def data(evaluate=False, verbose = 0):
from figure_analysis import FigureData
d13 = FigureData('Dabby (2013)\n4-way strand displacement')
d13.fname = 'Dabby2013-4way'
current = d13
pilp = [(0, 2), (2, 2), (2, 0),
(4, 2), (4, 0), (0, 4),
(2, 4), (6, 2), (0, 6),
(4, 4), (6, 0), (2, 6),
(4, 6), (6, 4), (6, 6)]
litr = [(0.047), (0.10), (0.033),
(0.93), (0.039), (0.97),
(56), (490), (58),
(770), (5.0), (9.4e3),
(7.0e4), (2.8e5), (6.9e5)]
for (pil, rate) in zip(pilp, litr):
pilstring = dabby2013_4way_displacement(pil)
exp_result = 'rep + clx -> pr1 + pr2 [k={}]'.format(rate)
current.add_reaction_rate_setup(pilstring, exp_result, pil)
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
return [d13]
def data(evaluate=False, verbose = 0):
from figure_analysis import FigureData
# Default pilsimulator call
psim = "pilsimulator --no-jacobian --nxy --header --atol 1e-10 --rtol 1e-10 --mxstep 10000 --t8 18000 --t-lin 18000"
rates = {'k_slow': 1e-5, 'k_fast': 0.1}
# Setup
F3 = FigureData('Yin et al. (2008) Fig. 3 - Autocatalytic hairpin system (varying initiator)')
F3.fname = 'Yin2008-F3'
current = F3
template = yin2008_F3_pil
sims = [psim + ' --pyplot-labels A B C D I --p0 A=20 B=20 C=20 D=20 I=20',
psim + ' --pyplot-labels A B C D I --p0 A=20 B=20 C=20 D=20 I=6',
psim + ' --pyplot-labels A B C D I --p0 A=20 B=20 C=20 D=20 I=2',
psim + ' --pyplot-labels A B C D I --p0 A=20 B=20 C=20 D=20 I=1',
psim + ' --pyplot-labels A B C D I --p0 A=20 B=20 C=20 D=20 I=0.6',
psim + ' --pyplot-labels A B C D I --p0 A=20 B=20 C=20 D=20 I=0.4',
psim + ' --pyplot-labels A B C D I --p0 A=20 B=20 C=20 D=20 I=0.2',
psim + ' --pyplot-labels A B C D I --p0 A=20 B=20 C=20 D=20 I=0.1',
psim + ' --pyplot-labels A B C D I --p0 A=20 B=20 C=20 D=20 I=0.06',
psim + ' --pyplot-labels A B C D I --p0 A=20 B=20 C=20 D=20 I=0.02',
psim + ' --pyplot-labels A B C D I --p0 A=20 B=20 C=20 D=20 I=0.01']
#psim + ' --pyplot-labels A B C D I --p0 A=20 B=20 C=20 D=20 I=0']
# Diagonal crossing
diagX = [
(297.38, 3.30),
(2256.56, 5.23),
(4411.66, 7.37),
(5811.08, 8.72),
(6930.61, 9.83),
(7546.36, 10.45),
(8302.04, 11.17),
(8973.76, 11.76),
(9281.63, 12.11),
(9561.52, 12.38),
(9701.46, 12.52),
(9841.40, 12.66)]
for (sim, res) in zip(sims, diagX):
pilstring = template(None)
simulation = sim
reporter = 'A'
metric = 'diagonal-crossing-time'
tmax = '18000'
cmax = '2;-20'
current.add_system_simulation_setup(pilstring, simulation, reporter, metric, ':'.join([tmax, cmax]), res, simargs=sim[sim.find('I='):])
# Half completion
halfC = [
(45.48, -10.00),
(1067.06, -10.00),
(3488.05, -10.00),
(5321.28, -10.00),
(6874.64, -10.00),
(7700.29, -10.00),
(8847.81, -10.00),
(9729.45, -10.00),
(10247.23, -10.00),
(10681.05, -10.00),
(10876.97, -10.00),
(11086.88, -10.00)]
for (sim, res) in zip(sims, halfC):
pilstring = template(None)
simulation = sim
reporter = 'A'
metric = 'completion-time'
current.add_system_simulation_setup(pilstring, simulation, reporter, metric, '-10', res, simargs=sim[sim.find('I='):])
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
current.pepperargs['default'].update(rates)
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
return [F3]
def data(evaluate=False, verbose=0):
from figure_analysis import FigureData
# Default pilsimulator call
psim = "pilsimulator --nxy --header --atol 1e-13 --rtol 1e-13 --mxstep 10000"
psim += " --t8 18000 --t-lin 18000"
# Setup
F1E = FigureData(
'Zhang et al. (2007) Fig. 1 - Single-layer catalytic DSD system (varying catalyst)'
)
F1E.fname = 'Zhang2007-F1'
current = F1E
template = zhang2007_F1_pil
sims = [
psim + ' --pyplot-labels ROX S F OR C --p0 S=10 F=13 OR=30 C=10',
psim + ' --pyplot-labels ROX S F OR C --p0 S=10 F=13 OR=30 C=5',
psim + ' --pyplot-labels ROX S F OR C --p0 S=10 F=13 OR=30 C=2',
psim + ' --pyplot-labels ROX S F OR C --p0 S=10 F=13 OR=30 C=1',
psim + ' --pyplot-labels ROX S F OR C --p0 S=10 F=13 OR=30 C=0.5',
psim + ' --pyplot-labels ROX S F OR C --p0 S=10 F=13 OR=30 C=0.2',
psim + ' --pyplot-labels ROX S F OR C --p0 S=10 F=13 OR=30 C=0.1',
psim + ' --pyplot-labels ROX S F OR C --p0 S=10 F=13 OR=30 C=0.05',
psim + ' --pyplot-labels ROX S F OR C --p0 S=10 F=13 OR=30 C=0.02'
]
# DIAGONAL CROSSING
diagX = [(1216.44, 7.44), (1660.27, 6.83), (2457.53, 5.78),
(3435.62, 4.49), (4364.38, 3.26), (5424.66, 1.88),
(6073.97, 1.03), (6386.30, 0.57), (6550.68, 0.32)]
#(6715.07, 0.09) 0 input
for (sim, res) in zip(sims, diagX):
pilstring = template(None)
simulation = sim
reporter = 'ROX'
metric = 'diagonal-crossing-time'
tmax = '7200'
cmax = '10'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
':'.join([tmax, cmax]),
res,
simargs=sim[sim.find('C='):])
# Half completion
halfC = [(550.68, 5.00), (953.42, 5.00), (1906.85, 5.00), (4076.71, 5.00)]
for (sim, res) in zip(sims, halfC):
pilstring = template(None)
simulation = sim
reporter = 'ROX'
metric = 'completion-time'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
'5',
res,
simargs=sim[sim.find('C='):])
current.pepperargs['default'] = current.pepperargs['Condensed'].copy()
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
# Setup
F3 = FigureData(
'Zhang et al. (2007) Fig. 3 - Two-layer feedforward DSD system (varying catalyst)'
)
F3.fname = 'Zhang2007-F3'
current = F3
template = zhang2007_F3_pil
sims = [
psim +
' --pyplot-labels ROX S0 S1 F0 F1 OR C0 --p0 S1=10 F1=13 S0=10 F0=13 OR=30 C0=10',
psim +
' --pyplot-labels ROX S0 S1 F0 F1 OR C0 --p0 S1=10 F1=13 S0=10 F0=13 OR=30 C0=5',
psim +
' --pyplot-labels ROX S0 S1 F0 F1 OR C0 --p0 S1=10 F1=13 S0=10 F0=13 OR=30 C0=2',
psim +
' --pyplot-labels ROX S0 S1 F0 F1 OR C0 --p0 S1=10 F1=13 S0=10 F0=13 OR=30 C0=1',
psim +
' --pyplot-labels ROX S0 S1 F0 F1 OR C0 --p0 S1=10 F1=13 S0=10 F0=13 OR=30 C0=0.5',
psim +
' --pyplot-labels ROX S0 S1 F0 F1 OR C0 --p0 S1=10 F1=13 S0=10 F0=13 OR=30 C0=0.2',
psim +
' --pyplot-labels ROX S0 S1 F0 F1 OR C0 --p0 S1=10 F1=13 S0=10 F0=13 OR=30 C0=0.1',
psim +
' --pyplot-labels ROX S0 S1 F0 F1 OR C0 --p0 S1=10 F1=13 S0=10 F0=13 OR=30 C0=0.05',
psim +
' --pyplot-labels ROX S0 S1 F0 F1 OR C0 --p0 S1=10 F1=13 S0=10 F0=13 OR=30 C0=0.02',
psim +
' --pyplot-labels ROX S0 S1 F0 F1 OR C0 --p0 S1=10 F1=13 S0=10 F0=13 OR=30 C0=0.01'
]
#Diagonal Dataset
diagX = [
(1860.53, 6.56), (2302.30, 5.98), (2744.07, 5.40), (3066.90, 4.98),
(3856.99, 3.92), (4519.65, 3.07), (4910.44, 2.54), (5607.08, 1.63),
(5904.42, 1.23), (6065.84, 1.02)
