def set_bng_path(dir):
""" Deprecated. Use pysb.pathfinder.set_path() instead. """
warn("Function %s() is deprecated; use pysb.pathfinder.set_path() "
"instead" % set_bng_path.__name__,
category=DeprecationWarning,
stacklevel=2)
pf.set_path('bng', dir)
def stochkit(model,
start=0,
finish=10,
points=10,
n_runs=20,
path='/opt/conda/bin/'):
set_path('stochkit_ssa', path)
sims = StochKitSimulator(model,
linspace(start, finish,
points + 1)).run(n_runs=n_runs).dataframe
sims = modes(sims, n_runs)
return {'sims': sims['sims'], 'avrg': sims['avrg'], 'stdv': sims['stdv']}
def bngNF(model,
start=0,
finish=10,
points=10,
n_runs=20,
path='/opt/conda/bin/'):
set_path('bng', path)
sims = BngSimulator(model,
linspace(start, finish,
points + 1)).run(method='nf',
n_runs=n_runs).dataframe
sims = modes(sims, n_runs)
return {'sims': sims['sims'], 'avrg': sims['avrg'], 'stdv': sims['stdv']}
def set_kappa_path(path):
"""Set the path to the KaSim and KaSa executables.
Deprecated. Use pysb.pathfinder.set_path() instead.
Parameters
----------
path: string
Directory containing KaSim and KaSa executables.
"""
warnings.warn("Function %s() is deprecated; use "
"pysb.pathfinder.set_path() instead" %
set_kappa_path.__name__, category=DeprecationWarning,
stacklevel=2)
pf.set_path('kasim', path)
pf.set_path('kasa', path)
from pysb import *
from pysb import pathfinder
# this is your pythonanywhere.com username
user_name = 'rah'
bngl_path = '/home/' + str(user_name) + '/BioNetGen-2.3.1/'
pathfinder.set_path('bng', bngl_path)
pathfinder.get_path('bng')
Model()
# Physical and geometric constants
Parameter('NA', 6.0e23) # Avogadro's num
Parameter('f', 0.01) # scaling factor
Expression('Vo', f * 1e-10) # L
Expression('V', f * 3e-12) # L
# Initial concentrations
Parameter('EGF_conc', 2e-9) # nM
Expression('EGF0', EGF_conc * NA * Vo) # nM
Expression('EGFR0', f * 1.8e5) # copy per cell
# Rate constants
Expression('kp1', 9.0e7 / (NA * Vo)) # input /M/sec
Parameter('km1', 0.06) # /sec
Monomer('EGF', ['R'])
Monomer('EGFR', ['L', 'CR1', 'Y1068'], {'Y1068': ['U', 'P']})
Initial(EGF(R=None), EGF0)
def cupsoda(model, start=0, finish=10, points=10, path='/opt/conda/bin/'):
set_path('cupsoda', path)
return CupSodaSimulator(model, linspace(start, finish,
points + 1)).run().dataframe
def bngODE(model, start=0, finish=10, points=10, path='/opt/conda/bin/'):
set_path('bng', path)
return BngSimulator(model,
linspace(start, finish,
points + 1)).run(method='ode').dataframe
def set_bng_path(dir):
""" Deprecated. Use pysb.pathfinder.set_path() instead. """
warn("Function %s() is deprecated; use pysb.pathfinder.set_path() "
"instead" % set_bng_path.__name__, category=DeprecationWarning,
stacklevel=2)
pf.set_path('bng', dir)
def test_get_set_path():
bng_path = get_path('bng')
assert os.path.exists(bng_path)
set_path('bng', bng_path)
from numpy import linspace
from pysb.bng import generate_network, generate_equations
from pysb.simulator import ScipyOdeSimulator, BngSimulator, KappaSimulator
# modify accordingly
from pysb.pathfinder import set_path
set_path('bng', '/opt/git-repositories/bionetgen.RuleWorld/bng2/')
set_path('kasim', '/opt/git-repositories/KaSim4.Kappa-Dev/')
## for network-based simulations:
## ScipyOdeSimulator and BngSimulator ode and ssa methods
# generate_network(model)
# generate_equations(model)
## set the number of stochastic simulations
runs = 100
# data1 = ScipyOdeSimulator(model, linspace(0, 100, 200)).run().dataframe
# data1 = BngSimulator(model, linspace(0, 200, 201)).run(method = 'ode').dataframe
# data2 = BngSimulator(model, linspace(0, 200, 201)).run(method = 'ssa', n_runs = runs).dataframe
# data2 = BngSimulator(model, linspace(0, 200, 201)).run(method = 'nf', n_runs = runs).dataframe
data2 = KappaSimulator(model, linspace(0, 100, 101)).run(n_runs = runs).dataframe
## process simulations
data = []
for i in range(0, runs):
data.append(data2.xs(i))
avrg = 0
for i in range(0, runs):
avrg += data[i]
avrg = avrg / runs
