add recipes

README.md

@@ -72,15 +72,32 @@ reconstructions using Refseq v84.
 
 ---
 
-**VMH high fat low carbs (AGORA)**
-
-[recipe](https://nbviewer.jupyter.org/github/micom-dev/media/blob/main/recipes/vmh_high_fat_low_carb_agora.ipynb) |
-[medium](https://github.com/micom-dev/media/raw/main/media/vmh_high_fat_low_carb_agora.qza)
-
-This is the completed [VMH](https://vmh.life) growth medium representing a high fat/protein low carb diet. Components
-commonly adsorbed in the small intestine were identified by matching reactions to metabolites adsorbed in the 
-Recon3 human model. As low carb diets usually allow for less bacterial growth this medium was only completed
-to allow for a minimal growth rate of 1e-4 in AGORA 1.03.
+**VMH diets**
+
+| Recipe | Medium |
+| ------ | ------ |
+| [Austrian average recipe](https://nbviewer.jupyter.org/github/micom-dev/media/blob/main/recipes/vmh_eu_average_agora.ipynb) |
+[Austrian average medium](https://github.com/micom-dev/media/raw/main/media/vmh_eu_average_agora.qza) |
+| [high fat low carb recipe](https://nbviewer.jupyter.org/github/micom-dev/media/blob/main/recipes/vmh_high_fat_low_carb_agora.ipynb) |
+[high fat low carb medium](https://github.com/micom-dev/media/raw/main/media/vmh_high_fat_low_carb_agora.qza) |
+
+[high fat low carb recipe](https://nbviewer.jupyter.org/github/micom-dev/media/blob/main/recipes/vmh_high_fiber_carb_agora.ipynb) |
+[high fat low carb medium](https://github.com/micom-dev/media/raw/main/media/vmh_high_fiber_agora.qza)<br>
+[fermented recipe](https://nbviewer.jupyter.org/github/micom-dev/media/blob/main/recipes/vmh_fermented_agora.ipynb) |
+[fermented medium](https://github.com/micom-dev/media/raw/main/media/vmh_fermented_agora.qza)<br>
+[formula recipe](https://nbviewer.jupyter.org/github/micom-dev/media/blob/main/recipes/vmh_formula_agora.ipynb) |
+[formula medium](https://github.com/micom-dev/media/raw/main/media/vmh_formula_agora.qza)
+
+These are the completed [VMH](https://vmh.life) growth medium representing a variety of diets. Components
+commonly adsorbed in the small intestine were identified by matching reactions to metabolites adsorbed in the
+Recon3 human model.
+
+**Provided diets**:
+- Austrian average diet
+- high fat/protein low carb diet
+- high fiber diet
+- fermented foods diet (80% high fiber diet + 20% fermented foods)
+- baby formula
 
 ---
 
@@ -90,4 +107,15 @@ to allow for a minimal growth rate of 1e-4 in AGORA 1.03.
 [medium](https://github.com/micom-dev/media/raw/main/media/breast_milk_agora.qza)
 
 This is a completed medium based on a breast milk-only diet of an infant. Lactose is the major carbon source here.
-Medium was depleted for components absorbed by human cells and mucin/primary bile acids were added to the medium.
+Medium was depleted for components absorbed by human cells and mucin/primary bile acids were added to the medium.
+
+---
+
+**Single meal diets (AGORA)**
+
+[]
+
+Those are ~1000kcal single meal media for a set of indigenous populations across the globe. Each of them
+tends to include 4-5 representative food items detailed in the [source mapping](https://github.com/micom-dev/media/raw/main/data/foods_diets.xslx).
+Those are not necessarily representative for the diverse diets of the respective poopulation, but are usually more
+realistic than an average European diet.

