Python generate_pathway Exemples

Exemple #1

from mEncoder.mechanistic_model import (
    add_monomer_synth_deg, generate_pathway, add_activation,
    add_abundance_observables, add_phospho_observables
)

model = Model('FLT3_MAPK')

# FLT3
for rtkf_name in ['FL']:
    add_monomer_synth_deg(rtkf_name)


rtk_cascade = [
    ('FLT3',  {'Y843': ['FL']}),
]
generate_pathway(model, rtk_cascade)

# ERK
for ras_name in ['HRAS', 'KRAS', 'NRAS']:
    add_monomer_synth_deg(ras_name, nsites=['N'])
    add_activation(
        model, ras_name, 'N', 'nucleotide_exchange',
        ['FLT3__Y843_p']
    )

mapk_cascade = [
    ('RAF1',   {'S338':      ['KRAS__N_gtp', 'HRAS__N_gtp', 'NRAS__N_gtp']}),
    ('BRAF',   {'S447':      ['KRAS__N_gtp', 'HRAS__N_gtp', 'NRAS__N_gtp']}),
    ('MAP2K1', {'S218_S222': ['RAF1__S338_p', 'BRAF__S447_p']}),
    ('MAP2K2', {'S222_S226': ['RAF1__S338_p', 'BRAF__S447_p']}),
    ('MAPK1', {'T185_Y187': ['MAP2K1__S218_p__S222_p',

Exemple #2

Fichier : pw_EGFR_MAPK_AKT_STAT.py Projet : meyer-lab/mechanismEncoder

rtkfs = ['EGF']

# EGFR
for rtkf_name in rtkfs:
    add_monomer_synth_deg(rtkf_name)
    add_gf_bolus(model, rtkf_name, [rtkf_name])

erbb_cascade = [
    ('EGFR', {
        'Y1173': ['EGF']
    }),
    ('ERBB2', {
        'Y1248': ['EGF']
    }),
]
generate_pathway(model, erbb_cascade)

active_rtks = ['EGFR__Y1173_p', 'ERBB2__Y1248_p']
stat_rtks = ['EGFR__Y1173_p', 'ERBB2__Y1248_p']

# MAPK
for ras_name in ['HRAS', 'KRAS', 'NRAS']:
    add_monomer_synth_deg(ras_name, nsites=['N'])
    add_activation(model, ras_name, 'N', 'nucleotide_exchange', active_rtks)

mapk_cascade = [
    ('RAF1', {
        'S338': ['KRAS__N_gtp', 'HRAS__N_gtp', 'NRAS__N_gtp']
    }),
    ('BRAF', {
        'S445': ['KRAS__N_gtp', 'HRAS__N_gtp', 'NRAS__N_gtp']

Exemple #3

Fichier : pw_EGFR_MAPK.py Projet : meyer-lab/mechanismEncoder

rtkfs = ['EGF']

# EGFR
for rtkf_name in rtkfs:
    add_monomer_synth_deg(rtkf_name)
    add_gf_bolus(model, rtkf_name, [rtkf_name])

erbb_cascade = [
    ('EGFR', {
        'Y1173': ['EGF']
    }),
    ('ERBB2', {
        'Y1248': ['EGFR__Y1173_p']
    }),
]
generate_pathway(model, erbb_cascade)

active_rtks = ['EGFR__Y1173_p', 'ERBB2__Y1248_p']

mapk_cascade = [
    ('RAF1', {
        'S338': active_rtks + ['EGF']
    }),
    ('BRAF', {
        'S445': active_rtks + ['EGF']
    }),
    ('MAP2K1', {
        'S218_S222': ['RAF1__S338_p', 'BRAF__S445_p']
    }),
    ('MAP2K2', {
        'S222_S226': ['RAF1__S338_p', 'BRAF__S445_p']

Exemple #4

Fichier : pw_FLT3_MAPK_AKT_STAT.py Projet : meyer-lab/mechanismEncoder

from mEncoder.mechanistic_model import (add_monomer_synth_deg,
                                        generate_pathway, add_activation,
                                        add_observables, add_inhibitor)

from pysb import Model

model = Model('FLT3_MAPK_AKT_STAT')

# FLT3
for rtkf_name in ['FL']:
    add_monomer_synth_deg(rtkf_name)

rtk_cascade = [('FLT3', {'Y843': ['FL']}), ('ABL2', {'Y1294': [], 'Y177': []})]
generate_pathway(model, rtk_cascade)

# ERK
for ras_name in ['HRAS', 'KRAS', 'NRAS']:
    add_monomer_synth_deg(ras_name, nsites=['N'])
    add_activation(model, ras_name, 'N', 'nucleotide_exchange',
                   ['FLT3__Y843_p', 'ABL2__Y177_p'])

mapk_cascade = [
    ('RAF1', {
        'S338': ['KRAS__N_gtp', 'HRAS__N_gtp', 'NRAS__N_gtp'],
        'S29_S289_S296_S301_S642':
        ['MAPK1__T185_p__Y187_p', 'MAPK3__T202_p__Y204_p']
    }),
    ('BRAF', {
        'S447': ['KRAS__N_gtp', 'HRAS__N_gtp', 'NRAS__N_gtp']
    }),
    ('MAP2K1', {