]
#(6320.71, 0.66), # 0x
#(6720.00, 0.15)] # control
for (sim, res) in zip(sims, diagX):
pilstring = template(None)
simulation = sim
reporter = 'ROX'
metric = 'diagonal-crossing-time'
tmax = '7200'
cmax = '10'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
':'.join([tmax, cmax]),
res,
simargs=sim[sim.find('C0='):])
# Half completion
halfC = [(1257.35, 5.00), (1852.04, 5.00), (2514.69, 5.00),
(3066.90, 5.00), (4850.97, 5.00)]
for (sim, res) in zip(sims, halfC):
pilstring = template(None)
simulation = sim
reporter = 'ROX'
metric = 'completion-time'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
'5',
res,
simargs=sim[sim.find('C0='):])
current.pepperargs['default'] = current.pepperargs['Condensed'].copy()
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
# Setup
F4 = FigureData(
'Zhang et al. (2007) Fig. 4 - Autocatalytic DSD system (varying autocatalyst)'
)
F4.fname = 'Zhang2007-F4'
current = F4
template = zhang2007_F4_pil
sims = [
psim + ' --pyplot-labels TET S F SR A --p0 S=10 F=13 SR=20 A=10',
psim + ' --pyplot-labels TET S F SR A --p0 S=10 F=13 SR=20 A=7',
psim + ' --pyplot-labels TET S F SR A --p0 S=10 F=13 SR=20 A=5',
psim + ' --pyplot-labels TET S F SR A --p0 S=10 F=13 SR=20 A=3',
psim + ' --pyplot-labels TET S F SR A --p0 S=10 F=13 SR=20 A=2',
psim + ' --pyplot-labels TET S F SR A --p0 S=10 F=13 SR=20 A=1',
psim + ' --pyplot-labels TET S F SR A --p0 S=10 F=13 SR=20 A=0.7',
psim + ' --pyplot-labels TET S F SR A --p0 S=10 F=13 SR=20 A=0.5',
psim + ' --pyplot-labels TET S F SR A --p0 S=10 F=13 SR=20 A=0.3',
psim + ' --pyplot-labels TET S F SR A --p0 S=10 F=13 SR=20 A=0.2',
psim + ' --pyplot-labels TET S F SR A --p0 S=10 F=13 SR=20 A=0.1'
]
#Diagonal Dataset
diagX = [(496.08, 7.62), (600.76, 7.32), (655.37, 7.16), (855.63, 6.61),
(910.24, 6.45), (1064.98, 6.04), (1206.07, 5.64), (1237.93, 5.54),
(1333.50, 5.26), (1392.67, 5.10), (1465.49, 4.91)]
#(1756.76, 4.10)]
for (sim, res) in zip(sims, diagX):
pilstring = template(None)
simulation = sim
reporter = 'TET'
metric = 'diagonal-crossing-time'
tmax = '3600'
cmax = '10'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
':'.join([tmax, cmax]),
res,
simargs=sim[sim.find('A='):])
#Half completion
halfC = [(241.21, 5.0), (350.44, 5.0), (393.68, 5.0), (609.86, 5.0),
(694.06, 5.0), (892.04, 5.0), (1087.74, 5.0), (1121.87, 5.0),
(1276.61, 5.0), (1376.74, 5.0), (1470.04, 5.0)]
#(1966.12, 5.0)]
for (sim, res) in zip(sims, halfC):
pilstring = template(None)
simulation = sim
reporter = 'TET'
metric = 'completion-time'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
'5',
res,
simargs=sim[sim.find('A='):])
current.pepperargs['default'] = current.pepperargs['Condensed'].copy()
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
return [F1E, F3, F4]
def data(evaluate=False, verbose=0):
from figure_analysis import FigureData
rates = {'k_slow': 0.01, 'k_fast': 1}
seesaw_on = {
'ssw_rxns': 'seesaw-T25-utbr-leak-reduced',
'ssw_expl': False,
'ssw_conc': 50e-9,
'dry_run': True
}
seesaw_off = {
'ssw_rxns': None,
'ssw_expl': False,
'ssw_conc': 50e-9,
'dry_run': False
}
# Default pilsimulator call
psim = "pilsimulator --no-jacobian --nxy --header --atol 1e-13 --rtol 1e-13 --mxstep 1000 --t8 36000 --t-lin 18000"
# Setup
SF31 = FigureData('Sup. Fig. 31: Integer 4-bit square-root circuit')
SF31.fname = 'Qian2011-SF31'
current = SF31
template = qian2011_SF31
sims = [
psim +
' --pyplot-labels y1_0 y1_1 y2_0 y2_1 --p0 x4_0=45 x4_1=5 x3_0=45 x3_1=5 x2_0=45 x2_1=5 x1_0=45 x1_1=5', # 0000
psim +
' --pyplot-labels y1_0 y1_1 y2_0 y2_1 --p0 x4_0=45 x4_1=5 x3_0=45 x3_1=5 x2_0=45 x2_1=5 x1_0=5 x1_1=45', # 0001
psim +
' --pyplot-labels y1_0 y1_1 y2_0 y2_1 --p0 x4_0=45 x4_1=5 x3_0=45 x3_1=5 x2_0=5 x2_1=45 x1_0=45 x1_1=5', # 0010
psim +
' --pyplot-labels y1_0 y1_1 y2_0 y2_1 --p0 x4_0=45 x4_1=5 x3_0=45 x3_1=5 x2_0=5 x2_1=45 x1_0=5 x1_1=45', # 0011
psim +
' --pyplot-labels y1_0 y1_1 y2_0 y2_1 --p0 x4_0=45 x4_1=5 x3_0=5 x3_1=45 x2_0=45 x2_1=5 x1_0=45 x1_1=5',
psim +
' --pyplot-labels y1_0 y1_1 y2_0 y2_1 --p0 x4_0=45 x4_1=5 x3_0=5 x3_1=45 x2_0=45 x2_1=5 x1_0=5 x1_1=45',
psim +
' --pyplot-labels y1_0 y1_1 y2_0 y2_1 --p0 x4_0=45 x4_1=5 x3_0=5 x3_1=45 x2_0=5 x2_1=45 x1_0=45 x1_1=5',
psim +
' --pyplot-labels y1_0 y1_1 y2_0 y2_1 --p0 x4_0=45 x4_1=5 x3_0=5 x3_1=45 x2_0=5 x2_1=45 x1_0=5 x1_1=45',
psim +
' --pyplot-labels y1_0 y1_1 y2_0 y2_1 --p0 x4_0=5 x4_1=45 x3_0=45 x3_1=5 x2_0=45 x2_1=5 x1_0=45 x1_1=5',
psim +
' --pyplot-labels y1_0 y1_1 y2_0 y2_1 --p0 x4_0=5 x4_1=45 x3_0=45 x3_1=5 x2_0=45 x2_1=5 x1_0=5 x1_1=45',
psim +
' --pyplot-labels y1_0 y1_1 y2_0 y2_1 --p0 x4_0=5 x4_1=45 x3_0=45 x3_1=5 x2_0=5 x2_1=45 x1_0=45 x1_1=5',
psim +
' --pyplot-labels y1_0 y1_1 y2_0 y2_1 --p0 x4_0=5 x4_1=45 x3_0=45 x3_1=5 x2_0=5 x2_1=45 x1_0=5 x1_1=45',
psim +
' --pyplot-labels y1_0 y1_1 y2_0 y2_1 --p0 x4_0=5 x4_1=45 x3_0=5 x3_1=45 x2_0=45 x2_1=5 x1_0=45 x1_1=5',
psim +
' --pyplot-labels y1_0 y1_1 y2_0 y2_1 --p0 x4_0=5 x4_1=45 x3_0=5 x3_1=45 x2_0=45 x2_1=5 x1_0=5 x1_1=45',
psim +
' --pyplot-labels y1_0 y1_1 y2_0 y2_1 --p0 x4_0=5 x4_1=45 x3_0=5 x3_1=45 x2_0=5 x2_1=45 x1_0=45 x1_1=5',
psim +
' --pyplot-labels y1_0 y1_1 y2_0 y2_1 --p0 x4_0=5 x4_1=45 x3_0=5 x3_1=45 x2_0=5 x2_1=45 x1_0=5 x1_1=45'
]
simargs = [
'0000', '0001', '0010', '0011', '0100', '0101', '0110', '0111', '1000',
'1001', '1010', '1011', '1100', '1101', '1110', '1111'
]
litr = [('y1_0', [(4.2 * 3600, 50 * 0.42), (7.1 * 3600, 50 * 0.1),
(7.1 * 3600, 50 * 0.1), (7.1 * 3600, 50 * 0.1),
(3.9 * 3600, 50 * 0.55), (4.1 * 3600, 50 * 0.45),
(4.1 * 3600, 50 * 0.45), (4.1 * 3600, 50 * 0.45),
(4.5 * 3600, 50 * 0.42), (7.3 * 3600, 50 * 0.1),
(7.3 * 3600, 50 * 0.1), (7.3 * 3600, 50 * 0.1),
(7.3 * 3600, 50 * 0.1), (7.3 * 3600, 50 * 0.1),
(7.3 * 3600, 50 * 0.1), (7.3 * 3600, 50 * 0.1)]),
('y1_1', [(7.1 * 3600, 50 * 0.1), (5.0 * 3600, 50 * 0.4),
(5.0 * 3600, 50 * 0.4), (4.2 * 3600, 50 * 0.42),
(7.3 * 3600, 50 * 0.08), (7.3 * 3600, 50 * 0.08),
(7.3 * 3600, 50 * 0.08), (7.3 * 3600, 50 * 0.08),
(6.9 * 3600, 50 * 0.1), (4.0 * 3600, 50 * 0.5),
(4.0 * 3600, 50 * 0.5), (3.8 * 3600, 50 * 0.6),
(6.0 * 3600, 50 * 0.25), (4.0 * 3600, 50 * 0.51),
(4.0 * 3600, 50 * 0.51), (3.5 * 3600, 50 * 0.6)]),
('y2_0', [(3.1 * 3600, 50 * 0.55), (3.0 * 3600, 50 * 0.6),
(3.0 * 3600, 50 * 0.6), (3.0 * 3600, 50 * 0.6),
(6.8 * 3600, 50 * 0.1), (6.8 * 3600, 50 * 0.1),
