Tutorial load model

Working with SBML models using basico

In [1]:

import basico

import basico

c:\Users\Wehling\code\AIAgents-Hackathon\.venv\Lib\site-packages\tqdm\auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
  from .autonotebook import tqdm as notebook_tqdm

In [9]:

# load SBML model
model = basico.load_model("./Dwivedi_Model537_annotated.xml")

# load SBML model model = basico.load_model("./Dwivedi_Model537_annotated.xml")

In [10]:

# get model species
species = basico.get_species()
species

# get model species species = basico.get_species() species

Out[10]:

	compartment	type	unit	initial_concentration	initial_particle_number	initial_expression	expression	concentration	particle_number	rate	particle_number_rate	key	sbml_id	transition_time	display_name
name
IL6	serum	reactions	nmol/l	4.356289e-04	2.623419e+11			4.356289e-04	2.623419e+11	-1.565877e-17	-9.429932e-03	Metabolite_88	mwf626e95e_543f_41e4_aad4_c6bf60ab345b	0.028719	IL6{serum}
sgp130	serum	reactions	nmol/l	3.900000e+00	2.348635e+15			3.900000e+00	2.348635e+15	0.000000e+00	0.000000e+00	Metabolite_89	mwbbbce920_e8dd_4320_9386_fc94bfb2fc99	0.997567	sgp130{serum}
sR_IL6_sgp130	serum	reactions	nmol/l	8.740607e-02	5.263716e+13			8.740607e-02	5.263716e+13	-2.367565e-16	-1.425781e-01	Metabolite_90	mw810ff751_fa4e_4143_bd50_169b3e325e1e	9.190533	sR_IL6_sgp130{serum}
CRP	serum	reactions	nmol/l	2.210637e+02	1.331277e+17			2.210637e+02	1.331277e+17	6.243627e-13	3.760000e+02	Metabolite_91	mw114aa90f_5f5b_4fe8_9406_361c8489b6a1	2.777778	CRP{serum}
sR	serum	reactions	nmol/l	4.253507e+00	2.561522e+15			4.253507e+00	2.561522e+15	1.307675e-14	7.875000e+00	Metabolite_92	mw30ae63db_6cd3_4b6f_93ad_3350cd360bcc	3.283772	sR{serum}
sR_IL6	serum	reactions	nmol/l	1.094243e-03	6.589683e+11			1.094243e-03	6.589683e+11	5.032090e-17	3.030396e-02	Metabolite_93	mw03db56ac_8dc6_4931_ae82_fef706d2ee3d	0.518949	sR_IL6{serum}
Ab	serum	reactions	nmol/l	2.381820e-29	1.434365e-14			2.381820e-29	1.434365e-14	5.129906e-26	3.089302e-11	Metabolite_94	mwf345ed7a_0622_403c_b816_c8749a2c9ded	0.000464	Ab{serum}
Ab_sR	serum	reactions	nmol/l	6.104391e-26	3.676150e-11			6.104391e-26	3.676150e-11	-5.097542e-26	-3.069812e-11	Metabolite_95	mw1da111f2_a036_4392_8512_015005bdcbb7	1.185348	Ab_sR{serum}
Ab_sR_IL6	serum	reactions	nmol/l	-7.413309e-29	-4.464399e-14			-7.413309e-29	-4.464399e-14	5.137413e-29	3.093822e-14	Metabolite_96	mw9947742a_0e4b_4636_9a4b_b6eef2a8f6ac	1.159408	Ab_sR_IL6{serum}
CRP Suppression (%)	serum	assignment	nmol/l	-0.000000e+00	-0.000000e+00		( [CRP{serum}] - {Values[Initial for CRP]} ) /...	-0.000000e+00	-0.000000e+00	NaN	NaN	Metabolite_97	CRP_Suppression___	NaN	CRP Suppression (%)
CRP (% of baseline)	serum	assignment	nmol/l	1.000000e+02	6.022141e+16		[CRP{serum}] / {Values[Initial for CRP]} * 100	1.000000e+02	6.022141e+16	NaN	NaN	Metabolite_98	CRP____of_baseline	NaN	CRP (% of baseline)
gp130	liver	reactions	nmol/l	3.889589e-01	2.342365e+14			3.889589e-01	2.342365e+14	6.486481e-17	3.906250e-02	Metabolite_99	mw80848184_e2dd_47ce_86d7_7a21479342bd	5.678232	gp130{liver}
R_IL6_gp130	liver	reactions	nmol/l	6.599359e-05	3.974227e+10			6.599359e-05	3.974227e+10	-5.270266e-18	-3.173828e-03	Metabolite_100	mwd2d9d93a_3bd1_4f17_bac1_baba9ef2d55a	0.006371	R_IL6_gp130{liver}
