def make_reaction_network(pysb_model, model_id):
"""Generate a PySB/BNG reaction network as a PNG file."""
try:
for m in pysb_model.monomers:
pysb_assembler.set_extended_initial_condition(pysb_model, m, 0)
fname = 'model%d_rxn' % model_id
diagram_dot = render_reactions.run(pysb_model)
# TODO: use specific PySB/BNG exceptions and handle them
# here to show meaningful error messages
except Exception as e:
logger.error('Could not generate model diagram.')
logger.error(e)
return None
try:
with open(fname + '.dot', 'wt') as fh:
fh.write(diagram_dot)
subprocess.call(
('dot -T png -o %s.png %s.dot' % (fname, fname)).split(' '))
abs_path = os.path.abspath(os.getcwd())
full_path = os.path.join(abs_path, fname + '.png')
except Exception as e:
logger.error('Could not save model diagram.')
logger.error(e)
return None
return full_path
def visualize():
for ACC_NO in ACC_NOs:
dot_r = render_reactions.run(models[ACC_NO])
dotfile_r = open('model_reactions-' + ACC_NO + '.dot', 'w')
dotfile_r.write(dot_r)
dotfile_r.close()
system('dot -T pdf model_reactions-' + ACC_NO +
'.dot -o model_reactions-' + ACC_NO + '.pdf')
dot_s = render_species.run(models[ACC_NO])
dotfile_s = open('model_species-' + ACC_NO + '.dot', 'w')
dotfile_s.write(dot_s)
dotfile_s.close()
system('ccomps -x model_species-' + ACC_NO +
'.dot | dot | gvpack -m0 | neato -n2 -T pdf -o model_species-' +
ACC_NO + '.pdf')
# Run the simulation
solver = Solver(models[ACC_NO], t)
solver.run()
yout = solver.yobs
# Plot simulation results for the observables in the model
pl.ion()
pl.figure()
for observ in outputs[ACC_NO]:
pl.plot(t, yout[observ], label=observ)
pl.legend()
pl.xlabel("Time (minutes)")
pl.ylabel("Distribution of radioactive iron/body compartments")
pl.savefig('model_results-' + ACC_NO + '.png')
pl.clf()
def get_model_diagram(model, model_id=None):
try:
for m in model.monomers:
pysb_assembler.set_extended_initial_condition(model, m, 0)
fname = "model%d" % ("" if model_id is None else model_id)
diagram_dot = render_reactions.run(model)
# TODO: use specific PySB/BNG exceptions and handle them
# here to show meaningful error messages
except Exception as e:
raise DiagramGenerationError(e)
try:
with open(fname + ".dot", "wt") as fh:
fh.write(diagram_dot)
subprocess.call(("dot -T png -o %s.png %s.dot" % (fname, fname)).split(" "))
abs_path = os.path.abspath(os.getcwd())
if abs_path[-1] != "/":
abs_path = abs_path + "/"
full_path = abs_path + fname + ".png"
except Exception as e:
raise DiagramConversionError(e)
return full_path
def get_model_diagram(model, model_id=None):
try:
for m in model.monomers:
pysb_assembler.set_extended_initial_condition(model, m, 0)
fname = 'model%d' % ('' if model_id is None else model_id)
diagram_dot = render_reactions.run(model)
#TODO: use specific PySB/BNG exceptions and handle them
# here to show meaningful error messages
except Exception as e:
raise DiagramGenerationError(e)
try:
with open(fname + '.dot', 'wt') as fh:
fh.write(diagram_dot)
subprocess.call(
('dot -T png -o %s.png %s.dot' % (fname, fname)).split(' '))
abs_path = os.path.abspath(os.getcwd())
if abs_path[-1] != '/':
abs_path = abs_path + '/'
full_path = abs_path + fname + '.png'
except Exception as e:
raise DiagramConversionError(e)
return full_path
def draw_reaction_network(pysb_model, model_id):
"""Generate a PySB/BNG reaction network as a PNG file."""
try:
for m in pysb_model.monomers:
pysb_assembler.set_extended_initial_condition(pysb_model, m, 0)
diagram_dot = render_reactions.run(pysb_model)
# TODO: use specific PySB/BNG exceptions and handle them
# here to show meaningful error messages
except Exception as e:
logger.error('Could not generate model diagram.')
logger.error(e)
return None
try:
fname_prefix = make_pic_name(model_id, 'rxn')
with open(fname_prefix + '.dot', 'wt') as fh:
fh.write(diagram_dot)
subprocess.call(('dot -T png -o %s.png %s.dot' %
(fname_prefix, fname_prefix)).split(' '))
fname = fname_prefix + '.png'
except Exception as e:
logger.error('Could not save model diagram.')
logger.error(e)
return None
return fname
def draw_reaction_network(pysb_model, model_id):
"""Generate a PySB/BNG reaction network as a PNG file."""
try:
for m in pysb_model.monomers:
pysb_assembler.set_extended_initial_condition(pysb_model, m, 0)
diagram_dot = render_reactions.run(pysb_model)
# TODO: use specific PySB/BNG exceptions and handle them
# here to show meaningful error messages
except Exception as e:
logger.error('Could not generate model diagram.')
logger.error(e)
return None
try:
fname_prefix = make_pic_name(model_id, 'rxn')
with open(fname_prefix + '.dot', 'wt') as fh:
fh.write(diagram_dot)
subprocess.call(('dot -T png -o %s.png %s.dot' %
(fname_prefix, fname_prefix)).split(' '))
fname = fname_prefix + '.png'
except Exception as e:
logger.error('Could not save model diagram.')
logger.error(e)
return None
return fname
RAF1 = model.monomers['RAF1']
HRAS = model.monomers['HRAS']
r1 = model.rules['RAF1_autophospho_RAF1_T491']
r1.rule_expression = (RAF1(HRAS=1, T491='u') % HRAS(RAF1=1) >> RAF1(HRAS=1, T491='p') % HRAS(RAF1=1))
r2 = model.rules['RAF1_autophospho_RAF1_S494']
r2.rule_expression = (RAF1(HRAS=1, S494='u') % HRAS(RAF1=1) >> RAF1(HRAS=1, S494='p') % HRAS(RAF1=1))
for r in (r1, r2):
r.reactant_pattern = r.rule_expression.reactant_pattern
r.product_pattern = r.rule_expression.product_pattern
# Rendering reactions and species
if args.render:
print 'Rendering reactions...'
gv_str = rr.run(model)
with open('reactions.dot', 'w') as f:
f.write(gv_str)
print 'Rendering species...'
gv_str = rs.run(model)
with open('species.dot', 'w') as f:
f.write(gv_str)
if args.simulate:
# Set parameters
print 'Setting model parameters...'
model.add_component(Parameter("kp1", 1.667e-06)) # ligand-monomer binding (scaled), units: /molecule/s
model.add_component(Parameter("km1", 0.06)) # ligand-monomer dissociation, units: /s
model.add_component(Parameter("kp2", 5.556e-06)) # aggregation of bound monomers (scaled), units: /molecule/s
model.add_component(Parameter("km2", 0.1)) # dissociation of bound monomers, units: /s
