def assemble_pysb(stmts, data_genes, out_file):
"""Return an assembled PySB model."""
base_file, _ = os.path.splitext(out_file)
#stmts = ac.load_statements('%s.pkl' % base_file)
stmts = preprocess_stmts(stmts, data_genes)
# This is the "final" set of statements going into the assembler so it
# makes sense to cache these.
# This is also the point where index cards can be generated
ac.dump_statements(stmts, '%s_before_pa.pkl' % base_file)
assemble_index_cards(stmts, 'output/index_cards')
# Save a version of statements with no evidence for faster loading
for s in stmts:
s.evidence = []
for ss in s.supports + s.supported_by:
ss.evidence = []
ac.dump_statements(stmts, '%s_no_evidence.pkl' % base_file)
# Assemble model
pa = PysbAssembler()
pa.add_statements(stmts)
pa.make_model(reverse_effects=False)
#ac.dump_statements(pa.statements, '%s_after_pa.pkl' % base_file)
# Set context
set_context(pa)
# Add observables
add_observables(pa.model)
pa.save_model(out_file)
with open('korkut_pysb.pkl', 'wb') as fh:
pickle.dump(pa.model, fh)
#pa.export_model('kappa', '%s.ka' % base_file)
return pa.model
def assemble_model(model_name, statements):
# Pysb assembly
pa = PysbAssembler()
pa.add_statements(statements)
ts = time.time()
model = pa.make_model()
te = time.time()
print('Assembly took %.2fs' % (te - ts))
model.name = model_name
add_observable(model)
set_parameters(model)
# Save and return model
pa.model = model
pa.save_model('%s.py' % model_name)
return model
def assemble_pysb(stmts, data_genes, out_file):
"""Return an assembled PySB model."""
stmts = ac.filter_direct(stmts)
stmts = ac.filter_belief(stmts, 0.95)
stmts = ac.filter_top_level(stmts)
stmts = ac.filter_gene_list(stmts, data_genes, 'all')
stmts = ac.reduce_activities(stmts)
pa = PysbAssembler()
pa.add_statements(stmts)
model = pa.make_model()
# Add observables
o = Observable('MAPK1p', model.monomers['MAPK1'](T185='p', Y187='p'))
model.add_component(o)
o = Observable('MAPK3p', model.monomers['MAPK3'](T202='p', Y204='p'))
model.add_component(o)
o = Observable('GSK3Ap', model.monomers['GSK3A'](S21='p'))
model.add_component(o)
o = Observable('GSK3Bp', model.monomers['GSK3B'](S9='p'))
model.add_component(o)
o = Observable('RPS6p', model.monomers['RPS6'](S235='p'))
model.add_component(o)
o = Observable('EIF4EBP1p', model.monomers['EIF4EBP1'](S65='p'))
model.add_component(o)
o = Observable('JUNp', model.monomers['JUN'](S73='p'))
model.add_component(o)
o = Observable('FOXO3p', model.monomers['FOXO3'](S315='p'))
model.add_component(o)
o = Observable('AKT1p', model.monomers['AKT1'](S473='p'))
model.add_component(o)
o = Observable('AKT2p', model.monomers['AKT2'](S474='p'))
model.add_component(o)
o = Observable('AKT3p', model.monomers['AKT3'](S='p'))
model.add_component(o)
o = Observable('ELK1', model.monomers['ELK1'](S383='p'))
model.add_component(o)
# Set context
pa.set_context('SKMEL28_SKIN')
pa.save_model(out_file)
ke = KappaExporter(model)
with open('%s.ka' % base_file, 'wb') as fh:
base_file, _ = os.path.splitext(out_file)
fh.write(ke.export().encode('utf-8'))
return model
def assemble_pysb(stmts, data_genes, out_file):
"""Return an assembled PySB model."""