data/vmh_eu_average.tsv

@@ -0,0 +1,92 @@
+Reaction	Flux Value
+EX_etoh[e]	234.434015507376
+EX_h2o[e]	165892.342500366
+EX_caro[e]	0.00358558063868411
+EX_retinol[e]	3.00225238748885
+EX_thm[e]	5.40785801339038
+EX_adpcbl[e]	0.00000360855006052868
+EX_ribflv[e]	0.00369323412792778
+EX_nac[e]	0.30861619226627
+EX_ncam[e]	0.145527600499817
+EX_pnto_R[e]	0.0255697049402686
+EX_pydam[e]	0.00317177006440072
+EX_pydxn[e]	0.00317220502138381
+EX_pydx[e]	0.00321045851728662
+EX_btn[e]	0.000178666327993894
+EX_10fthf[e]	0.000125752137038594
+EX_5mthf[e]	0.000129311313237557
+EX_thf[e]	0.000133695809304773
+EX_ascb_L[e]	0.58344116649402
+EX_vitd3[e]	0.00000876149165825399
+EX_avite1[e]	0.0368580802547259
+EX_phyQ[e]	0.000136877276619236
+EX_ca2[e]	18.549079295374
+EX_cl[e]	375.557498660198
+EX_k[e]	83.433806584941
+EX_mg2[e]	14.529932112734
+EX_na1[e]	172.446271718304
+EX_pi[e]	14.2266092792925
+EX_cu2[e]	0.0356749441349574
+EX_fe2[e]	0.109248813680723
+EX_fe3[e]	0.109248813680723
+EX_mn2(e)	0.07470233059804
+EX_zn2(e)	0.150963597430407
+EX_mnl(e)	0.170169038237532
+EX_xylt[e]	0.141969084917231
+EX_lcts[e]	4.12671470494148
+EX_malt[e]	8.41375824760113
+EX_sucr[e]	202.383021737003
+EX_fru[e]	106.505865197865
+EX_gal[e]	0.0299740391516459
+EX_cellul(e)	0.052346876171936
+EX_ala_L[e]	37.2085636165274
+EX_arg_L[e]	20.3518771021335
+EX_asp_L[e]	47.0867491277091
+EX_cys_L[e]	7.5118316383043
+EX_glu_L[e]	103.122200527918
+EX_gly[e]	36.7646862919061
+EX_urate[e]	2.91939280341538
+EX_his_L[e]	14.0240766306639
+EX_ile_L[e]	28.9216751325922
+EX_leu_L[e]	46.8878099058571
+EX_lys_L[e]	33.3115482470592
+EX_met_L[e]	10.7274046938804
+EX_phe_L[e]	20.7149866425811
+EX_pro_L[e]	53.8152791831878
+EX_ser_L[e]	37.3792255591735
+EX_thr_L[e]	25.8810502421104
+EX_trp_L[e]	4.55482477186948
+EX_tyr_L[e]	15.6468539670012
+EX_val_L[e]	37.7843773128131
+EX_dca[e]	10.7484261929606
+EX_ddca[e]	13.4590471717898
+EX_ttdca[e]	30.2113800398482
+EX_ttdcea[e]	3.78398479501178
+EX_ptdca[e]	2.89407662964767
+EX_hdca[e]	92.7850671903611
+EX_hpdca[e]	1.77952492310981
+EX_ocdca[e]	35.850866390117
+EX_ocdcea[e]	101.592732580242
+EX_lnlc[e]	54.9854618653545
+EX_lnlnca[e]	4.1633368983032
+EX_strdnc[e]	0
+EX_arach[e]	1.0330553972827
+EX_CE2510[e]	1.0866650339605
+EX_CE4843[e]	0.114865262591682
+EX_arachd[e]	0.536810750978139
+EX_docosac[e]	0.4540962307068
+EX_doco13ac[e]	0.560730442644664
+EX_adrn[e]	0
+EX_clpnd[e]	0.0483768856818379
+EX_crvnc[e]	0.166300079729987
+EX_but[e]	26.3342564399315
+EX_octa[e]	6.84557290848338
+EX_chsterol[e]	1.23218850986736
+EX_sbt_D[e]	0.0329359428846836
+EX_glc_D[e]	135.580350130082
+EX_lgnc[e]	0.222615855993872
+EX_fol[e]	0.0001346137907466
+EX_hdcea[e]	7.1204730223287
+EX_strch1[e]	33.0369997278473
+EX_i[e]	0.00201237986337282
+EX_starch1200(e)	0.305869770147688