(6.8 * 3600, 50 * 0.1), (6.8 * 3600, 50 * 0.1),
(7.0 * 3600, 50 * 0.11), (7.0 * 3600, 50 * 0.11),
(7.0 * 3600, 50 * 0.11), (7.0 * 3600, 50 * 0.11),
(7.2 * 3600, 50 * 0.08), (7.2 * 3600, 50 * 0.08),
(7.2 * 3600, 50 * 0.08), (7.2 * 3600, 50 * 0.08)]),
('y2_1', [(7.0 * 3600, 50 * 0.10), (7.0 * 3600, 50 * 0.10),
(7.0 * 3600, 50 * 0.10), (7.0 * 3600, 50 * 0.10),
(2.0 * 3600, 50 * 0.75), (2.0 * 3600, 50 * 0.75),
(2.0 * 3600, 50 * 0.75), (2.0 * 3600, 50 * 0.75),
(1.8 * 3600, 50 * 0.8), (1.8 * 3600, 50 * 0.8),
(1.8 * 3600, 50 * 0.8), (1.8 * 3600, 50 * 0.8),
(2.0 * 3600, 50 * 0.8), (2.0 * 3600, 50 * 0.8),
(2.0 * 3600, 50 * 0.8), (2.0 * 3600, 50 * 0.8),
(1.5 * 3600, 50 * 0.85), (1.5 * 3600, 50 * 0.85),
(1.5 * 3600, 50 * 0.85), (1.5 * 3600, 50 * 0.85)])]
for (rep, results) in litr:
for (sim, arg, res) in zip(sims, simargs, results):
pilstring = template(None)
simulation = sim
reporter = rep
metric = 'diagonal-crossing-time'
tmax = '36000'
cmax = '50'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
':'.join([tmax, cmax]),
res,
simargs=rep + '-' + arg)
current.pepperargs['default'] = current.pepperargs['CONDENSED'].copy()
#current.pepperargs['default'].update(rates)
current.pepperargs['default'].update(seesaw_off)
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
return [SF31]
def data(evaluate=False, verbose=0):
from figure_analysis import FigureData
# Setup Experiment 1
z09_3way = FigureData(
'Zhang and Winfree (2009)\n3-way strand displacement')
z09_3way.fname = 'Zhang2009-3way'
current = z09_3way
k3way_exp = [
#((n, m), k)
#((0, 15), 1.40),
((1, 14), 8.17),
((2, 13), 144),
((3, 12), 1.08e3),
((4, 11), 5.05e4),
((5, 10), 9.64e5),
((6, 9), 2.36e6),
((7, 8), 3.22e6),
((8, 9), 3.15e6),
((9, 8), 2.77e6),
((10, 7), 2.83e6),
((15, 0), 4.78e6)
]
for (pil, rate) in k3way_exp:
pilstring = zhang2009_3way_displacement(pil)
exp_result = 'X + S -> Y + L [k={}]'.format(rate)
current.add_reaction_rate_setup(pilstring, exp_result, pil)
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
# Setup Experiment 2
z09_3wayX = FigureData('Zhang and Winfree (2009)\n3-way toehold exchange')
z09_3wayX.fname = 'Zhang2009-3wayX'
current = z09_3wayX
k3wayX_exp = [((1, 4), 7.70), ((1, 3), 5.48), ((1, 2), 23.5),
((1, 1), 18.9), ((2, 5), 43.6), ((2, 4), 214.05),
((2, 3), 273.0), ((2, 2), 249.0), ((2, 1), 231.0),
((3, 6), 66.9), ((3, 5), 215.0), ((3, 4), 939.0),
((3, 3), 974.0), ((3, 2), 907.0), ((3, 1), 846.0),
((4, 7), 131.0), ((4, 6), 407.0), ((4, 5), 4.25e3),
((4, 4), 2.13e4), ((4, 3), 2.41e4), ((4, 2), 2.29e4),
((4, 1), 1.97e4), ((5, 7), 3.59e3), ((5, 6), 9.72e4),
((5, 5), 3.45e5), ((5, 4), 1.53e6), ((5, 3), 1.58e6),
((5, 2), 1.58e6), ((5, 1), 1.73e6), ((6, 7), 1.61e5),
((6, 6), 4.05e5), ((6, 5), 1.48e6), ((6, 4), 3.04e6),
((6, 3), 2.59e6), ((6, 2), 3.00e6), ((7, 7), 4.7e5),
((7, 6), 1.11e6), ((7, 5), 2.90e6), ((7, 4), 3.57e6),
((8, 7), 1.94e6), ((8, 6), 2.68e6), ((8, 5), 3.14e6),
((8, 4), 3.37e6)]
for (pil, rate) in k3wayX_exp:
pilstring = zhang2009_3way_exchange(pil)
exp_result = 'X + S -> Y + L [k={}]'.format(rate)
current.add_reaction_rate_setup(pilstring, exp_result, pil)
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
return [z09_3way, z09_3wayX]
def data(evaluate=False, verbose = 0):
from figure_analysis import FigureData
# Default pilsimulator call
psim = "pilsimulator --no-jacobian --nxy --header"
psim += " --atol 1e-12 --rtol 1e-12 --mxstep 1000"
psim += " --t8 18000 --t-lin 18000"
rates = {'k_slow': 1e-5, 'k_fast': 0.1}
rc = {'release_cutoff': 15}
# Setup
F3 = FigureData('Zhang & Winfree (2009) Fig. 3 - Single strand displacement reactions (varying toehold length)')
F3.fname = 'Zhang2009-F3'
current = F3
template = zhang2009_F1DF_displacement_pil
sims = [psim + ' --pyplot-labels F R S X --p0 R=3 S=1 X=0.6',
psim + ' --pyplot-labels F R S X --p0 R=3 S=1 X=0.4',
psim + ' --pyplot-labels F R S X --p0 R=3 S=1 X=0.2']
diagX = [(1260, 0.31), (1867, 0.27), (3498, 0.17)]
for (sim, res) in zip(sims, diagX):
pilstring = template(5)
simulation = sim
reporter = 'F'
metric = 'diagonal-crossing-time'
tmax = '7200'
cmax = '0.4'
current.add_system_simulation_setup(pilstring, simulation, reporter, metric,
':'.join([tmax, cmax]), res, simargs=sim[sim.find('X='):])
# Half completion
halfC = [(1241.01, 0.30), (2430.95, 0.30)]
for (sim, res) in zip(sims, halfC):
pilstring = template(5)
simulation = sim
reporter = 'F'
metric = 'completion-time'
current.add_system_simulation_setup(pilstring, simulation, reporter, metric, '0.3',
res, simargs=sim[sim.find('X='):])
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
# Setup
F4 = FigureData('Zhang & Winfree (2009) Fig. 4 - Single toehold exchange reactions (varying toehold lengths)')
F4.fname = 'Zhang2009-F4'
current = F4
template = zhang2009_F1DF_exchange_pil
pilp = [(4,7), (5,7), (6,7), (7,7)]
halfC = [
(527.64, 0.20),
(578.28, 0.20),
(983.36, 0.20),
(1877.93, 0.20)]
for (pip, res) in zip(pilp, halfC):
pilstring = template(pip)
simulation = psim + ' --pyplot-labels F R S X --p0 R=3 S=1 X=0.4'
reporter = 'F'
metric = 'completion-time'
current.add_system_simulation_setup(pilstring, simulation, reporter, metric, '0.2',
res, simargs=sim[sim.find('X='):])
diagX = [(785, 0.28), (823, 0.27), (1192, 0.23), (1622, 0.18)]
for (pip, res) in zip(pilp, diagX):
pilstring = template(pip)
simulation = psim + ' --pyplot-labels F R S X --p0 R=3 S=1 X=0.4'
reporter = 'F'
metric = 'diagonal-crossing-time'
tmax = '3600'
cmax = '0.4'
current.add_system_simulation_setup(pilstring, simulation, reporter, metric,
':'.join([tmax, cmax]), res, simargs=sim[sim.find('X='):])
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
# Setup
F5 = FigureData('Zhang & Winfree (2009) Fig. 5 - Catalytic DSD system (varying toehold lengths)')
F5.fname = 'Zhang2009-F5'
current = F5
template = zhang2009_F5_pil
pilp = [6,7,5,8,4,9,3,2]
diagX = [
(2825.85, 7.53),
(3485.78, 7.09),
(4737.96, 6.19),
(9103.64, 3.20),
(10728.08, 2.08),
(11269.57, 1.71),
(13300.12, 0.30),
(13672.39, 0.08)]
for (pip, res) in zip(pilp, diagX):
pilstring = template(pip)
simulation = psim + ' --pyplot-labels F R S Z X --p0 R=30 S=10 Z=100 X=1'
reporter = 'F'
metric = 'diagonal-crossing-time'
tmax = '14400'
cmax = '10'
current.add_system_simulation_setup(pilstring, simulation, reporter, metric,
':'.join([tmax, cmax]), res, simargs=sim[sim.find('X='):])
halfC = [ (1066.04, 5.01), (1472.15, 5.01), (3096.59, 5.01)]
