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SysBioChalmers / yeast-GEM

The consensus GEM for Saccharomyces cerevisiae
http://sysbiochalmers.github.io/yeast-GEM/
Creative Commons Attribution 4.0 International
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Fix/unbalanced_rxns #222

Closed eiden309 closed 4 years ago

eiden309 commented 4 years ago

Main improvements in this PR:

1. Added checkSmatrixMNX.m (script intended for automatic curation of reaction balance) into repository for documentation purposes

2. After manual curation of selected unbalanced reactions in the model (details found in modMetsandSmatrix.tsv), used script modMetsandSmatrix.m to balance reactions by:

*Addresses all reactions which can currently be balanced (based on information from existing databases) in issue #194 Script display_rxnMetInfo.m** utilized to facilitate manual curation

3. After reactions are elemental- and charge-balanced, identified that requirement of coenzyme A (CoA) in biomass equation for the anaerobic model is not necessary and removed the CoA requirement

4. After changes are made, checkRxnBalance.m committed in this PR is used to check the model before and after the changes. Exchange reactions, transport reactions, SLIMER reactions and reactions with missing information are excluded from the final output.

List of reactions balanced: r_0001 r_0002 r_0004 r_0014 r_0015 r_0034 r_0035 r_0038 r_0041 r_0043 r_0045 r_0063 r_0066 r_0067 r_0073 r_0074 r_0080 r_0082 r_0083 r_0088 r_0089 r_0092 r_0093 r_0094 r_0100 r_0105 r_0106 r_0107 r_0123 r_0124 r_0146 r_0150 r_0153 r_0157 r_0189 r_0195 r_0209 r_0210 r_0212 r_0213 r_0215 r_0219 r_0223 r_0224 r_0228 r_0234 r_0240 r_0263 r_0264 r_0265 r_0266 r_0271 r_0274 r_0282 r_0312 r_0313 r_0315 r_0319 r_0322 r_0335 r_0340 r_0341 r_0342 r_0343 r_0344 r_0345 r_0357 r_0358 r_0360 r_0361 r_0362 r_0363 r_0364 r_0437 r_0441 r_0442 r_0446 r_0447 r_0449 r_0450 r_0454 r_0455 r_0457 r_0461 r_0463 r_0464 r_0465 r_0466 r_0467 r_0477 r_0478 r_0490 r_0499 r_0501 r_0502 r_0503 r_0504 r_0506 r_0507 r_0508 r_0509 r_0511 r_0512 r_0518 r_0524 r_0525 r_0530 r_0531 r_0534 r_0535 r_0539 r_0540 r_0545 r_0550 r_0551 r_0552 r_0555 r_0558 r_0559 r_0560 r_0571 r_0572 r_0573 r_0574 r_0575 r_0616 r_0617 r_0618 r_0619 r_0620 r_0621 r_0622 r_0623 r_0624 r_0625 r_0646 r_0647 r_0648 r_0649 r_0650 r_0651 r_0652 r_0653 r_0654 r_0655 r_0665 r_0666 r_0672 r_0673 r_0681 r_0682 r_0683 r_0687 r_0690 r_0695 r_0701 r_0702 r_0703 r_0704 r_0705 r_0706 r_0711 r_0712 r_0722 r_0723 r_0727 r_0728 r_0729 r_0730 r_0737 r_0747 r_0748 r_0749 r_0750 r_0751 r_0752 r_0753 r_0754 r_0755 r_0756 r_0758 r_0760 r_0763 r_0768 r_0769 r_0785 r_0797 r_0798 r_0799 r_0800 r_0802 r_0803 r_0804 r_0813 r_0831 r_0832 r_0842 r_0852 r_0853 r_0855 r_0882 r_0883 r_0886 r_0888 r_0890 r_0905 r_0907 r_0911 r_0912 r_0916 r_0919 r_0920 r_0921 r_0922 r_0941 r_0967 r_0968 r_0969 r_0970 r_0971 r_0972 r_0973 r_0974 r_0975 r_0976 r_0977 r_0978 r_0979 r_0982 r_0993 r_0995 r_0998 r_0999 r_1000 r_1004 r_1006 r_1027 r_1029 r_1031 r_1032 r_1033 r_1034 r_1035 r_1036 r_1037 r_1038 r_1039 r_1042 r_1043 r_1045 r_1049 r_1057 r_1058 r_1066 r_1067 r_1069 r_1076 r_1078 r_1089 r_1090 r_1095 r_1617 r_1690 r_1725 r_1797 r_1975 r_2064 r_2074 r_2112 r_2113 r_2116 r_2126 r_2147 r_2148 r_2150 r_2151 r_2154 r_2156 r_2157 r_2162 r_2168 r_2172 r_2176 r_2177 r_2179 