data/vmh_fermented.tsv

@@ -0,0 +1,81 @@
+EX_but(e)	1.865731619386157
+EX_octa(e)	0.5237302160910873
+EX_dca(e)	1.1917781902839424
+EX_ddca(e)	1.0606603388293
+EX_ttdca(e)	2.978057115713639
+EX_hdca(e)	8.238321703291218
+EX_ocdca(e)	2.5318438363519435
+EX_hdcea(e)	0.46093078816402355
+EX_ocdcea(e)	6.0745402258420045
+EX_CE2510(e)	0.06881921096351419
+EX_lnlc(e)	2.7390740326548877
+EX_arachd(e)	0.03624873088250172
+EX_clpnd(e)	0.01669215001569062
+EX_chsterol(e)	0.1034517985741756
+EX_ca2(e)	18.7609162133839
+EX_fe2(e)	0.05363953800698362
+EX_fe3(e)	0.05363953800698362
+EX_mg2(e)	4.254268668998148
+EX_pi(e)	7.75688091077972
+EX_k(e)	33.51296603688651
+EX_na1(e)	72.26692794369792
+EX_zn2(e)	0.050688283878862046
+EX_cu2(e)	0.0033629182009882602
+EX_h2o(e)	43473.207188564375
+EX_ascb_L(e)	0.08440110052639334
+EX_thm(e)	0.0007917707098350657
+EX_ribflv(e)	0.004237919736722889
+EX_nac(e)	0.012597715834776807
+EX_ncam(e)	0.012595332963219534
+EX_pydam(e)	0.0016101165674749754
+EX_pydx(e)	0.0016297563640859365
+EX_pydxn(e)	0.0016103373689298085
+EX_5mthf(e)	0.00009232237730830484
+EX_fol(e)	0.00009610810430312258
+EX_thf(e)	0.00009545270744021437
+EX_chol[e]	1.1845929953499448
+EX_adpcbl(e)	0.000001835928978163714
+EX_retinol(e)	0.001656126200726406
+EX_caro(e)	0.00020712548936190818
+EX_avite1(e)	0.0009565687599966662
+EX_phyQ(e)	0.0001909714248438581
+EX_glc_D(e)	5.41753003926044
+EX_fru(e)	28.841686561472592
+EX_lcts(e)	51.50797627203317
+EX_gal(e)	24.42329116060035
+EX_ptdca(e)	0.3260289589940909
+EX_hpdca(e)	0.18074343821524946
+EX_arach(e)	0.030495389578601872
+EX_ttdcea(e)	0.29687535362114703
+EX_lnlnca(e)	0.12039433108513142
+EX_mn2(e)	0.005808361036509397
+EX_pnto_R(e)	0.010384141284075757
+EX_vitd3(e)	0.000006499622891879814
+EX_trp_L(e)	0.21887602509386697
+EX_thr_L(e)	2.4429311143795456
+EX_ile_L(e)	2.8656833842966036
+EX_leu_L(e)	5.23050111722772
+EX_lys_L(e)	4.184231175545448
+EX_met_L(e)	1.3511041053861201
+EX_phe_L(e)	2.2864704753521874
+EX_tyr_L(e)	1.899127152109543
+EX_val_L(e)	4.865710654113702
+EX_arg_L(e)	1.4023260233926473
+EX_his_L(e)	1.1369305196236528
+EX_ala_D[e]	1.7257209304413805
+EX_ala_L(e)	1.7257209304413805
+EX_asp_D[e]	2.2665557361498987
+EX_asp_L(e)	2.2665557361498987
+EX_glu_L(e)	10.074506591441494
+EX_gly(e)	2.3499132770100153
+EX_pro_D[e]	3.5073242972105567
+EX_pro_L(e)	3.5073242972105567
+EX_ser_L(e)	4.184880762299153
+EX_sucr(e)	19.41299429003802
+EX_malt(e)	0
+EX_docosac(e)	0
+EX_lgnc(e)	0
+EX_CE4843(e)	0
+EX_starch1200(e)	0
+EX_strch1(e)	0
+EX_strch2[e]	0

data/vmh_formula_fluxes.tsv

@@ -0,0 +1,47 @@
+EX_lcts(e)	230.35000357876876
+EX_but(e)	0
+EX_octa(e)	4.2278296270691715
+EX_dca(e)	2.6309043675371537
+EX_ddca(e)	17.660947931310954
+EX_ttdca(e)	6.8739416703685325
+EX_hdca(e)	32.52418308791028
+EX_ocdca(e)	5.3643904295809115
+EX_hdcea(e)	0
+EX_ocdcea(e)	51.52682468927362
+EX_CE2510(e)	0
+EX_doco13ac(e)	0
+EX_lnlc(e)	25.949273093267728
+EX_strdnc(e)	0
+EX_arachd(e)	0
+EX_tmndnc[e]	0
+EX_clpnd(e)	0
+EX_crvnc(e)	0
+EX_chsterol(e)	0.06190555626678667
+EX_ca2(e)	14.052597435001747
+EX_fe2(e)	0.11723878592532903
+EX_fe3(e)	0.11723878592532903
+EX_mg2(e)	2.3751491462662004
+EX_pi(e)	3.9608540591565067
+EX_k(e)	20.166605709199636
+EX_na1(e)	8.513004093967142
+EX_zn2(e)	0.11198531661058429
+EX_cu2(e)	0.00864129921631574
+EX_h2o(e)	257.91439267111025
+EX_etoh(e)	0
+EX_ascb_L(e)	0.4985032795366735
+EX_thm(e)	0.0021755040236724746
+EX_ribflv(e)	0.002693563330595734
+EX_nac(e)	0.029981613657489872
+EX_ncam(e)	0.029975942602882628
+EX_pydam(e)	0.0008598845948507003
+EX_pydx(e)	0.0008703732506989228
+EX_pydxn(e)	0.000860002514120253
+EX_5mthf(e)	0.00006372807029980943
+EX_fol(e)	0.0003317063644796255
+EX_thf(e)	0.00006588886711336805
+EX_chol[e]	1.6760166956575167
+EX_adpcbl(e)	0.0000013816315179118931
+EX_retinol(e)	0.0023101983022611847
+EX_caro(e)	0
+EX_avite1(e)	0.02255644858524177
+EX_phyQ(e)	0.00012808642283474196