for (pip, res) in zip(pilp, halfC):
pilstring = template(pip)
simulation = psim + ' --pyplot-labels F R S Z X --p0 R=30 S=10 Z=100 X=1'
reporter = 'F'
metric = 'completion-time'
current.add_system_simulation_setup(pilstring, simulation, reporter, metric, '5.01',
res, simargs=sim[sim.find('X='):])
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
return [F3, F4, F5]
def data(evaluate=False, verbose=0):
from figure_analysis import FigureData
# Default pilsimulator call
psim = "pilsimulator --no-jacobian --nxy --header"
psim += " --atol 1e-10 --rtol 1e-10 --mxstep 1000"
psim += " --t8 54000 --t-lin 54000"
rates = {'k_slow': 0.001, 'k_fast': 0.1}
# Setup
F3A = FigureData('Zhang (2011) Fig. 3A - Cooperative strand displacement')
F3A.fname = 'Zhang2011-F3A'
current = F3A
template = zhang2011_F1_pil
sims = [
psim + ' --pyplot-labels R D1 T1 T2 F --p0 R=60 D1=20 T1=18 T2=18',
psim + ' --pyplot-labels R D1 T1 T2 F --p0 R=60 D1=20 T1=12 T2=12',
psim + ' --pyplot-labels R D1 T1 T2 F --p0 R=60 D1=20 T1=6 T2=6'
]
diagX = [(409.46, 9.15), (425.68, 6.14), (300.00, 3.25)]
diagXe = [('1800', '12'), ('1800', '8'), ('1800', '4')]
for (sim, res, tc) in zip(sims, diagX, diagXe):
pilstring = template(None)
simulation = sim
reporter = 'F'
metric = 'diagonal-crossing-time'
tmax = tc[0]
cmax = tc[1]
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
':'.join([tmax, cmax]),
res,
simargs=sim[sim.find('T1='):])
halfC = [(381.08, 9.02), (385.14, 6.01), (263.51, 3.02)]
for (sim, res) in zip(sims, halfC):
pilstring = template(None)
simulation = sim
reporter = 'F'
metric = 'completion-time'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
'50%',
res,
simargs=sim[sim.find('T1='):])
current.pepperargs['default'] = current.pepperargs['Condensed'].copy()
current.pepperargs['default'].update(rates)
if evaluate:
current.eval(verbose=verbose)
if verbose:
for df in current.get_dataframes():
print(df)
return [F3A]
def data(evaluate=False, verbose=0):
from figure_analysis import FigureData
psim = "pilsimulator --no-jacobian --header --nxy --atol 1e-13 --rtol 1e-13 --mxstep 10000 "
psim += "--t-lin 10000 --t8 1000"
rates = {'k_slow': 1e-10, 'k_fast': 0.01}
G11_F3 = FigureData('Fig. 3: |a|=14, |b|=22, varying: |n|, |m|')
G11_F3.fname = 'Genot2011-F3'
current = G11_F3
template = genot2011_F3_pil
pilp = [(8, 7), (17, 17), (20, 20), (23, 23)] # original
# After 30% of the reaction has gone to completion, the signal dropped to 70%.
litr = [(42, 1.98), (48, 1.98), (100, 1.98), (91, 1.98)] # seconds
for (pil, res) in zip(pilp, litr):
pilstring = template(pil)
simulation = psim + " --pyplot-labels S I T W --p0 S=6.6 I=660"
reporter = 'T'
metric = 'completion-time'
current.add_system_simulation_setup(pilstring, simulation, reporter,
metric, '1.98',
res) #, simargs='pilname')
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
current.pepperargs['default'].update(rates)
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
G11_F4A = FigureData('Fig. 4A: |n|=|m|=0, either |a|=11 or |a|=9')
G11_F4A.fname = 'Genot2011-F4A'
current = G11_F4A
template = genot2011_F4A_pil
pilp = [11, 9]
#litr = [(32, 0.58*6.6), (38, 0.58*6.6)]
litr = [(2, 1.98), (3, 1.98)]
for (pil, res) in zip(pilp, litr):
pilstring = template(pil)
simulation = psim + " --pyplot-labels S I T W --p0 S=6.6 I=22"
reporter = 'T'
metric = 'completion-time'
current.add_system_simulation_setup(pilstring, simulation, reporter,
metric, '1.98',
res) #, simargs='pilname')
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
current.pepperargs['default'].update(rates)
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
G11_F4B = FigureData('Fig. 4B: |n|=|m|=1, either |a|=11 or |a|=9')
G11_F4B.fname = 'Genot2011-F4B'
current = G11_F4B
template = genot2011_F4B_pil
pilp = [11, 9]
#litr = [(44, 3.3), (182, 3.3)]
litr = [(15, 1.98), (75, 1.98)]
for (pil, res) in zip(pilp, litr):
pilstring = template(pil)
simulation = psim + " --pyplot-labels S I T W --p0 S=6.6 I=22"
reporter = 'T'
metric = 'completion-time'
current.add_system_simulation_setup(pilstring, simulation, reporter,
metric, '1.98',
res) #, simargs='pilname')
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
current.pepperargs['default'].update(rates)
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
G11_F4C = FigureData('Fig. 4C: |n|=|m|=0, |a|=6, varying: [invader]$_0$')
G11_F4C.fname = 'Genot2011-F4C'
current = G11_F4C
template = genot2011_F4C_pil
sims = [
psim + " --pyplot-labels S I T W --p0 S=6.6 I=330",
psim + " --pyplot-labels S I T W --p0 S=6.6 I=145",
psim + " --pyplot-labels S I T W --p0 S=6.6 I=66"
]
#litr = [(69, 3.3), (177, 3.3), (347, 3.3)]
litr = [(25, 1.98), (75, 1.98), (150, 1.98)]
for (sim, res) in zip(sims, litr):
pilstring = template(None)
simulation = sim
reporter = 'T'
metric = 'completion-time'
current.add_system_simulation_setup(
pilstring, simulation, reporter, metric, '1.98',
res) #, simargs=sim[sim.find('I='):])
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
current.pepperargs['default'].update(rates)
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
G11_F4D = FigureData('Fig. 4D: |n|=|m|=17, |a|=14, varying: [invader]$_0$')
G11_F4D.fname = 'Genot2011-F4D'
current = G11_F4D
template = genot2011_F4D_pil
sims = [
psim + " --pyplot-labels S I T W --p0 S=6.6 I=330",
psim + " --pyplot-labels S I T W --p0 S=6.6 I=145",
psim + " --pyplot-labels S I T W --p0 S=6.6 I=66"
]
#litr = [(176, 3.3), (213, 3.3), (248, 3.3)]
litr = [(51, 1.98), (55, 1.98), (60, 1.98)]
for (sim, res) in zip(sims, litr):
pilstring = template(None)
simulation = sim
reporter = 'T'
metric = 'completion-time'
current.add_system_simulation_setup(
pilstring, simulation, reporter, metric, '1.98',
res) #, simargs=sim[sim.find('I='):])
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
current.pepperargs['default'].update(rates)
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
G11_SF4A = FigureData('Sup. Fig. 4A: |a|=14, |b|=22 varying: |n|,|m|')
G11_SF4A.fname = 'Genot2011-SF4A'
current = G11_SF4A
template = genot2011_SF4A_pil
pilp = [17, 20, 23]
#litr = [(9088, 5), (13927, 5), (28681, 5)]
litr = [(4249, 3), (6492, 3), (12157, 3)]
psim = "pilsimulator --nxy --header --atol 1e-12 --rtol 1e-12 --mxstep 10000 --t-lin 100000 --t8 1e5"
for (pil, res) in zip(pilp, litr):
pilstring = template(pil)
simulation = psim + " --pyplot-labels S X R F --p0 R=30 X=40 S=10"