r_2209 r_2210 r_2211 r_2212 r_2213 r_2214 r_2215 r_2216 r_2217 r_2218 r_2232 r_2233 r_2238 r_2240 r_2242 r_2244 r_2245 r_2248 r_2249 r_2250 r_2258 r_2260 r_2268 r_2271 r_2275 r_2277 r_2280 r_2281 r_2282 r_2286 r_2289 r_2290 r_2292 r_2293 r_2294 r_2295 r_2296 r_2297 r_2298 r_2300 r_2302 r_2304 r_2308 r_2309 r_2310 r_2311 r_2312 r_2313 r_2315 r_2316 r_2317 r_2318 r_2319 r_2320 r_2321 r_2323 r_2325 r_2326 r_2327 r_2329 r_2330 r_2331 r_2332 r_2344 r_2345 r_2346 r_2347 r_2348 r_2349 r_2350 r_2351 r_2352 r_2353 r_2354 r_2355 r_2356 r_2357 r_2358 r_2359 r_2360 r_2361 r_2362 r_2363 r_2364 r_2365 r_2366 r_2367 r_2368 r_2376 r_2384 r_2392 r_2400 r_2408 r_2416 r_2424 r_2432 r_2438 r_2440 r_2446 r_2447 r_2448 r_2449 r_2450 r_2451 r_2452 r_2453 r_2454 r_2455 r_2456 r_2457 r_2458 r_2459 r_2460 r_2461 r_2462 r_2463 r_2464 r_2465 r_2466 r_2467 r_2468 r_2469 r_2470 r_2471 r_2472 r_2473 r_2474 r_2475 r_2476 r_2477 r_2478 r_2479 r_2480 r_2481 r_2482 r_2483 r_2484 r_2485 r_2486 r_2487 r_2506 r_2507 r_2510 r_2511 r_2512 r_2513 r_2514 r_2515 r_2516 r_2517 r_2518 r_2519 r_2520 r_2528 r_2529 r_2530 r_2531 r_2532 r_2533 r_2534 r_2535 r_2536 r_2537 r_2538 r_2539 r_2540 r_2541 r_2542 r_2543 r_2544 r_2545 r_2546 r_2547 r_2548 r_2549 r_2550 r_2551 r_2552 r_2553 r_2554 r_2555 r_2556 r_2557 r_2558 r_2559 r_2560 r_2561 r_2562 r_2563 r_2564 r_2565 r_2566 r_2567 r_2568 r_2569 r_2570 r_2571 r_2572 r_2573 r_2574 r_2575 r_2576 r_2577 r_2578 r_2579 r_2580 r_2581 r_2582 r_2583 r_2584 r_2586 r_2588 r_2590 r_2592 r_2594 r_2596 r_2598 r_2600 r_2602 r_2603 r_2604 r_2605 r_2606 r_2607 r_2608 r_2609 r_2610 r_2611 r_2612 r_2613 r_2614 r_2615 r_2616 r_2617 r_2618 r_2619 r_2620 r_2621 r_2622 r_2623 r_2624 r_2625 r_2626 r_2627 r_2628 r_2629 r_2630 r_2631 r_2632 r_2633 r_2634 r_2635 r_2636 r_2637 r_2638 r_2639 r_2640 r_2641 r_2642 r_2643 r_2644 r_2645 r_2646 r_2647 r_2648 r_2649 r_2650 r_2651 r_2652 r_2653 r_2654 r_2655 r_2656 r_2657 r_2658 r_2659 r_2660 r_2661 r_2662 r_2663 r_2664 r_2665 r_2666 r_2667 r_2668 r_2669 r_2670 r_2671 r_2672 r_2673 r_2674 r_2675 r_2676 r_2677 r_2678 r_2679 r_2680 r_2681 r_2682 r_2683 r_2684 r_2685 r_2686 r_2687 r_2688 r_2689 r_2690 r_2691 r_2692 r_2693 r_2694 r_2695 r_2696 r_2697 r_2698 r_2699 r_2700 r_2701 r_2702 r_2703 r_2704 r_2705 r_2706 r_2707 r_2708 r_2709 r_2710 r_2711 r_2712 r_2713 r_2714 r_2715 r_2716 r_2717 r_2718 r_2719 r_2720 r_2721 r_2722 r_2723 r_2724 r_2725 r_2726 r_2727 r_2728 r_2729 r_2730 r_2731 r_2732 r_2733 r_2734 r_2735 r_2736 r_2737 r_2738 r_2739 r_2740 r_2741 r_2742 r_2743 r_2744 r_2745 r_2746 r_2747 r_2748 r_2749 r_2750 r_2751 r_2752 r_2753 r_2754 r_2755 r_2756 r_2757 r_2758 r_2759 r_2760 r_2761 r_2762 r_2763 r_2764 r_2765 r_2766 r_2767 r_2768 r_2769 r_2770 r_2771 r_2772 r_2773 r_2774 r_2775 r_2776 r_2777 r_2778 r_2779 r_2780 r_2781 r_2782 r_2783 r_2784 r_2785 r_2786 r_2787 r_2788 r_2789 r_2790 r_2791 r_2792 r_2793 r_2794 r_2795 r_2796 r_2797 r_2798 r_2799 r_2800 r_2801 r_2802 r_2803 r_2804 r_2805 r_2806 r_2807 r_2808 r_2809 r_2810 r_2811 r_2812 r_2813 r_2814 r_2815 r_2816 r_2817 r_2818 r_2819 r_2820 r_2821 r_2822 r_2823 r_2824 r_2825 r_2826 r_2827 r_2828 r_2829 r_2830 r_2831 r_2832 r_2833 r_2834 r_2835 r_2836 r_2837 r_2838 r_2839 r_2840 r_2841 r_2842 r_2843 r_2844 r_2845 r_2846 r_2847 r_2848 r_2849 r_2850 r_2851 r_2852 r_2853 r_2854 r_2855 r_2856 r_2857 r_2858 r_2859 r_2860 r_2861 r_2862 r_2863 