sR_IL6	liver	reactions	nmol/l	9.761649e-04	5.878603e+11			9.761649e-04	5.878603e+11	-2.918916e-16	-1.757812e-01	Metabolite_101	mw4638f126_8cb8_4021_ab41_6ae195743ba0	0.123541	sR_IL6{liver}
R	liver	reactions	nmol/l	4.382358e-01	2.639118e+14			4.382358e-01	2.639118e+14	-6.486481e-17	-3.906250e-02	Metabolite_102	mw10315fa3_6f13_4618_bda8_a8694bd3c374	6.397603	R
IL6	liver	reactions	nmol/l	7.256658e-04	4.370062e+11			7.256658e-04	4.370062e+11	1.444255e-18	8.697510e-04	Metabolite_103	mw0adf3eb4_a196_4c48_b10d_4e9e9faaf9e1	4.075710	IL6{liver}
R_IL6	liver	reactions	nmol/l	1.600365e-05	9.637625e+09			1.600365e-05	9.637625e+09	-6.334454e-21	-3.814697e-06	Metabolite_104	mw7d86cc23_a1af_44c3_bdb9_71e9b1bb2a83	0.175114	R_IL6
Ractive	liver	reactions	nmol/l	7.654165e-01	4.609446e+14			7.654165e-01	4.609446e+14	2.432430e-18	1.464844e-03	Metabolite_105	mw0eb6c959_d408_45a0_a450_928b8c5876bb	74.828042	Ractive{liver}
STAT3	liver	reactions	nmol/l	7.775373e-01	4.682439e+14			7.775373e-01	4.682439e+14	1.556755e-16	9.375000e-02	Metabolite_106	mw42054cd7_17af_46da_970c_7f99151906ad	1.980238	STAT3{liver}
pSTAT3	liver	reactions	nmol/l	9.222463e+00	5.553897e+15			9.222463e+00	5.553897e+15	-1.556755e-16	-9.375000e-02	Metabolite_107	mw39c2e431_fdc3_4964_be29_6ca856620b1b	23.487843	pSTAT3{liver}
CRP	liver	assignment	nmol/l	1.583258e+02	9.534605e+16		Values[VmProtSynth] * [pSTAT3{liver}] / ( Valu...	1.583258e+02	9.534605e+16	NaN	NaN	Metabolite_108	mwd5313618_89eb_4c8c_bc82_66f10f966349	NaN	CRP{liver}
sR	liver	reactions	nmol/l	6.087047e+00	3.665705e+15			6.087047e+00	3.665705e+15	-7.654706e-15	-4.609772e+00	Metabolite_109	mw2e464cf3_a09c_4b7c_9f3c_06720016a48e	34187.965404	sR{liver}
CRPExtracellular	liver	reactions	nmol/l	4.097753e+02	2.467725e+17			4.097753e+02	2.467725e+17	-5.048039e-13	-3.040000e+02	Metabolite_110	mw36ea78c1_ed71_4def_96d3_857a442d7195	5.176354	CRPExtracellular
sgp130	liver	reactions	nmol/l	5.589699e+00	3.366195e+15			5.589699e+00	3.366195e+15	3.468646e-15	2.088867e+00	Metabolite_111	mw147d30ec_478e_4090_b496_128a131d29eb	755.173729	sgp130{liver}
sR_IL6_sgp130	liver	reactions	nmol/l	1.163437e-01	7.006379e+13			1.163437e-01	7.006379e+13	5.416211e-16	3.261719e-01	Metabolite_112	mwab41493c_6349_45f1_a226_3030cfed0e06	15.718141	sR_IL6_sgp130{liver}
Ab_sR	liver	reactions	nmol/l	8.616193e-26	5.188793e-11			8.616193e-26	5.188793e-11	-8.215556e-26	-4.947523e-11	Metabolite_113	mwf405687b_7401_44ec_a0d6_4a2b35c13e8a	1.048766	Ab_sR{liver}
Ab	liver	reactions	nmol/l	2.200207e-29	1.324996e-14			2.200207e-29	1.324996e-14	7.691938e-26	4.632193e-11	Metabolite_114	mw3667a5e1_02c9_44a0_acb4_b0431faa822d	0.000270	Ab{liver}
Ab_R	liver	reactions	nmol/l	2.033720e-27	1.224735e-12			2.033720e-27	1.224735e-12	4.554136e-27	2.742565e-12	Metabolite_115	mw772cbf20_3fc1_4800_ae59_77884f1ae333	0.446207	Ab_R
Ab_sR_IL6	liver	reactions	nmol/l	-3.077935e-29	-1.853576e-14			-3.077935e-29	-1.853576e-14	-6.375163e-29	-3.839213e-14	Metabolite_116	mw2ba2b802_9f07_4f4d_94c6_24c8de1a95cf	0.482382	Ab_sR_IL6{liver}
sR_IL6	gut	reactions	nmol/l	1.306824e-03	7.869877e+11			1.306824e-03	7.869877e+11	1.281080e-16	7.714844e-02	Metabolite_117	mw7becb5fe_8da8_4285_a821_0d77ad811b62	0.067090	sR_IL6{gut}