reporter = 'F'
metric = 'completion-time'
current.add_system_simulation_setup(pilstring, simulation, reporter,
metric, '3', res)
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
current.pepperargs['default'].update(rates)
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
G11_SF5 = FigureData('Sup. Fig. 5: |m|=|n|=20, varying: |a|')
G11_SF5.fname = 'Genot2011-SF5'
current = G11_SF5
template = genot2011_SF5_pil
pilp = [14, 10, 8, 6, 4, 2]
litr = [(25382, 6.94), (35273, 5.76), (68655, 1.87), (77018, 0.91),
(76218, 0.99), (77818, 0.79)]
psim = "pilsimulator --nxy --header --atol 1e-12 --rtol 1e-12 --mxstep 10000 --t-lin 100000 --t8 1e5"
for (pil, res) in zip(pilp, litr):
pilstring = template(pil)
simulation = psim + " --pyplot-labels S X R F --p0 R=30 X=40 S=10"
reporter = 'F'
metric = 'diagonal-crossing-time'
tmax = '86400'
cmax = '10'
current.add_system_simulation_setup(pilstring, simulation, reporter,
metric, ':'.join([tmax,
cmax]), res)
current.pepperargs['default'] = current.pepperargs['detailed'].copy()
current.pepperargs['default'].update({'k_slow': 1e-10, 'k_fast': 1e-5})
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
return [G11_F3, G11_F4A, G11_F4B, G11_F4C, G11_F4D, G11_SF4A] #, G11_SF5]
def data(evaluate=False, verbose=0):
from figure_analysis import FigureData
# Default pilsimulator call
psim = "pilsimulator --no-jacobian --nxy --header"
psim += " --atol 1e-10 --rtol 1e-10 --mxstep 1000"
psim += " --t8 86500 --t-lin 86500"
rates = {'k_slow': 1e-5, 'k_fast': 0.1}
# Setup
F3A = FigureData(
'Zhang & Winfree (2010) Fig. 3A - Catalytic DSD system with 100 nM substrates (varying catalyst)'
)
F3A.fname = 'Zhang2010-F3A'
current = F3A
template = zhang2007_F1_pil
sims = [
psim + ' --pyplot-labels S F OR C ROX --p0 S=100 F=200 OR=300 C=10',
psim + ' --pyplot-labels S F OR C ROX --p0 S=100 F=200 OR=300 C=1'
]
diagX = [(2557.53, 88.07), (11842.47, 44.61)]
for (sim, res) in zip(sims, diagX):
pilstring = template(None)
simulation = sim
reporter = 'ROX'
metric = 'diagonal-crossing-time'
tmax = '21600'
cmax = '100'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
':'.join([tmax, cmax]),
res,
simargs=sim[sim.find('C='):])
halfC = [(611.58, 50.00), (15956.76, 50.00)]
for (sim, res) in zip(sims, halfC):
pilstring = template(None)
simulation = sim
reporter = 'ROX'
metric = 'completion-time'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
'50',
res,
simargs=sim[sim.find('C='):])
current.pepperargs['default'] = current.pepperargs['Condensed'].copy()
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
# Setup
F3B = FigureData(
'Zhang & Winfree (2010) Fig. 3B - Catalytic DSD system 30 nM substrates (varying catalyst)'
)
F3B.fname = 'Zhang2010-F3B'
current = F3B
template = zhang2007_F1_pil
sims = [
psim + ' --pyplot-labels S F OR C ROX --p0 S=30 F=60 OR=90 C=3',
psim + ' --pyplot-labels S F OR C ROX --p0 S=30 F=60 OR=90 C=0.9'
]
diagX = [(4200.75, 24.15), (9051.94, 17.45)]
for (sim, res) in zip(sims, diagX):
pilstring = template(None)
simulation = sim
reporter = 'ROX'
metric = 'diagonal-crossing-time'
tmax = '21600'
cmax = '30'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
':'.join([tmax, cmax]),
res,
simargs=sim[sim.find('C='):])
halfC = [(1571.89, 15), (6938.02, 15)]
for (sim, res) in zip(sims, halfC):
pilstring = template(None)
simulation = sim
reporter = 'ROX'
metric = 'completion-time'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
'15',
res,
simargs=sim[sim.find('C='):])
current.pepperargs['default'] = current.pepperargs['Condensed'].copy()
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
# Setup
F3C = FigureData(
'Zhang & Winfree (2010) Fig. 3C - Catalytic DSD system with 3 nM substrates (varying catalyst)'
)
F3C.fname = 'Zhang2010-F3C'
current = F3C
template = zhang2007_F1_pil
sims = [
psim + ' --pyplot-labels S F OR C ROX --p0 S=3 F=6 OR=9 C=0.9',
psim + ' --pyplot-labels S F OR C ROX --p0 S=3 F=6 OR=9 C=0.3'
]
diagX = [(10199.26, 2.30), (17034.36, 1.82)]
for (sim, res) in zip(sims, diagX):
pilstring = template(None)
simulation = sim
reporter = 'ROX'
metric = 'diagonal-crossing-time'
tmax = '43200'
cmax = '3'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
':'.join([tmax, cmax]),
res,
simargs=sim[sim.find('C='):])
halfC = [(4485.54, 1.50), (12388.63, 1.50)]
for (sim, res) in zip(sims, halfC):
pilstring = template(None)
simulation = sim
reporter = 'ROX'
metric = 'completion-time'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
'1.5',
res,
simargs=sim[sim.find('C='):])
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
# Setup
F3D = FigureData(
'Zhang & Winfree (2010) Fig. 3D - Catalytic DSD system with 1 nM substrates (varying catalyst)'
)
F3D.fname = 'Zhang2010-F3D'
current = F3D
template = zhang2007_F1_pil
sims = [
psim + ' --pyplot-labels S F OR C ROX --p0 S=1 F=2 OR=3 C=1',
psim + ' --pyplot-labels S F OR C ROX --p0 S=1 F=2 OR=3 C=0.1'
]
diagX = [(14382.50, 0.83), (40417.98, 0.53)]
for (sim, res) in zip(sims, diagX):
pilstring = template(None)
simulation = sim
reporter = 'ROX'
metric = 'diagonal-crossing-time'
tmax = '86400'
cmax = '1'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
':'.join([tmax, cmax]),
res,
simargs=sim[sim.find('C='):])
halfC = [(5354.07, 0.50), (36323.69, 0.50)]
for (sim, res) in zip(sims, halfC):
pilstring = template(None)
simulation = sim
reporter = 'ROX'
metric = 'completion-time'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
'0.5',
res,
simargs=sim[sim.find('C='):])
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
# Setup
F10C = FigureData(
'Zhang & Winfree (2010) Fig. 10C -- Catalytic DSD system with four-letter alphabet (varying catalyst)'
)
F10C.fname = 'Zhang2010-F10C'
current = F10C
template = zhang2010_F10A_pil
sims = [
psim +
' --pyplot-labels S4 F4 OR4 C4 ROX --p0 S4=30 F4=60 OR4=90 C4=3',
psim +
' --pyplot-labels S4 F4 OR4 C4 ROX --p0 S4=30 F4=60 OR4=90 C4=0.09',
psim +
' --pyplot-labels S4 F4 OR4 C4 ROX --p0 S4=30 F4=60 OR4=90 C4=0.03'
]
diagX = [(14893.10, 11.70), (25416.48, 5.91), (31189.31, 2.72)]
for (sim, res) in zip(sims, diagX):
pilstring = template(None)
simulation = sim
reporter = 'ROX'
metric = 'diagonal-crossing-time'
tmax = '36000'
cmax = '20'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
':'.join([tmax, cmax]),
res,
simargs=sim[sim.find('C4='):])
#NOTE: That doesn't make sense!