r_2864 r_2865 r_2866 r_2867 r_2868 r_2869 r_2870 r_2871 r_2872 r_2873 r_2874 r_2875 r_2876 r_2877 r_2878 r_2879 r_2880 r_2881 r_2882 r_2883 r_2884 r_2885 r_2886 r_2887 r_2888 r_2889 r_2890 r_2891 r_2948 r_2949 r_2950 r_2951 r_2952 r_2953 r_2954 r_2955 r_2956 r_2957 r_2958 r_2959 r_2960 r_2961 r_2962 r_2963 r_2964 r_2965 r_2966 r_2967 r_2968 r_2969 r_2970 r_2971 r_2972 r_2973 r_2974 r_2975 r_2976 r_2977 r_2978 r_2979 r_2980 r_2981 r_2982 r_2983 r_2984 r_2985 r_2986 r_2987 r_2988 r_2989 r_2990 r_2991 r_2992 r_2993 r_2994 r_2995 r_2996 r_2997 r_2998 r_2999 r_3000 r_3001 r_3002 r_3003 r_3004 r_3005 r_3006 r_3007 r_3008 r_3009 r_3010 r_3011 r_3022 r_3023 r_3024 r_3025 r_3026 r_3027 r_3028 r_3029 r_3030 r_3031 r_3032 r_3033 r_3034 r_3035 r_3036 r_3037 r_3038 r_3039 r_3040 r_3041 r_3042 r_3043 r_3044 r_3045 r_3058 r_3059 r_3060 r_3061 r_3062 r_3063 r_3064 r_3065 r_3066 r_3067 r_3068 r_3069 r_3078 r_3079 r_3080 r_3081 r_3082 r_3083 r_3084 r_3085 r_3086 r_3087 r_3088 r_3089 r_3090 r_3091 r_3092 r_3093 r_3094 r_3095 r_3096 r_3097 r_3098 r_3099 r_3100 r_3101 r_3102 r_3103 r_3105 r_3106 r_3107 r_3108 r_3109 r_3110 r_3111 r_3112 r_3113 r_3114 r_3115 r_3116 r_3117 r_3118 r_3119 r_3120 r_3121 r_3122 r_3123 r_3124 r_3125 r_3126 r_3127 r_3128 r_3129 r_3130 r_3131 r_3132 r_3133 r_3134 r_3135 r_3136 r_3137 r_3138 r_3139 r_3140 r_3141 r_3142 r_3143 r_3144 r_3145 r_3146 r_3147 r_3148 r_3149 r_3150 r_3151 r_3152 r_3153 r_3154 r_3155 r_3156 r_3157 r_3158 r_3159 r_3160 r_3161 r_3162 r_3163 r_3164 r_3165 r_3166 r_3167 r_3168 r_3169 r_3170 r_3171 r_3172 r_3173 r_3174 r_3175 r_3176 r_3177 r_3178 r_3179 r_3180 r_3181 r_3182 r_3183 r_3184 r_3185 r_3186 r_3187 r_3188 r_3189 r_3190 r_3191 r_3192 r_3193 r_3194 r_3195 r_3196 r_3197 r_3198 r_3199 r_3200 r_3201 r_3202 r_3203 r_3204 r_3205 r_3206 r_3207 r_3208 r_3209 r_3210 r_3211 r_3212 r_3213 r_3214 r_3215 r_3216 r_3217 r_3218 r_3219 r_3220 r_3221 r_3222 r_3223 r_3224 r_3225 r_3226 r_3227 r_3228 r_3229 r_3230 r_3231 r_3232 r_3233 r_3234 r_3235 r_3236 r_3237 r_3238 r_3239 r_3240 r_3241 r_3242 r_3243 r_3244 r_3245 r_3246 r_3247 r_3248 r_3249 r_3250 r_3251 r_3264 r_3265 r_3266 r_3267 r_3296 r_3316 r_3317 r_3318 r_3319 r_3320 r_3321 r_3322 r_3323 r_3332 r_3333 r_3334 r_3335 r_3336 r_3337 r_3338 r_3339 r_3340 r_3341 r_3342 r_3343 r_3344 r_3345 r_3346 r_3347 r_3348 r_3356 r_3364 r_3372 r_3380 r_3388 r_3396 r_3404 r_3412 r_3420 r_3428 r_3436 r_3444 r_3452 r_3460 r_3468 r_3476 r_3484 r_3492 r_3500 r_4042 r_4186 r_4202 r_4219 r_4235 r_4239 r_4245 r_4267 r_4268 r_4279 r_4286 r_4303 r_4304 r_4313 r_4382 r_4495 r_4567 r_4571 r_4577 r_4578
Remaining unbalanced reactions: model.rxns | Imbalance issue(s) to check | Charge difference | Elemental difference -- | -- | -- | -- r_0013 | checkMetCharge | 4 | [] r_0229 | checkMetCharge | 2 | [] r_0365 | checkMetCharge | -1 | [] r_0438 | checkMetChargeAndFormula | -0.633 | H0.633 r_0439 | checkMetChargeAndFormula | 1.266 | H-1.266 r_0532 | checkMetCharge | -2 | [] r_1603 | checkMetFormula | [] | H-2 r_2070 | checkMetCharge | -2 | [] r_2071 | checkMetCharge | -2 | [] r_4170 | checkMetFormula | [] | R-1 r_4250 | checkMetFormula | [] | R1 r_4253 | checkMetFormula | [] | R1 r_4271 | checkMetFormula | [] | R1 r_4320 | checkMetChargeAndFormula | 2 | R1 r_4321 | checkMetChargeAndFormula | -2 | R1 r_4328 | checkMetFormula | [] | R-1 r_4568 | checkMetFormula | [] | O-1

