JonathanRob
commented
4 years ago Hi @raphyz, thanks for posting the issue.
Here is the list of metabolite IDs and names corresponding to those in Ham's media as defined in the Human-GEM metabolic task list, as well as their corresponding exchange reaction that should be opened to enable biomass flux.
| mets | metNames | rxns | rxnEqns |
|---|---|---|---|
| m01365s | arginine | HMR_9066 | arginine[s] <=> |
| m02125s | histidine | HMR_9038 | histidine[s] <=> |
| m02426s | lysine | HMR_9041 | lysine[s] <=> |
| m02471s | methionine | HMR_9042 | methionine[s] <=> |
| m02724s | phenylalanine | HMR_9043 | phenylalanine[s] <=> |
| m03089s | tryptophan | HMR_9045 | tryptophan[s] <=> |
| m03101s | tyrosine | HMR_9064 | tyrosine[s] <=> |
| m01307s | alanine | HMR_9061 | alanine[s] <=> |
| m01986s | glycine | HMR_9067 | glycine[s] <=> |
| m02896s | serine | HMR_9069 | serine[s] <=> |
| m02993s | threonine | HMR_9044 | threonine[s] <=> |
| m01370s | aspartate | HMR_9070 | aspartate[s] <=> |
| m01974s | glutamate | HMR_9071 | glutamate[s] <=> |
| m01369s | asparagine | HMR_9062 | asparagine[s] <=> |
| m01975s | glutamine | HMR_9063 | glutamine[s] <=> |
| m02184s | isoleucine | HMR_9039 | isoleucine[s] <=> |
| m02360s | leucine | HMR_9040 | leucine[s] <=> |
| m02770s | proline | HMR_9068 | proline[s] <=> |
| m03135s | valine | HMR_9046 | valine[s] <=> |
| m01628s | cysteine | HMR_9065 | cysteine[s] <=> |
| m02982s | thiamin | HMR_9159 | thiamin[s] <=> |
| m02159s | hypoxanthine | HMR_9358 | hypoxanthine[s] <=> |
| m01830s | folate | HMR_9146 | folate[s] <=> |
| m01401s | biotin | HMR_9109 | biotin[s] <=> |
| m02680s | pantothenate | HMR_9145 | pantothenate[s] <=> |
| m01513s | choline | HMR_9083 | choline[s] <=> |
| m02171s | inositol | HMR_9361 | inositol[s] <=> |
| m02583s | nicotinamide | HMR_9378 | nicotinamide[s] <=> |
| m02817s | pyridoxine | HMR_9144 | pyridoxine[s] <=> |
| m02842s | riboflavin | HMR_9143 | riboflavin[s] <=> |
| m02996s | thymidine | HMR_9423 | thymidine[s] <=> |
| m01361s | aquacob(III)alamin | HMR_9269 | aquacob(III)alamin[s] <=> |
| m02394s | lipoic acid | HMR_9167 | lipoic acid[s] <=> |
| m01965s | glucose | HMR_9034 | glucose[s] <=> |
| m02946s | sulfate | HMR_9074 | sulfate[s] <=> |
| m02387s | linoleate | HMR_9035 | linoleate[s] <=> |
| m02389s | linolenate | HMR_9036 | linolenate[s] <=> |
| m02630s | O2 | HMR_9048 | O2[s] <=> |
| m02040s | H2O | HMR_9047 | H2O[s] <=> |
| m02833s | retinoate | HMR_9404 | retinoate[s] <=> |
| m01821s | Fe2+ | HMR_9076 | Fe2+[s] <=> |
| m02751s | Pi | HMR_9072 | Pi[s] <=> |
| m01327s | alpha-tocopherol | HMR_9151 | alpha-tocopherol[s] <=> |
| m01935s | gamma-tocopherol | HMR_9153 | gamma-tocopherol[s] <=> |
Also, make sure that you are using the most recent version of the model (1.4.0), otherwise you may have boundary metabolites that will need to be removed prior to performing flux simulations.