#halfC = [(10663.70, 10.01)]
#for (sim, res) in zip(sims, halfC):
# pilstring = template(None)
# simulation = sim
# reporter = 'ROX'
# metric = 'completion-time'
# current.add_system_simulation_setup(pilstring, simulation, reporter, metric, '10',
# res, simargs=sim[sim.find('C4='):])
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
# Setup
F10F = FigureData(
'Zhang & Winfree (2010) Fig. 10F -- Catalytic DSD system with three and four-letter alphabet (varying catalyst)'
)
F10F.fname = 'Zhang2010-F10F'
current = F10F
template = zhang2010_F10D_pil
sims = [
psim +
' --pyplot-labels S43 F43 OR43 C43 RG --p0 S43=10 F43=20 OR43=30 C43=3',
psim +
' --pyplot-labels S43 F43 OR43 C43 RG --p0 S43=10 F43=20 OR43=30 C43=0.09',
psim +
' --pyplot-labels S43 F43 OR43 C43 RG --p0 S43=10 F43=20 OR43=30 C43=0.03'
]
diagX = [(3545.01, 4.06), (5321.74, 2.07), (6277.79, 1.01)]
for (sim, res) in zip(sims, diagX):
pilstring = template(None)
simulation = sim
reporter = 'RG'
metric = 'diagonal-crossing-time'
tmax = '7200'
cmax = '8'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
':'.join([tmax, cmax]),
res,
simargs=sim[sim.find('C43='):])
#NOTE: That doesn't make sense!
#halfC = [(3426.56, 4.00)]
#for (sim, res) in zip(sims, halfC):
# pilstring = template(None)
# simulation = sim
# reporter = 'RG'
# metric = 'completion-time'
# current.add_system_simulation_setup(pilstring, simulation, reporter, metric, '4',
# res, simargs=sim[sim.find('C43='):])
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
return [F3A, F3B, F3C, F3D] #, F10C, F10F]
def data(evaluate=False, verbose=0):
from figure_analysis import FigureData
# Default pilsimulator call
psim = "pilsimulator --no-jacobian --nxy --header --atol 1e-12 --rtol 1e-12 --mxstep 1000"
h10l = " --t0 0 --t8 36000 --t-lin 18000"
h20l = " --t0 0 --t8 72000 --t-lin 18000"
h30log = " --t0 0.1 --t8 108000 --t-log 18000"
# Setup
k17_F2 = FigureData(
'Kotani & Hughes (2017) Fig. 2 - Single-layer catalytic DSD with 4-way branch migration (varying catalyst)'
)
k17_F2.fname = 'Kotani2017-F2'
current = k17_F2
template = kotani2017_F2_pil
sims = [
psim + h10l +
" --pyplot-labels D S1 S2 R C1 --p0 S1=10 S2=10 R=20 C1=1", psim +
h10l + " --pyplot-labels D S1 S2 R C1 --p0 S1=10 S2=10 R=20 C1=0.5",
psim + h10l +
" --pyplot-labels D S1 S2 R C1 --p0 S1=10 S2=10 R=20 C1=0.05"
]
#litr = [(7733, 7.42), (11333, 6.18), (25533, 1.40)]
diagX = [(4893.97, 7.49), (9388.93, 6.29), (27435.62, 1.35)]
for (sim, res) in zip(sims, diagX):
pilstring = template(None)
simulation = sim
reporter = 'D'
metric = 'diagonal-crossing-time'
cmax = '10'
tmax = '32400'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
':'.join([tmax, cmax]),
res,
simargs=sim[sim.find('C1='):])
halfC = [(555.34, 5.00), (4514.48, 5.00)]
for (sim, res) in zip(sims, halfC):
pilstring = template(None)
simulation = sim
reporter = 'D'
metric = 'completion-time'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
'5',
res,
simargs=sim[sim.find('C1='):])
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
current.pepperargs['default']['release_cutoff'] = 7
current.pepperargs['default']['max_complex_size'] = 8
if evaluate:
current.eval(cmpfig=True)
if verbose:
for df in current.get_dataframes():
print(df)
# Setup
k17_F3 = FigureData(
'Kotani & Hughes (2017) Fig. 3 - Two-layer feedforward DSD system with 4-way branch migration (varying catalyst)'
)
k17_F3.fname = 'Kotani2017-F3'
current = k17_F3
template = kotani2017_F3_pil
sims = [
psim + h30log +
" --pyplot-labels D S1 S2 S3 S4 R C1 --p0 S1=10 S2=10 S3=10 S4=10 R=20 C1=0.1",
psim + h30log +
" --pyplot-labels D S1 S2 S3 S4 R C1 --p0 S1=10 S2=10 S3=10 S4=10 R=20 C1=0.01",
psim + h30log +
" --pyplot-labels D S1 S2 S3 S4 R C1 --p0 S1=10 S2=10 S3=10 S4=10 R=20 C1=0.001"
]
#litr = [(21220, 7.72), (64203, 3.12), (86996, 0.69)]
diagX = [(21370.60, 7.78), (66095.66, 3.17), (90663.66, 0.74)]
for (sim, res) in zip(sims, diagX):
pilstring = template(None)
simulation = sim
reporter = 'D'
metric = 'diagonal-crossing-time'
cmax = '10'
tmax = '97200'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
':'.join([tmax, cmax]),
res,
simargs=sim[sim.find('C1='):])
halfC = [(12994.28, 5)]
for (sim, res) in zip(sims, halfC):
pilstring = template(None)
simulation = sim
reporter = 'D'
metric = 'completion-time'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
'5',
res,
simargs=sim[sim.find('C1='):])
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
current.pepperargs['default']['release_cutoff'] = 7
current.pepperargs['default']['max_complex_size'] = 8
if evaluate:
current.eval(cmpfig=True)
if verbose:
for df in current.get_dataframes():
print(df)
# Setup
k17_F4 = FigureData(
'Kotani & Hughes (2017) Fig. 4 - Autocatalytic DSD system with 4-way branch migration (varying autocatalyst)'
)
k17_F4.fname = 'Kotani2017-F4'
current = k17_F4
template = kotani2017_F4_pil
sims = [
psim + h20l +
" --pyplot-labels D S5 S6 R C1 --p0 S5=10 S6=10 R=20 C1=0.1", psim +
h20l + " --pyplot-labels D S5 S6 R C1 --p0 S5=10 S6=10 R=20 C1=0.01",
psim + h20l +
" --pyplot-labels D S5 S6 R C1 --p0 S5=10 S6=10 R=20 C1=0.001", psim +
h20l + " --pyplot-labels D S5 S6 R C1 --p0 S5=10 S6=10 R=20 C1=0"
]
diagX = [(6800.87, 6.11), (9054.78, 4.88), (10322.61, 4.21),
(10921.30, 3.85)]
for (sim, res) in zip(sims, diagX):
pilstring = template(None)
simulation = sim
reporter = 'D'
metric = 'diagonal-crossing-time'
cmax = '10'
tmax = '18000'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
':'.join([tmax, cmax]),
res,
simargs=sim[sim.find('C1='):])
halfC = [(6131.74, 5), (9125.22, 5), (10780.43, 5), (11520.00, 5)]
for (sim, res) in zip(sims, halfC):
pilstring = template(None)
simulation = sim
reporter = 'D'
metric = 'completion-time'
current.add_system_simulation_setup(pilstring,
simulation,
reporter,
metric,
'5',
res,
simargs=sim[sim.find('C1='):])
current.pepperargs['default'] = current.pepperargs['CONDENSED'].copy()
current.pepperargs['default']['max_complex_size'] = 24
current.pepperargs['default']['k_slow'] = 1e-4
current.pepperargs['default']['k_fast'] = 1e-3
if evaluate:
current.eval(cmpfig=True)
if verbose:
for df in current.get_dataframes():
print(df)
return [k17_F2, k17_F3, k17_F4]
def data(evaluate=False, verbose = 0):
""" """
from figure_analysis import FigureData