base_file, _ = os.path.splitext(out_file)
#stmts = ac.load_statements('%s.pkl' % base_file)
stmts = preprocess_stmts(stmts, data_genes)
# Make a SIF model equivalent to the PySB model
# Useful for making direct comparisons in pathfinding
sa = SifAssembler(stmts)
sa.make_model(use_name_as_key=True,
include_mods=True,
include_complexes=True)
sif_str = sa.print_model(include_unsigned_edges=True)
with open('%s_pysb.sif' % base_file, 'wt') as f:
f.write(sif_str)
# This is the "final" set of statements going into the assembler so it
# makes sense to cache these.
# This is also the point where index cards can be generated
ac.dump_statements(stmts, '%s_before_pa.pkl' % base_file)
assemble_index_cards(stmts, 'output/index_cards')
# Save a version of statements with no evidence for faster loading
for s in stmts:
s.evidence = []
for ss in s.supports + s.supported_by:
ss.evidence = []
ac.dump_statements(stmts, '%s_no_evidence.pkl' % base_file)
# Assemble model
pa = PysbAssembler()
pa.add_statements(stmts)
pa.make_model(reverse_effects=False)
#ac.dump_statements(pa.statements, '%s_after_pa.pkl' % base_file)
# Set context
set_context(pa)
# Add observables
add_observables(pa.model)
pa.save_model(out_file)
with open('korkut_pysb.pkl', 'wb') as fh:
pickle.dump(pa.model, fh)
#pa.export_model('kappa', '%s.ka' % base_file)
return pa.model
def assemble_model(model_name, reread=False):
xml_fname = model_name + '.xml'
if not reread:
print('Processing %s' % xml_fname)
if os.path.exists(xml_fname):
with open(xml_fname, 'rb') as fh:
tp = trips.process_xml(fh.read())
else:
reread = True
if reread:
fname = model_name + '.txt'
print('Reading %s' % fname)
with open(fname, 'rb') as fh:
ts = time.time()
tp = trips.process_text(fh.read(), xml_fname)
te = time.time()
print('Reading took %.2fs' % (te - ts))
print('Assembling statements:')
for i, st in enumerate(tp.statements):
print('%d: %s' % (i, st))
print('----------------------')
pa = PysbAssembler()
pa.add_statements(tp.statements)
ts = time.time()
model = pa.make_model()
te = time.time()
print('Assembly took %.2fs' % (te - ts))
model.name = model_name
add_observable(model)
set_parameters(model)
# Save and return model
pa.model = model
pa.save_model('%s.py' % model_name)
return model
def assemble_model(model_id, reread=False):
model_name = 'model%d' % model_id
# If model has already been read, just process the EKB XML
if os.path.exists(model_name + '.xml') and not reread:
tp = trips.process_xml(open(model_name + '.xml').read())
else:
# Start with the basic model
model_txt = open('model1.txt').read()
# Apply patches one by one to get to the current model text
for j in range(1, model_id):
patch_txt = open('model%d_from%d.txt' % (j + 1, j)).read()
model_txt = apply_patch(model_txt, patch_txt)
print('Reading model %d text:' % model_id)
print(model_txt)
# Process model text and save result EKB XML
tp = trips.process_text(model_txt, model_name + '.xml')
print('Assembling statements:')
for i, st in enumerate(tp.statements):
print('%d: %s' % (i, st))
# Assemble the PySB model
pa = PysbAssembler()
pa.add_statements(tp.statements)
model = pa.make_model(policies='two_step')
# Set initial conditions
erk = model.monomers['ERK']
obs = Observable(b'ERK_p', erk(phospho='p'))
model.add_component(obs)
vem = model.monomers['VEMURAFENIB']
obs = Observable(b'Vem_free', vem(map3k=None))
model.add_component(obs)
ras = model.monomers['RAS']
obs = Observable(b'RAS_active', ras(gtp=ANY))
model.add_component(obs)
braf = model.monomers['BRAF']
obs = Observable(b'BRAF_active', braf(vemurafenib=None))
model.add_component(obs)