Description of the issue:
I am trying to grow the model with the "ham" minimal media
The metabolites I was given of the Ham MM are: arginine histidine lysine methionine phenylalanine tryptophan tyrosine alanine glycine serine threonine aspartate glutamate asparagine glutamine isoleucine leucine proline valine cysteine thiamin hypoxanthine folate biotin pantothenate choline inositol nicotinamide pyridoxine riboflavin thymidine aquacob(III)alamin lipoic acid glucose sulfate linoleate linolenate O2 H2O retinoate Fe2+ Pi alpha-tocopherol gamma-tocopherol
converting them to exchange reactions in my model the list is: R_EX_HMR_9455,D-arginine_C6H15N4O2=-50.0 R_EX_HMR_9038,histidine_C6H9N3O2=-50.0 R_EX_HMR_9041,lysine_C6H15N2O2=-50.0 R_EX_HMR_9042,methionine_C5H11NO2S=-50.0 R_EX_HMR_9043,phenylalanine_C9H11NO2=-50.0 R_EX_HMR_9045,tryptophan_C11H12N2O2=-50.0 R_EX_HMR_9064,tyrosine_C9H11NO3=-50.0 R_EX_HMR_9061,alanine_C3H7NO2=-50.0 R_EX_HMR_9067,glycine_C2H5NO2=-50.0 R_EX_HMR_9069,serine_C3H7NO3=-50.0 R_EX_HMR_9044,threonine_C4H9NO3=-50.0 R_EX_HMR_9070,aspartate_C4H6NO4=-50.0 R_EX_HMR_9071,glutamate_C5H8NO4=-50.0 R_EX_HMR_9062,asparagine_C4H8N2O3=-50.0 R_EX_HMR_9063,glutamine_C5H10N2O3=-50.0 R_EX_HMR_9039,isoleucine_C6H13NO2=-50.0 R_EX_HMR_9040,leucine_C6H13NO2=-50.0 R_EX_HMR_9394,D-proline_C5H9NO2=-50.0 R_EX_HMR_9046,valine_C5H11NO2=-50.0 R_EX_HMR_9065,cysteine_C3H7NO2S=-50.0 R_EX_HMR_9159,thiamin_C12H17N4OS=-50.0 R_EX_HMR_9358,hypoxanthine_C5H4N4O=-50.0 R_EX_HMR_9146,folate_C19H18N7O6=-50.0 R_EX_HMR_9109,biotin_C10H15N2O3S=-50.0 R_EX_HMR_9145,pantothenate_C9H16NO5=-50.0 R_EX_HMR_9083,choline_C5H14NO=-50.0 R_EX_HMR_9361,inositol_C6H12O6=-50.0 R_EX_HMR_9378,nicotinamide_C6H6N2O=-50.0 R_EX_HMR_9144,pyridoxine_C8H11NO3=-50.0 R_EX_HMR_9143,riboflavin_C17H20N4O6=-50.0 R_EX_HMR_9423,thymidine_C10H14N2O5=-50.0 R_EX_HMR_9269,aquacob(III)alamin_C62H90CoN13O15P=-50.0 R_EX_HMR_9167,lipoic acid_C8H13O2S2=-50.0 R_EX_HMR_9034,glucose_C6H12O6=-50.0 R_EX_HMR_9074,sulfate_O4S=-50.0 R_EX_HMR_9033,NEFA blood pool in_CHO2R=-50.0 R_EX_HMR_9035,linoleate_C18H31O2=-50.0 R_EX_HMR_9036,linolenate_C18H29O2=-50.0 R_EX_HMR_9048,O2_O2=-50.0 R_EX_HMR_9047,H2O_H2O=-50.0 R_EX_HMR_9404,retinoate_C20H27O2=-50.0 R_EX_HMR_9076,Fe2+_Fe=-50.0 R_EX_HMR_9072,Pi_HO4P=-50.0 R_EX_HMR_9151,alpha-tocopherol_C29H50O2=-50.0 R_EX_HMR_9153,gamma-tocopherol_C28H48O2=-50.0
However when trying to grow the model on this media I have zero biomass.
Do I have a mistake, as some of the metabolites are taken in the D- format. Thanks Raphy