rates = {'k_slow': 0.01, 'k_fast': 1}
seesaw = {'ssw_rxns': None, #'T20-utbr-leak-reduced',
'ssw_expl': False,
'ssw_conc': 100e-9,
'dry_run': False}
# Default pilsimulator call
psim = "pilsimulator --no-jacobian --nxy --header"
psim += " --atol 1e-12 --rtol 1e-12" # + " --mxstep 10000"
h1l = " --t8 3600 --t-lin 3600"
h5l = " --t8 18000 --t-lin 9000"
h10l = " --t8 36000 --t-lin 18000"
h12l = " --t8 43200 --t-lin 21600"
# Setup
SF22 = FigureData('Sup. Fig. 22: Single catalyst, no threshold')
SF22.fname='Qian2011-SF22'
current = SF22
template = qian2011_SF22
sims = [psim + h1l + " --pyplot-labels I O --p0 I=100",
psim + h1l + " --pyplot-labels I O --p0 I=90",
psim + h1l + " --pyplot-labels I O --p0 I=80",
psim + h1l + " --pyplot-labels I O --p0 I=70",
psim + h1l + " --pyplot-labels I O --p0 I=60",
psim + h1l + " --pyplot-labels I O --p0 I=50",
psim + h1l + " --pyplot-labels I O --p0 I=40",
psim + h1l + " --pyplot-labels I O --p0 I=30",
psim + h1l + " --pyplot-labels I O --p0 I=20",
psim + h1l + " --pyplot-labels I O --p0 I=10"]
litr = [(738.55, 72.89), (766.03, 71.75), (796.95, 70.62), (834.73, 69.18),
(886.26, 67.22), (951.53, 65.05), (1040.84, 61.75), (1157.63, 57.32),
(1353.44, 50.31), (1700.38, 37.53)]
for (sim, res) in zip(sims, litr):
pilstring = template(None)
simulation = sim
reporter = 'O'
metric = 'diagonal-crossing-time'
tmax = '2700'
cmax = '100'
current.add_system_simulation_setup(pilstring, simulation, reporter, metric,
':'.join([tmax, cmax]), res)
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
current.pepperargs['default'].update(rates)
current.pepperargs['default'].update(seesaw)
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
# Setup
SF23 = FigureData('Sup. Fig. 23: Single catalyst and threshold')
SF23.fname='Qian2011-SF23'
current = SF23
template = qian2011_SF23
sims = [psim + h5l + " --pyplot-labels I O --p0 I=100",
psim + h5l + " --pyplot-labels I O --p0 I=90",
psim + h5l + " --pyplot-labels I O --p0 I=80",
psim + h5l + " --pyplot-labels I O --p0 I=70",
psim + h5l + " --pyplot-labels I O --p0 I=60",
psim + h5l + " --pyplot-labels I O --p0 I=50",
psim + h5l + " --pyplot-labels I O --p0 I=40",
psim + h5l + " --pyplot-labels I O --p0 I=30",
psim + h5l + " --pyplot-labels I O --p0 I=20",
psim + h5l + " --pyplot-labels I O --p0 I=10"]
litr = [(1808, 83.24), (2081, 80.66), (2587, 76.28), (3516, 67.37),
(6590, 39.12), (9828, 9.05), (10115, 6.21), (10265, 4.41),
(10497, 2.47), (10648, 1.31)]
for (sim, res) in zip(sims, litr):
pilstring = template(None)
simulation = sim
reporter = 'O'
metric = 'diagonal-crossing-time'
tmax = '10800'
cmax = '100'
current.add_system_simulation_setup(pilstring, simulation, reporter, metric,
':'.join([tmax, cmax]), res)
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
current.pepperargs['default'].update(rates)
current.pepperargs['default'].update(seesaw)
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
# Setup
F2C_OR = FigureData('Fig. 2C: Two-input OR gate')
F2C_OR.fname='Qian2011-F2C-OR'
current = F2C_OR
template = qian2011_F2
sims = [psim + h5l + " --pyplot-labels x1 x2 y --p0 x1=90 x2=90",
psim + h5l + " --pyplot-labels x1 x2 y --p0 x1=10 x2=90",
psim + h5l + " --pyplot-labels x1 x2 y --p0 x1=90 x2=10",
psim + h5l + " --pyplot-labels x1 x2 y --p0 x1=10 x2=10"]
litr = [(3245, 85), (4733, 68), (4733, 68), (10530, 0.4)]
for (sim, res) in zip(sims, litr):
pilstring = template(None)
simulation = sim
reporter = 'y'
metric = 'diagonal-crossing-time'
tmax = '18000'
cmax = '100'
current.add_system_simulation_setup(pilstring, simulation, reporter, metric,
':'.join([tmax, cmax]), res)
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
current.pepperargs['default'].update(rates)
current.pepperargs['default'].update(seesaw)
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
# Setup
F2C_AND = FigureData('Fig. 2C: Two-input AND gate')
F2C_AND.fname='Qian2011-F2C-AND'
current = F2C_AND
template = qian2011_F2
sims = [ #T2_5 = 120 * 1.1 = 132
psim + h12l + " --t8 45000 --pyplot-labels x1 x2 y --p0 x1=90 x2=90 T2_5=132",
psim + h12l + " --t8 45000 --pyplot-labels x1 x2 y --p0 x1=10 x2=90 T2_5=132",
psim + h12l + " --t8 45000 --pyplot-labels x1 x2 y --p0 x1=90 x2=10 T2_5=132",
psim + h12l + " --t8 45000 --pyplot-labels x1 x2 y --p0 x1=10 x2=10 T2_5=132"]
litr = [(13797, 68), (41022, 0.7), (41022, 0.7), (42239, 0.4)]
for (sim, res) in zip(sims, litr):
pilstring = template(None)
simulation = sim
reporter = 'y'
metric = 'diagonal-crossing-time'
tmax = '43200'
cmax = '100'
current.add_system_simulation_setup(pilstring, simulation, reporter, metric,
':'.join([tmax, cmax]), res)
current.pepperargs['default'] = current.pepperargs['condensed'].copy()
current.pepperargs['default'].update(rates)
current.pepperargs['default'].update(seesaw)
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
# Setup
SF26 = FigureData('Sup. Fig. 26: Three-layer OR cascade')
SF26.fname = 'Qian2011-SF26'
current = SF26
template = qian2011_SF26
sims = [psim + h10l + " --pyplot-labels x1 x2 x3 x4 y --p0 x1=90 x2=90 x3=90 x4=90",
psim + h10l + " --pyplot-labels x1 x2 x3 x4 y --p0 x1=10 x2=10 x3=90 x4=10",
psim + h10l + " --pyplot-labels x1 x2 x3 x4 y --p0 x1=10 x2=90 x3=10 x4=10",
psim + h10l + " --pyplot-labels x1 x2 x3 x4 y --p0 x1=10 x2=10 x3=10 x4=10"]
simargs = ['((1 or 1) or 1) or 1',
'((0 or 0) or 1) or 0',
'((0 or 1) or 0) or 0',
'((0 or 0) or 0) or 0']
litr = [(3326.32, 84.49), (7368.42, 65.71), (9557.89, 55.51), (20842.11, 3.67)]
for (sim, arg, res) in zip(sims, simargs, litr):
pilstring = template(None)
simulation = sim
reporter = 'y'
metric = 'diagonal-crossing-time'
tmax = '21600'
cmax = '100'
current.add_system_simulation_setup(pilstring, simulation, reporter, metric,
':'.join([tmax, cmax]), res, simargs=arg)
current.pepperargs['default'] = current.pepperargs['Condensed'].copy()
current.pepperargs['default'].update(rates)
current.pepperargs['default'].update(seesaw)
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
# Setup
SF27 = FigureData('Sup. Fig. 27: Four-layer OR cascade')
SF27.fname = 'Qian2011-SF27'
current = SF27
template = qian2011_SF27
sims = [psim + h10l + " --pyplot-labels x1 x2 x3 x4 x5 y --p0 x1=90 x2=90 x3=90 x4=90 x5=90",
psim + h10l + " --pyplot-labels x1 x2 x3 x4 x5 y --p0 x1=10 x2=10 x3=90 x4=10 x5=10",
