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fix: bug in sumBioMass, redefine biomass equation and fit energetics #33

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Jul 29, 2019
Merged

fix: bug in sumBioMass, redefine biomass equation and fit energetics #33

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2 changes: 1 addition & 1 deletion ComplementaryScripts/experimental/sumBioMass.m
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@
[C,X] = getFraction(model,comps,'C',X);
[R,X] = getFraction(model,comps,'R',X);
[D,X] = getFraction(model,comps,'D',X);
[L,X] = getFraction(model,comps,'L',X);
[L,~] = getFraction(model,comps,'L',X);

%Add up any remaining components:
bioPos = strcmp(model.rxns,'r_4041');
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2 changes: 1 addition & 1 deletion ComplementaryScripts/reconstruction/r5_lipids_curation.m
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Expand Up @@ -134,7 +134,7 @@
sol=solveLP(model,1)

% Rescale carbohydrates
model = changeOtherComp(model,expData,1)
model = changeOtherComp(model,expData,1);
cd ../reconstruction
save([root '/scrap/model_r5.mat'],'model');

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6 changes: 3 additions & 3 deletions ModelFiles/txt/rhto.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -1763,14 +1763,14 @@ r_4005 s_3712 <=> s_1351 -1000.00 1000.00 0.00
r_4038 s_3713 <=> s_1524 -1000.00 1000.00 0.00
r_4039 s_0365 + s_1464 <=> s_0376 + s_1460 RHTO_07106 -1000.00 1000.00 0.00
r_4040 s_0811 <=> s_3714 -1000.00 1000.00 0.00
r_4041 160 s_0434 + 160 s_0803 + s_1096 + 0.00099 s_1405 + 0.02 s_1467 + 1e-06 s_3714 + s_3717 + s_3718 + s_3719 + s_3720 -> 160 s_0394 + s_0450 + 160 s_0794 + 160 s_1322 0.00 1000.00 0.00
r_4041 129.7 s_0434 + 129.7 s_0803 + s_1096 + 0.00099 s_1405 + 0.02 s_1467 + 1e-06 s_3714 + s_3717 + s_3718 + s_3719 + s_3720 -> 129.7 s_0394 + s_0450 + 129.7 s_0794 + 129.7 s_1322 0.00 1000.00 0.00
r_4042 s_3715 -> s_0554 + s_3716 RHTO_00551 0.00 1000.00 0.00
r_4043 s_3715 -> 0.00 1000.00 0.00
r_4044 s_3716 -> 0.00 1000.00 0.00
r_4045 s_0803 + s_1556 -> s_0575 + s_1550 RHTO_04784 0.00 1000.00 0.00
r_4046 s_0434 + s_0803 -> s_0394 + s_0794 + s_1322 3.39 1000.00 0.00
r_4047 0.2637 s_0404 + 0.16785 s_0428 + 0.06194 s_0430 + 0.13504 s_0432 + 0.024008 s_0542 + 0.088752 s_0747 + 0.15698 s_0748 + 0.17539 s_0757 + 0.054167 s_0832 + 0.087117 s_0847 + 0.22803 s_1077 + 0.10757 s_1099 + 0.041001 s_1148 + 0.082446 s_1314 + 0.17682 s_1379 + 0.22318 s_1428 + 0.14034 s_1491 + 0.031622 s_1527 + 0.05519 s_1533 + 0.15206 s_1561 -> 0.2637 s_1582 + 0.16785 s_1583 + 0.06194 s_1585 + 0.13504 s_1587 + 0.024008 s_1589 + 0.088752 s_1590 + 0.15698 s_1591 + 0.17539 s_1593 + 0.054167 s_1594 + 0.087117 s_1596 + 0.22803 s_1598 + 0.10757 s_1600 + 0.041001 s_1602 + 0.082446 s_1604 + 0.17682 s_1606 + 0.22318 s_1607 + 0.14034 s_1608 + 0.031622 s_1610 + 0.05519 s_1612 + 0.15206 s_1614 + s_3717 0.00 1000.00 0.00
r_4048 0.78301 s_0001 + 0.26154 s_0004 + 0.31239 s_0773 + 0.74371 s_1107 + 0.1258 s_1520 -> s_3718 0.00 1000.00 0.00
r_4048 1.0783 s_0001 + 0.36019 s_0004 + 0.43021 s_0773 + 1.0242 s_1107 + 0.17325 s_1520 -> s_3718 0.00 1000.00 0.00
r_4049 0.0342 s_0423 + 0.0613 s_0526 + 0.0523 s_0782 + 0.0324 s_1545 -> s_3719 0.00 1000.00 0.00
r_4050 0.0023 s_0584 + 0.0037 s_0589 + 0.0037 s_0615 + 0.0023 s_0649 -> s_3720 0.00 1000.00 0.00
r_4058 s_3732 -> s_3733 0.00 1000.00 0.00
Expand All @@ -1779,7 +1779,7 @@ r_4061 s_3738 -> s_3739 0.00 1000.00 0.00
r_4062 s_3746 -> 0.00 0.00 0.00
r_4063 0.0018455 m_0100 + 0.0026558 s_0089 + 0.02002 s_0666 + 0.052459 s_0694 + 0.0041483 s_1346 + 0.0032045 s_1351 + 0.036212 s_1524 + 0.010514 s_3710 + 0.012329 s_3733 + 0.00048288 s_3738 -> s_3746 0.00 1000.00 0.00
r_4064 s_3747 -> 0.00 0.00 0.00
r_4065 0.027769 m_0102 + 0.013992 m_0103 + 0.019661 s_3740 + 0.0092674 s_3742 + 0.043835 s_3743 -> s_3747 0.00 1000.00 0.00
r_4065 0.027769 m_0102 + 0.013992 m_0103 + 0.019661 s_3740 + 0.0092673 s_3742 + 0.043834 s_3743 -> s_3747 0.00 1000.00 0.00
r_4152 s_3748 <=> s_0712 + s_3749 RHTO_02286 or RHTO_07696 -1000.00 1000.00 0.00
r_4153 s_0020 + s_1198 <=> s_0794 + s_1203 + s_3750 RHTO_04102 -1000.00 1000.00 0.00