data/vmh_high_fiber.tsv

@@ -0,0 +1,92 @@
+Reaction	Flux Value
+EX_etoh[e]	22.792195952106
+EX_h2o[e]	181671.336776337
+EX_caro[e]	0.0131316070144016
+EX_retinol[e]	1.0996622116965
+EX_thm[e]	7.23560096565124
+EX_adpcbl[e]	0.00000256713517463926
+EX_ribflv[e]	0.00689492270645511
+EX_nac[e]	0.479928584005929
+EX_ncam[e]	0.216377371962733
+EX_pnto_R[e]	0.0548511412428343
+EX_pydam[e]	0.00499406031879244
+EX_pydxn[e]	0.0049947451734211
+EX_pydx[e]	0.00505497660951652
+EX_btn[e]	0.00047921786318031
+EX_10fthf[e]	0.000254696733339923
+EX_5mthf[e]	0.00026190544225418
+EX_thf[e]	0.000270785743233232
+EX_ascb_L[e]	1.51385194516555
+EX_vitd3[e]	0.0000153391100248364
+EX_avite1[e]	0.0685386160075281
+EX_phyQ[e]	0.000936308023351454
+EX_ca2[e]	33.0201107839713
+EX_cl[e]	231.445011705638
+EX_k[e]	116.447773944136
+EX_mg2[e]	31.1553178358363
+EX_na1[e]	147.911880218747
+EX_pi[e]	22.3360662142775
+EX_cu2[e]	0.0473279199320177
+EX_fe2[e]	0.424456083803384
+EX_fe3[e]	0.424456083803384
+EX_mn2(e)	0.174378247351175
+EX_zn2(e)	0.244799632915265
+EX_mnl(e)	2.6911958931075
+EX_xylt[e]	0.276050998450171
+EX_lcts[e]	26.574680138418
+EX_malt[e]	0.803397054892469
+EX_sucr[e]	137.117966441375
+EX_fru[e]	157.32729263932
+EX_gal[e]	1.01023613437029
+EX_cellul(e)	0.237688252970771
+EX_ala_L[e]	59.0612976074493
+EX_arg_L[e]	40.6717067454907
+EX_asp_L[e]	80.1605212018348
+EX_cys_L[e]	13.8267983512466
+EX_glu_L[e]	130.815459484688
+EX_gly[e]	60.7824918139359
+EX_urate[e]	6.31918448780354
+EX_his_L[e]	17.2196634840346
+EX_ile_L[e]	41.9322512500677
+EX_leu_L[e]	63.3179185639717
+EX_lys_L[e]	46.3467633181721
+EX_met_L[e]	12.6699519406372
+EX_phe_L[e]	29.6979340646568
+EX_pro_L[e]	50.90466904947
+EX_ser_L[e]	52.1149443443211
+EX_thr_L[e]	38.2589456611529
+EX_trp_L[e]	6.19299185409048
+EX_tyr_L[e]	21.2683752004128
+EX_val_L[e]	50.9786480665629
+EX_dca[e]	0.0434435557849707
+EX_ddca[e]	0.101851489490231
+EX_ttdca[e]	0.78750720213931
+EX_ttdcea[e]	0.0312850708972958
+EX_ptdca[e]	0.0721033549084136
+EX_hdca[e]	34.4471433085072
+EX_hpdca[e]	0.202603373555862
+EX_ocdca[e]	9.42414222633633
+EX_ocdcea[e]	130.212461458984
+EX_lnlc[e]	66.4728248713934
+EX_lnlnca[e]	22.7631796647487
+EX_strdnc[e]	0
+EX_arach[e]	0.667592228490719
+EX_CE2510[e]	1.00671520413458
+EX_CE4843[e]	0.0380336706118266
+EX_arachd[e]	0.359587410354417
+EX_docosac[e]	0.394315728220756
+EX_doco13ac[e]	0.0498874717568477
+EX_adrn[e]	0
+EX_clpnd[e]	0.0501674981380665
+EX_crvnc[e]	0.384328461895265
+EX_but[e]	0.0723329797054326
+EX_octa[e]	0.0155024143962962
+EX_chsterol[e]	1.05303585768653
+EX_sbt_D[e]	6.5699521001604
+EX_glc_D[e]	120.210995032636
+EX_hdcea[e]	3.61698466813181
+EX_lgnc[e]	0.166975492670868
+EX_fol[e]	0.000272645010836998
+EX_strch1[e]	45.1139619460203
+EX_i[e]	0.00366062755709078
+EX_starch1200(e)	0.417683121486647