model.parameters[b'BRAF_0'].value = 0
egf = model.monomers['EGF']
obs = Observable(b'EGF_free', egf(erbb=None))
model.add_component(obs)
# Add mutated form of BRAF as initial condition
sites_dict = {}
for site in braf.sites:
if site in braf.site_states:
sites_dict[site] = braf.site_states[site][0]
else:
sites_dict[site] = None
sites_dict['V600'] = 'E'
model.add_component(Parameter('BRAF_mut_0', 1e5))
model.initial(braf(**sites_dict), model.parameters['BRAF_mut_0'])
# Set up model parameters
model.parameters['kf_ee_bind_1'].value = 1
model.parameters['kr_ee_bind_1'].value = 0.1
model.parameters['kf_ee_bind_2'].value = 1
model.parameters['kr_ee_bind_2'].value = 0.1
model.parameters['kf_eg_bind_1'].value = 1
model.parameters['kr_eg_bind_1'].value = 0.1
model.parameters['kf_gs_bind_1'].value = 1
model.parameters['kr_gs_bind_1'].value = 0.1
model.parameters['kf_sr_bind_1'].value = 1
model.parameters['kr_sr_bind_1'].value = 50
model.parameters['kf_rg_bind_1'].value = 50
model.parameters['kr_rg_bind_1'].value = 0.5
model.parameters['kf_rb_bind_1'].value = 1
model.parameters['kr_rb_bind_1'].value = 0.5
model.parameters['kf_vb_bind_1'].value = 10
model.parameters['kr_vb_bind_1'].value = 1
model.parameters['kf_bm_bind_1'].value = 1
model.parameters['kr_bm_bind_1'].value = 0.1
model.parameters['kc_bm_phosphorylation_1'].value = 3
model.parameters['kf_pm_bind_1'].value = 1
model.parameters['kr_pm_bind_1'].value = 0.001
model.parameters['kc_pm_dephosphorylation_1'].value = 10
model.parameters['kf_me_bind_1'].value = 1
model.parameters['kr_me_bind_1'].value = 0.1
model.parameters['kc_me_phosphorylation_1'].value = 10
model.parameters['kf_de_bind_1'].value = 1
model.parameters['kr_de_bind_1'].value = 0.001
model.parameters['kc_de_dephosphorylation_1'].value = 10
model.parameters['VEMURAFENIB_0'].value = 0
model.parameters['EGF_0'].value = 1e3
model.parameters['EGFR_0'].value = 1e5
model.parameters['SOS_0'].value = 1e3
model.parameters['GRB2_0'].value = 1e5
model.parameters['RAS_0'].value = 2e5
model.parameters['GTP_0'].value = 1e7
model.parameters['MEK_0'].value = 1e5
model.parameters['ERK_0'].value = 1e5
model.parameters['DUSP6_0'].value = 1e3
model.parameters['PPP2CA_0'].value = 1e5
if model_id >= 2:
model.parameters['Phosphatase_0'].value = 1e2
model.parameters['kf_es_bind_1'].value = 1e-05
model.parameters['kr_es_bind_1'].value = 1e-04
model.parameters['kc_es_phosphorylation_1'].value = 1
model.parameters['kf_ps_bind_1'].value = 1
model.parameters['kr_ps_bind_1'].value = 0.1
model.parameters['kc_ps_dephosphorylation_1'].value = 1e-04
if model_id >= 3:
model.parameters['kf_bb_bind_1'].value = 10
model.parameters['kr_bb_bind_1'].value = 1
model.parameters['kf_vb_bind_2'].value = 1e-04
pa.model = model
pa.save_model('model%d.py' % model_id)
return model
def test_print_model():
st = Phosphorylation(Agent("MAP2K1"), Agent("MAPK3"))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
pa.save_model("/dev/null")
def assemble_model(model_name, reread=False):
xml_fname = model_name + '.xml'
if not reread:
print('Processing %s' % xml_fname)
if os.path.exists(xml_fname):
with open(xml_fname, 'rb') as fh:
tp = trips.process_xml(fh.read())
else:
reread = True
if reread:
fname = model_name + '.txt'
print('Reading %s' % fname)
with open(fname, 'rb') as fh:
tp = trips.process_text(fh.read(), xml_fname)
print('Assembling statements:')
for i, st in enumerate(tp.statements):
print('%d: %s' % (i, st))
print('----------------------')
pa = PysbAssembler()
pa.add_statements(tp.statements)
model = pa.make_model()
model.name = model_name
