Getting and setting reaction parameters and reactions

[1]:

import sys
sys.path.append('../..')
%matplotlib inline

[2]:

from basico import *

Load model

[3]:

biomod = load_example("LM-test1")

Getting/setting global quantities

It is possible to set:
    'initial_value'
    'initial_expression'
    'expression'
    'status'
    'type'

[4]:

get_parameters()

[4]:

	type	initial_value	expression	value	rate	key
name
epsilon	fixed	0.78		NaN	0.0	ModelValue_0
offset	fixed	0.10		NaN	0.0	ModelValue_1
signal	assignment	0.10	[P] * Values[epsilon] + Values[offset]	NaN	NaN	ModelValue_2

[5]:

set_parameters(name= 'offset', initial_value = 50)

[6]:

set_parameters('signal', expression='[P] * Values[epsilon] + Values[offset]')

[7]:

get_parameters()

[7]:

	type	initial_value	expression	value	rate	key
name
epsilon	fixed	0.78		NaN	0.0	ModelValue_0
offset	fixed	50.00		NaN	0.0	ModelValue_1
signal	assignment	50.00	[P] * Values[epsilon] + Values[offset]	NaN	NaN	ModelValue_2

Getting/setting species (metabolites)

[8]:

get_species()

[8]:

	compartment	type	unit	initial_concentration	initial_particle_number	concentration	particle_number	rate	particle_number_rate	key
name
E	compartment	reactions	mmol/ml	0.010000	6.022142e+18	NaN	NaN	NaN	NaN	Metabolite_1
S	compartment	reactions	mmol/ml	10.000001	6.022142e+21	NaN	NaN	NaN	NaN	Metabolite_0
ES	compartment	reactions	mmol/ml	0.000000	0.000000e+00	NaN	NaN	NaN	NaN	Metabolite_2
P	compartment	reactions	mmol/ml	0.000000	0.000000e+00	NaN	NaN	NaN	NaN	Metabolite_3

[9]:

get_species(name = 'E')['initial_concentration']

[9]:

name
E     0.01
ES    0.00
Name: initial_concentration, dtype: float64

Setting

if 'name' in kwargs:
    metab.setObjectName(kwargs['name'])

if 'unit' in kwargs:
    metab.setUnitExpression(kwargs['unit'])

if 'initial_concentration' in kwargs:
    metab.setInitialConcentration(kwargs['initial_concentration']),

if 'initial_particle_number' in kwargs:
    metab.setInitialValue(kwargs['initial_particle_number']),

if 'initial_expression' in kwargs:
    metab.setInitialExpression(kwargs['initial_expression'])

if 'expression' in kwargs:
    metab.setExpression(kwargs['expression'])

[10]:

set_species(name = 'E', new_name = 'Lilija')

[11]:

set_species(name = 'Lilija', initial_concentration = 123456)

[12]:

get_species(name = 'Lilija')

[12]:

	compartment	type	unit	initial_concentration	initial_particle_number	initial_expression	expression	concentration	particle_number	rate	particle_number_rate	key
name
Lilija	compartment	reactions	mmol/ml	123456.0	7.434694e+25			NaN	NaN	NaN	NaN	Metabolite_1

[13]:

# change it back
set_species(new_name = 'E', name = 'Lilija')

Getting/setting reaction parameters

[14]:

get_reaction_parameters()

[14]:

	value	reaction	type
name
(R1).k1	130.0	R1	local
(R1).k2	1.0	R1	local
(R2).k1	1.0	R2	local

Setting only the following is possible:
'new_name'
'value'

[15]:

set_reaction_parameters(name = '(R1).k1', value=123)

[16]:

get_reaction_parameters()

[16]:

	value	reaction	type
name
(R1).k1	123.0	R1	local
(R1).k2	1.0	R1	local
(R2).k1	1.0	R2	local

Getting/setting reactions

[17]:

get_reactions()

[17]:

	scheme	flux	particle_flux	function
name
R1	S + E = ES	NaN	NaN	Mass action (reversible)
R2	ES -> E + P	NaN	NaN	Mass action (irreversible)

Setting scheme

[18]:

set_reaction(name = 'R1', scheme = 'S + E + F = ES')

[19]:

get_reactions()

[19]:

	scheme	flux	particle_flux	function
name
R1	S + E + F = ES	NaN	NaN	Mass action (reversible)
R2	ES -> E + P	NaN	NaN	Mass action (irreversible)

Setting reaction name

[20]:

set_reaction(name = 'R1', new_name = 'Reaction 1')

[21]:

get_reactions()

[21]:

	scheme	flux	particle_flux	function
name
Reaction 1	S + E + F = ES	NaN	NaN	Mass action (reversible)
R2	ES -> E + P	NaN	NaN	Mass action (irreversible)

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