE_1348 Bigg value: 2766 Toolbox value: 2770 Model iECSF_1327 Bigg value: 2740 Toolbox value: 2746 Model iECSP_1301 Bigg value: 2710 Toolbox value: 2714 Model iECUMN_1333 Bigg value: 2738 Toolbox value: 2742 Model iECW_1372 Bigg value: 2781 Toolbox value: 2783 Model iECs_1301 Bigg value: 2719 Toolbox value: 2723 Model iEKO11_1354 Bigg value: 2776 Toolbox value: 2780 Model iETEC_1333 Bigg value: 2754 Toolbox value: 2758 Model iEcDH1_1363 Bigg value: 2748 Toolbox value: 2752 Model iEcE24377_1341 Bigg value: 2761 Toolbox value: 2765 Model iEcHS_1320 Bigg value: 2751 Toolbox value: 2755 Model iEcSMS35_1347 Bigg value: 2745 Toolbox value: 2749 Model iEcolC_1368 Bigg value: 2766 Toolbox value: 2770 Model iG2583_1286 Bigg value: 2702 Toolbox value: 2706 Model iJO1366 Bigg value: 2644 Toolbox value: 2645 Model iLF82_1304 Bigg value: 2724 Toolbox value: 2728 Model iMM1415 Bigg value: 3726 Toolbox value: 3727 Model iNRG857_1313 Bigg value: 2733 Toolbox value: 2737 Model iSBO_1134 Bigg value: 2589 Toolbox value: 2593 Model iSDY_1059 Bigg value: 2537 Toolbox value: 2541 Model iSFV_1184 Bigg value: 2619 Toolbox value: 2623 Model iSF_1195 Bigg value: 2628 Toolbox value: 2632 Model iSFxv_1172 Bigg value: 2636 Toolbox value: 2640 Model iSSON_1240 Bigg value: 2691 Toolbox value: 2695 Model iS_1188 Bigg value: 2617 Toolbox value: 2621 Model iSbBS512_1146 Bigg value: 2590 Toolbox value: 2594 Model iUMN146_1321 Bigg value: 2733 Toolbox value: 2737 Model iUMNK88_1353 Bigg value: 2775 Toolbox value: 2779 Model iUTI89_1310 Bigg value: 2723 Toolbox value: 2727 Model iWFL_1372 Bigg value: 2781 Toolbox value: 2783 Model iY75_1357 Bigg value: 2757 Toolbox value: 2761 Model iZ_1308 Bigg value: 2720 Toolbox value: 2724 Model ic_1306 Bigg value: 2724 Toolbox value: 2728

zakandrewking commented 9 years ago

Thanks for checking these. We are implementing tests right now for all the models, in the latest PR #168