p53 = model.monomers['TP53']
obs = Observable(b'p53_active', p53(activity='active'))
model.add_component(obs)
if not model_name.endswith('var'):
model.parameters['kf_aa_act_1'].value = 5e-06
model.parameters['kf_pt_act_1'].value = 1e-05
if model_name == 'p53_ATM':
model.add_component(Parameter('ATMa_0', 1))
atm = model.monomers['ATM']
model.initial(atm(activity='active'),
model.parameters['ATMa_0'])
model.parameters['kf_pa_act_1'].value = 1e-04
obs = Observable(b'atm_active', atm(activity='active'))
model.add_component(obs)
if model_name == 'p53_ATR':
model.add_component(Parameter('ATRa_0', 1))
atr = model.monomers['ATR']
model.initial(atr(activity='active'),
model.parameters['ATRa_0'])
obs = Observable(b'atr_active', atr(activity='active'))
model.add_component(obs)
if model_name == 'p53_ATM_var':
#model.add_component(Parameter('ATMa_0', 1))
#atm = model.monomers['ATM']
#model.initial(atm(activity='active'),
# model.parameters['ATMa_0'])
model.add_component(Parameter('ATMa_0', 1))
atm = model.monomers['ATM']
model.initial(atm(phospho='p'),
model.parameters['ATMa_0'])
model.parameters['kf_pa_dephosphorylation_1'].value = 1e-04
model.parameters['MDM2_0'].value = 0
model.parameters['kf_m_deg_1'].value = 8e-01
model.parameters['kf_tm_synth_1'].value = 0.2
model.parameters['kf_aa_phosphorylation_1'].value = 5e-06
obs = Observable(b'atm_active', atm(phospho='p'))
model.add_component(obs)
pa.model = model
pa.save_model('%s.py' % model_name)
return model
def assemble_model(model_name, reread=False):
xml_fname = model_name + '.xml'
if not reread:
print('Processing %s' % xml_fname)
if os.path.exists(xml_fname):
with open(xml_fname, 'rb') as fh:
tp = trips.process_xml(fh.read())
else:
reread = True
if reread:
fname = model_name + '.txt'
print('Reading %s' % fname)
with open(fname, 'rb') as fh:
tp = trips.process_text(fh.read(), xml_fname)
print('Assembling statements:')
for i, st in enumerate(tp.statements):
print('%d: %s' % (i, st))
print('----------------------')
pa = PysbAssembler()
pa.add_statements(tp.statements)
model = pa.make_model()
model.name = model_name
p53 = model.monomers['TP53']
obs = Observable(b'p53_active', p53(activity='active'))
model.add_component(obs)
if not model_name.endswith('var'):
model.parameters['kf_aa_act_1'].value = 5e-06
model.parameters['kf_pt_act_1'].value = 1e-05
if model_name == 'p53_ATM':
model.add_component(Parameter('ATMa_0', 1))
atm = model.monomers['ATM']
model.initial(atm(activity='active'), model.parameters['ATMa_0'])
model.parameters['kf_pa_act_1'].value = 1e-04
obs = Observable(b'atm_active', atm(activity='active'))
model.add_component(obs)
if model_name == 'p53_ATR':
model.add_component(Parameter('ATRa_0', 1))
atr = model.monomers['ATR']
model.initial(atr(activity='active'), model.parameters['ATRa_0'])
obs = Observable(b'atr_active', atr(activity='active'))
model.add_component(obs)
if model_name == 'p53_ATM_var':
#model.add_component(Parameter('ATMa_0', 1))
#atm = model.monomers['ATM']
#model.initial(atm(activity='active'),
# model.parameters['ATMa_0'])
model.add_component(Parameter('ATMa_0', 1))
atm = model.monomers['ATM']
model.initial(atm(phospho='p'), model.parameters['ATMa_0'])
model.parameters['kf_pa_dephosphorylation_1'].value = 1e-04
model.parameters['MDM2_0'].value = 0
model.parameters['kf_m_deg_1'].value = 8e-01
model.parameters['kf_tm_synth_1'].value = 0.2
model.parameters['kf_aa_phosphorylation_1'].value = 5e-06
obs = Observable(b'atm_active', atm(phospho='p'))
model.add_component(obs)
pa.model = model
pa.save_model('%s.py' % model_name)
return model
