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_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.""" 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_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('ERK_p', erk(phospho='p')) model.add_component(obs) vem = model.monomers['VEMURAFENIB'] obs = Observable('Vem_free', vem(map3k=None)) model.add_component(obs) ras = model.monomers['RAS'] obs = Observable('RAS_active', ras(gtp=ANY)) model.add_component(obs) braf = model.monomers['BRAF'] obs = Observable('BRAF_active', braf(vemurafenib=None)) model.add_component(obs) model.parameters['BRAF_0'].value = 0 egf = model.monomers['EGF'] obs = Observable('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