I hereby confirm that I have:

feiranl commented 4 years ago

@BenjaSanchez When I rerun this commit, all bigg IDs for mets and rxns cannot be saved. So I try only loadYeastModel and saveYeastModel function in devel branch, it is same, all bigg IDs are removed. And even though that I want to rerun the addBiGGidentifiers.m, there is a problem here for my matlab using xlsread. Could you help to check that? I think it is beacuse that when loadYeastModel, biggID field was loaded in a different field. After using the below code, it can be saved again. I noticed that in ravenCobraWrapper: as for metBiGGID, I noticed that that metBiGGID and metBiGGID are present in the function.

model.metBiGGID = model.metisbigg__46__metaboliteID
model.rxnBIGGID = model.rxnisbigg__46__reactionID

Dependencies: matlab 2019b cobra 3.1 raven 2.3.1

BenjaSanchez commented 4 years ago

@feiranl as I wrote in PR #188:

NOTE that after this branch is merged and until new versions for (RAVEN & COBRA) toolboxes are released, any further development in yeast-GEM should be conducted with the corresponding (development) toolbox branches (otherwise the BiGG fields will be removed) @feiranl.

So please revert your changes and switch to devel in RAVEN & COBRA

edkerk commented 4 years ago

By running the code below:

code


bs       = getElementalBalance(model);
idx      = find(bs.balanceStatus==0);
[~,exch] = getExchangeRxns(model);
slime    = find(contains(model.rxnNames,'SLIME'));
idx(ismember(idx,[exch;slime]))=[];
out = model.rxns(idx);
for i=1:length(idx)
    dif = bs.leftComp(idx(i),:) - bs.rightComp(idx(i),:);
    mets = find(~dif==0);
    difference = '';
    for j=1:length(mets)
        difference = strcat(difference,bs.elements.abbrevs(mets(j)));
        difference = strcat(difference,num2str(dif(mets(j))));
    end
    out(i,2) = difference;
end
out

There are still ~90 unbalanced reactions (filtered out are SLIME and exchange reactions). Some of these seem easy to fix, e.g.:

Not all of them seem so trivial, but there might be a few more from this list that could be fixed 'easily'.

eiden309 commented 4 years ago

@edkerk noted on the reactions. I will look through those and see if there was any reason for not correcting them previously

feiranl commented 4 years ago

@eiden309, Could you document the newly balanced reactions of this pull request and also the remaining unbalanced reactions list here? Thanks!

eiden309 commented 4 years ago

@feiranl I have edited the PR comment to include the requested lists of reactions!