gp130	gut	reactions	nmol/l	3.749627e-01	2.258078e+14			3.749627e-01	2.258078e+14	6.486481e-17	3.906250e-02	Metabolite_118	mw8c9107e6_f51d_442d_b2dc_2bfdbb8482ca	5.473908	gp130{gut}
R_IL6_gp130	gut	reactions	nmol/l	8.448905e-05	5.088050e+10			8.448905e-05	5.088050e+10	-2.997464e-17	-1.805115e-02	Metabolite_119	mw824bc3d4_1ac3_4912_9b51_8f14ff1c96b9	0.006371	R_IL6_gp130{gut}
Ractive	gut	reactions	nmol/l	9.802725e-01	5.903339e+14			9.802725e-01	5.903339e+14	1.135134e-17	6.835938e-03	Metabolite_120	mw6cce2109_0e32_4dd9_98ec_41173e8ef07d	74.853946	Ractive{gut}
STAT3	gut	reactions	nmol/l	6.106360e-01	3.677336e+14			6.106360e-01	3.677336e+14	-1.037837e-16	-6.250000e-02	Metabolite_121	mw2b255f94_8018_4b99_bde8_918eeac45446	1.545036	STAT3{gut}
pSTAT3	gut	reactions	nmol/l	9.389364e+00	5.654407e+15			9.389364e+00	5.654407e+15	1.037837e-16	6.250000e-02	Metabolite_122	mw48867e93_f170_44e8_ac7a_185b23e1bf3b	23.757039	pSTAT3{gut}
geneProduct	gut	assignment	nmol/l	1.598036e+02	9.623598e+16		Values[VmProtSynth] * [pSTAT3{gut}] / ( Values...	1.598036e+02	9.623598e+16	NaN	NaN	Metabolite_123	mw0083d743_836f_4238_a17f_4602193d5bc0	NaN	geneProduct
sR	gut	reactions	nmol/l	6.064107e+00	3.651890e+15			6.064107e+00	3.651890e+15	-5.510265e-15	-3.318359e+00	Metabolite_124	mwd31f52cc_04e7_40e0_885f_c7b2d9e62215	314.866866	sR{gut}
IL6	gut	reactions	nmol/l	9.348199e-03	5.629617e+12			9.348199e-03	5.629617e+12	0.000000e+00	0.000000e+00	Metabolite_125	mw2c9b0499_3325_4394_8af3_bbf653a944a0	0.259672	IL6{gut}
sgp130	gut	reactions	nmol/l	5.569739e+00	3.354175e+15			5.569739e+00	3.354175e+15	-3.747564e-15	-2.256836e+00	Metabolite_126	mwd65b5b39_dc1b_4e77_a999_67277a880e5e	585.644296	sgp130{gut}
sR_IL6_sgp130	gut	reactions	nmol/l	1.363039e-01	8.208413e+13			1.363039e-01	8.208413e+13	-1.654053e-16	-9.960938e-02	Metabolite_127	mw6335d5d7_c7b0_4bc0_b883_f7ee4915c2c3	14.332020	sR_IL6_sgp130{gut}
Ab	gut	reactions	nmol/l	2.158790e-29	1.300053e-14			2.158790e-29	1.300053e-14	-6.539663e-26	-3.938277e-11	Metabolite_128	mwf7796221_1fea_4274_a93e_c00adbf5778c	0.000330	Ab{gut}
Ab_sR	gut	reactions	nmol/l	2.620597e-26	1.578160e-11			2.620597e-26	1.578160e-11	6.543913e-26	3.940837e-11	Metabolite_129	mw5d764bb8_5693_4ac8_9557_f65992cc5eb0	0.400175	Ab_sR{gut}
Ab_sR_IL6	gut	reactions	nmol/l	-1.209167e-28	-7.281774e-14			-1.209167e-28	-7.281774e-14	1.278399e-29	7.698701e-15	Metabolite_130	mwedc1bc00_adf7_4144_a1c2_7dc1a9565dc2	9.458444	Ab_sR_IL6{gut}
Ab	peripheral	reactions	nmol/l	1.679209e-29	1.011244e-14			1.679209e-29	1.011244e-14	-2.088274e-32	-1.257588e-17	Metabolite_131	mwbc2f5464_81e5_43fd_8b39_f5a2756af72f	804.113764	Ab{peripheral}

In [11]:

# get annotations
basico.get_miriam_annotation(name="IL6")

# get annotations basico.get_miriam_annotation(name="IL6")

Out[11]:

{'descriptions': [{'id': '3569',
   'qualifier': 'is version of',
   'uri': 'http://identifiers.org/ncbigene/3569',
   'resource': 'NCBI Gene'},
  {'id': 'P05231',
   'qualifier': 'is version of',
   'uri': 'http://identifiers.org/uniprot/P05231',
   'resource': 'UniProt Knowledgebase'},
  {'id': 'BTO:0001239',
   'qualifier': 'is version of',
   'uri': 'http://identifiers.org/BTO:0001239',
   'resource': 'Brenda Tissue Ontology'}]}

In [ ]: