FRresults

papers/Fleming_FR_2015/checkGrowthBeforeAfter.m

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+function checkGrowthBeforeAfter(FRresults)
+% compares the growth of models before and after eliminating rows and
+% columns from the models that do not satisfy the conditions:
+% 1. All rows of S := R − F correspond to molecular species in stoichiometrically consistent
+% reactions, with the exception of exchange reactions.
+% 2. No two rows in [F, R] are identical up to scalar multiplication.
+% 3. All rows of S correspond to molecular species in net flux consistent reactions, assuming
+% all reactions are reversible, including exchange reactions.
+% 4. No row of [F, R] is all zeros.
+%
+%INPUT
+% FRresults     output from checkRankFRdriver.m
+
+for k=1:length(FRresults)  
+    model=FRresults(k).model;
+
+    %test if models support nonzero growth
+    FBAsolutionBefore = optimizeCbModel(model);
+
+    modelFR=model;
+    modelFR.lb(~model.FRVcols)=0;
+    modelFR.ub(~model.FRVcols)=0;
+    modelFR.S(~model.FRrows,:)=0;
+    modelFR.b(~model.FRrows,:)=0;
+
+    %test if the after model supports nonzero growth
+    FBAsolutionAfter = optimizeCbModel(modelFR);
+
+    if k==1
+        fprintf('%25s\t%s\t%s\t%s\n','ModelID','Before      ','After     ','Fractional Change')
+    end
+    fprintf('%25s\t%f\t%f\t%f\n',FRresults(k).modelID,FBAsolutionBefore.f,FBAsolutionAfter.f,(FBAsolutionAfter.f-FBAsolutionBefore.f)/abs(FBAsolutionBefore.f));
+end
+

papers/Fleming_FR_2015/results/FRresults_20151201T090029_rowDependencies.txt

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+121114_Recon2betaModel.mat
+cys_L[m] is dependent on:  10 or more metabolites, will not be displayed
+The reactions are:
+r1097	348 h2o[m] + 9 glu_L[m] + 13 asp_L[m] + 348 atp[m] + 3 ala_L[m] + 3 gly[m] + 7 lys_L[m] + arg_L[m] + asn_L[m] + cys_L[m] + 3 ser_L[m] + 3 gln_L[m] + 8 ile_L[m] + 10 leu_L[m] + 5 pro_L[m] + 3 phe_L[m] + 4 tyr_L[m] + 6 val_L[m] + 5 met_L[m] + his_L[m] + thr_L[m]  => 261 adp[m] + 261 pi[m] + 87 amp[m] + 87 ppi[m] + HC02222[m] 
+r1359	43 h2o[m] + 43 atp[m] + HC02222[m]  => 9 glu_L[m] + 13 asp_L[m] + 43 adp[m] + 43 pi[m] + 3 ala_L[m] + 3 gly[m] + 7 lys_L[m] + arg_L[m] + asn_L[m] + cys_L[m] + 3 ser_L[m] + 3 gln_L[m] + 8 ile_L[m] + 10 leu_L[m] + 5 pro_L[m] + 3 phe_L[m] + 4 tyr_L[m] + 6 val_L[m] + 5 met_L[m] + his_L[m] + thr_L[m] 
+
+phe_L[m] is dependent on:  10 or more metabolites, will not be displayed
+The reactions are:
+r1097	348 h2o[m] + 9 glu_L[m] + 13 asp_L[m] + 348 atp[m] + 3 ala_L[m] + 3 gly[m] + 7 lys_L[m] + arg_L[m] + asn_L[m] + cys_L[m] + 3 ser_L[m] + 3 gln_L[m] + 8 ile_L[m] + 10 leu_L[m] + 5 pro_L[m] + 3 phe_L[m] + 4 tyr_L[m] + 6 val_L[m] + 5 met_L[m] + his_L[m] + thr_L[m]  => 261 adp[m] + 261 pi[m] + 87 amp[m] + 87 ppi[m] + HC02222[m] 