r_4154 s_1201 + s_3751 <=> s_0794 + s_3752 + s_3753 RHTO_04102 -1000.00 1000.00 0.00
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34 changes: 17 additions & 17 deletions ModelFiles/xml/rhto.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -24,10 +24,10 @@
</rdf:Bag>
</dcterms:creator>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2019-07-23T11:38:11Z</dcterms:W3CDTF>
<dcterms:W3CDTF>2019-07-29T15:06:39Z</dcterms:W3CDTF>
</dcterms:created>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2019-07-23T11:38:11Z</dcterms:W3CDTF>
<dcterms:W3CDTF>2019-07-29T15:06:39Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:is>
<rdf:Bag>
Expand Down Expand Up @@ -91865,8 +91865,8 @@
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="M_s_0434" stoichiometry="160" constant="true"/>
<speciesReference species="M_s_0803" stoichiometry="160" constant="true"/>
<speciesReference species="M_s_0434" stoichiometry="129.7" constant="true"/>
<speciesReference species="M_s_0803" stoichiometry="129.7" constant="true"/>
<speciesReference species="M_s_1096" stoichiometry="1" constant="true"/>
<speciesReference species="M_s_1405" stoichiometry="0.00099" constant="true"/>
<speciesReference species="M_s_1467" stoichiometry="0.02" constant="true"/>
Expand All @@ -91877,10 +91877,10 @@
<speciesReference species="M_s_3720" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_s_0394" stoichiometry="160" constant="true"/>
<speciesReference species="M_s_0394" stoichiometry="129.7" constant="true"/>
<speciesReference species="M_s_0450" stoichiometry="1" constant="true"/>
<speciesReference species="M_s_0794" stoichiometry="160" constant="true"/>
<speciesReference species="M_s_1322" stoichiometry="160" constant="true"/>
<speciesReference species="M_s_0794" stoichiometry="129.7" constant="true"/>
<speciesReference species="M_s_1322" stoichiometry="129.7" constant="true"/>
</listOfProducts>
</reaction>
<reaction metaid="R_r_4042" sboTerm="SBO:0000176" id="R_r_4042" name="raffinose invertase" reversible="false" fast="false" fbc:lowerFluxBound="FB3N0" fbc:upperFluxBound="FB5N1000">
Expand Down Expand Up @@ -92122,11 +92122,11 @@
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="M_s_0001" stoichiometry="0.783010132868516" constant="true"/>
<speciesReference species="M_s_0004" stoichiometry="0.261542814004972" constant="true"/>
<speciesReference species="M_s_0773" stoichiometry="0.312388337861451" constant="true"/>
<speciesReference species="M_s_1107" stoichiometry="0.743711463462025" constant="true"/>
<speciesReference species="M_s_1520" stoichiometry="0.125801667090062" constant="true"/>
<speciesReference species="M_s_0001" stoichiometry="1.07834557720538" constant="true"/>
<speciesReference species="M_s_0004" stoichiometry="0.360191426513086" constant="true"/>
<speciesReference species="M_s_0773" stoichiometry="0.430214844435485" constant="true"/>
<speciesReference species="M_s_1107" stoichiometry="1.02422425161117" constant="true"/>
<speciesReference species="M_s_1520" stoichiometry="0.173251488859611" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_s_3718" stoichiometry="1" constant="true"/>
Expand Down Expand Up @@ -92360,11 +92360,11 @@
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="M_m_0102" stoichiometry="0.0277689653667153" constant="true"/>
<speciesReference species="M_m_0103" stoichiometry="0.0139919933252827" constant="true"/>
<speciesReference species="M_s_3740" stoichiometry="0.0196610394080864" constant="true"/>
<speciesReference species="M_s_3742" stoichiometry="0.00926736988751031" constant="true"/>
<speciesReference species="M_s_3743" stoichiometry="0.0438346137524661" constant="true"/>
<speciesReference species="M_m_0102" stoichiometry="0.0277687045397886" constant="true"/>
<speciesReference species="M_m_0103" stoichiometry="0.0139918619019988" constant="true"/>
<speciesReference species="M_s_3740" stoichiometry="0.0196608547368746" constant="true"/>
<speciesReference species="M_s_3742" stoichiometry="0.00926728284142939" constant="true"/>
<speciesReference species="M_s_3743" stoichiometry="0.0438342020249337" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_s_3747" stoichiometry="1" constant="true"/>
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