+r1359	43 h2o[m] + 43 atp[m] + HC02222[m]  => 9 glu_L[m] + 13 asp_L[m] + 43 adp[m] + 43 pi[m] + 3 ala_L[m] + 3 gly[m] + 7 lys_L[m] + arg_L[m] + asn_L[m] + cys_L[m] + 3 ser_L[m] + 3 gln_L[m] + 8 ile_L[m] + 10 leu_L[m] + 5 pro_L[m] + 3 phe_L[m] + 4 tyr_L[m] + 6 val_L[m] + 5 met_L[m] + his_L[m] + thr_L[m] 
+
+thr_L[m] is dependent on:  10 or more metabolites, will not be displayed
+The reactions are:
+r1097	348 h2o[m] + 9 glu_L[m] + 13 asp_L[m] + 348 atp[m] + 3 ala_L[m] + 3 gly[m] + 7 lys_L[m] + arg_L[m] + asn_L[m] + cys_L[m] + 3 ser_L[m] + 3 gln_L[m] + 8 ile_L[m] + 10 leu_L[m] + 5 pro_L[m] + 3 phe_L[m] + 4 tyr_L[m] + 6 val_L[m] + 5 met_L[m] + his_L[m] + thr_L[m]  => 261 adp[m] + 261 pi[m] + 87 amp[m] + 87 ppi[m] + HC02222[m] 
+r1359	43 h2o[m] + 43 atp[m] + HC02222[m]  => 9 glu_L[m] + 13 asp_L[m] + 43 adp[m] + 43 pi[m] + 3 ala_L[m] + 3 gly[m] + 7 lys_L[m] + arg_L[m] + asn_L[m] + cys_L[m] + 3 ser_L[m] + 3 gln_L[m] + 8 ile_L[m] + 10 leu_L[m] + 5 pro_L[m] + 3 phe_L[m] + 4 tyr_L[m] + 6 val_L[m] + 5 met_L[m] + his_L[m] + thr_L[m] 
+
+FR subset of dimension 2388 x 9306, of rank 2382.
+More than 15 rows or columns in the dependency, so will not display.
+-------------------------------
+iMM904.mat
+amp[x] is dependent on: hexccoa[r] and pi[r] and psphings[r] and sphgn[r] and ttccoa[r].
+The reactions are:
+ACSp	ac[x] + atp[x] + coa[x]  => accoa[x] + amp[x] + ppi[x] 
+FACOAL100p	atp[x] + coa[x] + dca[x]  <=> amp[x] + dcacoa[x] + ppi[x] 
+FACOAL120p	atp[x] + coa[x] + ddca[x]  <=> amp[x] + ddcacoa[x] + ppi[x] 
+FACOAL140p	atp[x] + coa[x] + ttdca[x]  <=> amp[x] + ppi[x] + tdcoa[x] 
+FACOAL141p	atp[x] + coa[x] + ttdcea[x]  <=> amp[x] + ppi[x] + tdecoa[x] 
+FACOAL160p	atp[x] + coa[x] + hdca[x]  <=> amp[x] + pmtcoa[x] + ppi[x] 
+FACOAL161p	atp[x] + coa[x] + hdcea[x]  <=> amp[x] + hdcoa[x] + ppi[x] 
+FACOAL240p	atp[x] + coa[x] + ttc[x]  <=> amp[x] + ppi[x] + ttccoa[x] 
+FACOAL260p	atp[x] + coa[x] + hexc[x]  <=> amp[x] + hexccoa[x] + ppi[x] 
+FACOAL80p	atp[x] + coa[x] + octa[x]  <=> amp[x] + occoa[x] + ppi[x] 
+
+coa[r] is dependent on:  10 or more metabolites, will not be displayed
+The reactions are:
+CERASE124er	cer1_24[r] + coa[r] + h[r]  => sphgn[r] + ttccoa[r] 
+CERASE126er	cer1_26[r] + coa[r] + h[r]  => hexccoa[r] + sphgn[r] 
+CERASE224er	cer2_24[r] + coa[r] + h[r]  => psphings[r] + ttccoa[r] 
+CERASE226er	cer2_26[r] + coa[r] + h[r]  => hexccoa[r] + psphings[r] 
+
+psphings[r] is dependent on:  10 or more metabolites, will not be displayed
+The reactions are:
+CERASE224er	cer2_24[r] + coa[r] + h[r]  => psphings[r] + ttccoa[r] 
+CERASE226er	cer2_26[r] + coa[r] + h[r]  => hexccoa[r] + psphings[r] 
+SBPP2er	h2o[r] + psph1p[r]  => pi[r] + psphings[r] 
+
+FR subset of dimension 810 x 2235, of rank 804.
+More than 15 rows or columns in the dependency, so will not display.
+-------------------------------
+iND750.mat
+h[r] is dependent on: 6pgl[r] and dolp[r] and ergtetrol[r] and h[r] and nadph[r] and o2[r] and sql[r].
+The reactions are:
+C24STRer	ergtetrol[r] + h[r] + nadph[r]  => ergst[r] + nadp[r] 
+SQLEr	h[r] + nadph[r] + o2[r] + sql[r]  => Ssq23epx[r] + h2o[r] + nadp[r] 
+DOLPMMer	dolmanp[r]  => dolp[r] + h[r] + mannan[r] 
+DOLPt2er	dolp[c] + h[c]  <=> dolp[r] + h[r] 
+G6PDH2er	g6p[r] + nadp[r]  => 6pgl[r] + h[r] + nadph[r] 
+
+pi[x] is dependent on:  10 or more metabolites, will not be displayed
+The reactions are:
+FA140COAabcp	atp[x] + h2o[x] + tdcoa[c]  => adp[x] + h[x] + pi[x] + tdcoa[x] 
+FA141COAabcp	atp[x] + h2o[x] + tdecoa[c]  => adp[x] + h[x] + pi[x] + tdecoa[x] 
+FA160COAabcp	atp[x] + h2o[x] + pmtcoa[c]  => adp[x] + h[x] + pi[x] + pmtcoa[x] 
+FA161COAabcp	atp[x] + h2o[x] + hdcoa[c]  => adp[x] + h[x] + hdcoa[x] + pi[x] 
+FA180COAabcp	atp[x] + h2o[x] + stcoa[c]  => adp[x] + h[x] + pi[x] + stcoa[x] 
+FA181COAabcp	atp[x] + h2o[x] + odecoa[c]  => adp[x] + h[x] + odecoa[x] + pi[x] 
+FA182COAabcp	atp[x] + h2o[x] + ocdycacoa[c]  => adp[x] + h[x] + ocdycacoa[x] + pi[x] 
+
+ppi[x] is dependent on:  10 or more metabolites, will not be displayed
+The reactions are:
+ACSp	ac[x] + atp[x] + coa[x]  => accoa[x] + amp[x] + ppi[x] 
+FACOAL100p	atp[x] + coa[x] + dca[x]  <=> amp[x] + dcacoa[x] + ppi[x] 
+FACOAL120p	atp[x] + coa[x] + ddca[x]  <=> amp[x] + ddcacoa[x] + ppi[x] 
+FACOAL140p	atp[x] + coa[x] + ttdca[x]  <=> amp[x] + ppi[x] + tdcoa[x] 
+FACOAL141p	atp[x] + coa[x] + ttdcea[x]  <=> amp[x] + ppi[x] + tdecoa[x] 
+FACOAL160p	atp[x] + coa[x] + hdca[x]  <=> amp[x] + pmtcoa[x] + ppi[x] 
+FACOAL161p	atp[x] + coa[x] + hdcea[x]  <=> amp[x] + hdcoa[x] + ppi[x] 
+FACOAL240p	atp[x] + coa[x] + ttc[x]  <=> amp[x] + ppi[x] + ttccoa[x] 
+FACOAL260p	atp[x] + coa[x] + hexc[x]  <=> amp[x] + hexccoa[x] + ppi[x] 
+FACOAL80p	atp[x] + coa[x] + octa[x]  <=> amp[x] + occoa[x] + ppi[x] 
+
+FR subset of dimension 688 x 1776, of rank 682.
+More than 15 rows or columns in the dependency, so will not display.
+-------------------------------