psim + h10l + " --pyplot-labels x1 x2 x3 x4 x5 y --p0 x1=10 x2=90 x3=10 x4=10 x5=10",
psim + h10l + " --pyplot-labels x1 x2 x3 x4 x5 y --p0 x1=10 x2=10 x3=10 x4=10 x5=10"]
simargs = ['(((1 or 1) or 1) or 1) or 1',
'(((0 or 0) or 1) or 0) or 0',
'(((0 or 1) or 0) or 0) or 0',
'(((0 or 0) or 0) or 0) or 0']
litr = [(3558.62, 82.89), (9848.28, 53.83), (12082.76, 43.88), (20937.93, 3.28)]
for (sim, arg, res) in zip(sims, simargs, litr):
pilstring = template(None)
simulation = sim
reporter = 'y'
metric = 'diagonal-crossing-time'
tmax = '21600'
cmax = '100'
current.add_system_simulation_setup(pilstring, simulation, reporter, metric,
':'.join([tmax, cmax]), res, simargs=arg)
current.pepperargs['default'] = current.pepperargs['Condensed'].copy()
current.pepperargs['default'].update(rates)
current.pepperargs['default'].update(seesaw)
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
# Setup
SF28 = FigureData('Sup. Fig. 28: Five AND/OR gates, four layers')
SF28.fname = 'Qian2011-SF28'
current = SF28
template = qian2011_SF28
sims = [psim + h10l + " --pyplot-labels x1 x2 x3 x4 x5 x6 y --p0 x1=90 x2=90 x3=90 x4=90 x5=90 x6=90",
psim + h10l + " --pyplot-labels x1 x2 x3 x4 x5 x6 y --p0 x1=90 x2=10 x3=90 x4=90 x5=10 x6=10",
psim + h10l + " --pyplot-labels x1 x2 x3 x4 x5 x6 y --p0 x1=90 x2=90 x3=10 x4=90 x5=10 x6=10",
psim + h10l + " --pyplot-labels x1 x2 x3 x4 x5 x6 y --p0 x1=10 x2=10 x3=10 x4=90 x5=10 x6=90",
psim + h10l + " --pyplot-labels x1 x2 x3 x4 x5 x6 y --p0 x1=10 x2=10 x3=10 x4=10 x5=90 x6=90",
psim + h10l + " --pyplot-labels x1 x2 x3 x4 x5 x6 y --p0 x1=90 x2=10 x3=90 x4=10 x5=90 x6=10",
psim + h10l + " --pyplot-labels x1 x2 x3 x4 x5 x6 y --p0 x1=10 x2=90 x3=90 x4=10 x5=10 x6=10",
psim + h10l + " --pyplot-labels x1 x2 x3 x4 x5 x6 y --p0 x1=90 x2=90 x3=10 x4=10 x5=10 x6=90",
psim + h10l + " --pyplot-labels x1 x2 x3 x4 x5 x6 y --p0 x1=90 x2=10 x3=10 x4=10 x5=90 x6=10",
psim + h10l + " --pyplot-labels x1 x2 x3 x4 x5 x6 y --p0 x1=10 x2=90 x3=10 x4=10 x5=10 x6=90",
psim + h10l + " --pyplot-labels x1 x2 x3 x4 x5 x6 y --p0 x1=10 x2=10 x3=90 x4=10 x5=90 x6=10",
psim + h10l + " --pyplot-labels x1 x2 x3 x4 x5 x6 y --p0 x1=10 x2=10 x3=10 x4=10 x5=10 x6=10"]
simargs = ['(((1 or 1) and 1) or 1) or (1 and 1)',
'(((1 or 0) and 1) or 1) or (0 and 0)',
'(((1 or 1) and 0) or 1) or (0 and 0)',
'(((0 or 0) and 0) or 1) or (0 and 1)',
'(((0 or 0) and 0) or 0) or (1 and 1)',
'(((1 or 0) and 1) or 0) or (1 and 0)',
'(((0 or 1) and 1) or 0) or (0 and 0)',
'(((1 or 1) and 0) or 0) or (0 and 1)',
'(((1 or 0) and 0) or 0) or (1 and 0)',
'(((0 or 1) and 0) or 0) or (0 and 1)',
'(((0 or 0) and 1) or 0) or (1 and 0)',
'(((0 or 0) and 0) or 0) or (0 and 0)']
litr = [(4467.98, 83.76), (7541.50, 73.47), (8224.51, 71.49), (8822.13, 69.50), (12151.78, 57.23), (13944.66, 51.29),
(16420.55, 42.57), (28031.62, 2.57), (28031.62, 2.57), (28031.62, 2.57), (28031.62, 2.57), (28031.62, 2.57)]
for (sim, arg, res) in zip(sims, simargs, litr):
pilstring = template(None)
simulation = sim
reporter = 'y'
metric = 'diagonal-crossing-time'
tmax = '28800'
cmax = '100'
current.add_system_simulation_setup(pilstring, simulation, reporter, metric,
':'.join([tmax, cmax]), res, simargs=arg)
current.pepperargs['default'] = current.pepperargs['Condensed'].copy()
current.pepperargs['default'].update(rates)
current.pepperargs['default'].update(seesaw)
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
# Setup
SF29_OR = FigureData('Sup. Fig. 29: Four-input OR gates')
SF29_OR.fname = 'Qian2011-SF29-OR'
current = SF29_OR
template = qian2011_SF29_OR
sims = [ # Threshold = 60 * 1.1
psim + h5l + " --pyplot-labels x1 x2 x3 x4 x5 x6 x7 x8 y --p0 x1=90 x2=10 x3=90 x4=10 x5=90 x6=10 x7=90 x8=10 T2_5=66",
psim + h5l + " --pyplot-labels x1 x2 x3 x4 x5 x6 x7 x8 y --p0 x1=90 x2=10 x3=90 x4=10 x5=90 x6=10 x7=10 x8=10 T2_5=66",
psim + h5l + " --pyplot-labels x1 x2 x3 x4 x5 x6 x7 x8 y --p0 x1=90 x2=10 x3=90 x4=10 x5=10 x6=10 x7=10 x8=10 T2_5=66",
psim + h5l + " --pyplot-labels x1 x2 x3 x4 x5 x6 x7 x8 y --p0 x1=10 x2=10 x3=10 x4=10 x5=10 x6=10 x7=90 x8=10 T2_5=66",
psim + h5l + " --pyplot-labels x1 x2 x3 x4 x5 x6 x7 x8 y --p0 x1=10 x2=10 x3=10 x4=10 x5=90 x6=10 x7=10 x8=10 T2_5=66",
psim + h5l + " --pyplot-labels x1 x2 x3 x4 x5 x6 x7 x8 y --p0 x1=10 x2=10 x3=90 x4=10 x5=10 x6=10 x7=10 x8=10 T2_5=66",
psim + h5l + " --pyplot-labels x1 x2 x3 x4 x5 x6 x7 x8 y --p0 x1=90 x2=10 x3=10 x4=10 x5=10 x6=10 x7=10 x8=10 T2_5=66",
psim + h5l + " --pyplot-labels x1 x2 x3 x4 x5 x6 x7 x8 y --p0 x1=10 x2=10 x3=10 x4=10 x5=10 x6=10 x7=10 x8=10 T2_5=66"]
simargs = ['(1 or 0) or (1 or 0) or (1 or 0) or (1 or 0)',
'(1 or 0) or (1 or 0) or (1 or 0) or (0 or 0)',
'(1 or 0) or (1 or 0) or (0 or 0) or (0 or 0)',
'(0 or 0) or (0 or 0) or (0 or 0) or (1 or 0)',
'(0 or 0) or (0 or 0) or (1 or 0) or (0 or 0)',
'(0 or 0) or (1 or 0) or (0 or 0) or (0 or 0)',
'(1 or 0) or (0 or 0) or (0 or 0) or (0 or 0)',
'(0 or 0) or (0 or 0) or (0 or 0) or (0 or 0)']
litr = [(1925.58, 81.20), (2302.33, 78.40), (2679.07, 74.80), (3809.30, 63.60), (4102.33, 61.20), (4311.63, 59.20), (4479.07, 58.00), (10548.84, 3.60)]
for (sim, arg, res) in zip(sims, simargs, litr):
pilstring = template(None)
simulation = sim
reporter = 'y'
metric = 'diagonal-crossing-time'
tmax = '10800'
cmax = '100'
current.add_system_simulation_setup(pilstring, simulation, reporter, metric,
':'.join([tmax, cmax]), res, simargs=arg)
current.pepperargs['default'] = current.pepperargs['Condensed'].copy()
current.pepperargs['default'].update(rates)
current.pepperargs['default'].update(seesaw)
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
# Setup
SF29_AND = FigureData('Sup. Fig. 29: Four-input AND gates')
SF29_AND.fname = 'Qian2011-SF29-AND'
current = SF29_AND
template = qian2011_SF29_AND
sims = [ # Threshold = 320 * 1.1
psim + h10l + " --pyplot-labels x1 x2 x3 x4 x5 x6 x7 x8 y --p0 x1=90 x2=10 x3=90 x4=10 x5=90 x6=10 x7=90 x8=10 T2_5=352",
psim + h10l + " --pyplot-labels x1 x2 x3 x4 x5 x6 x7 x8 y --p0 x1=90 x2=10 x3=90 x4=10 x5=90 x6=10 x7=10 x8=10 T2_5=352",
psim + h10l + " --pyplot-labels x1 x2 x3 x4 x5 x6 x7 x8 y --p0 x1=90 x2=10 x3=90 x4=10 x5=10 x6=10 x7=10 x8=10 T2_5=352",
psim + h10l + " --pyplot-labels x1 x2 x3 x4 x5 x6 x7 x8 y --p0 x1=90 x2=10 x3=10 x4=10 x5=10 x6=10 x7=10 x8=10 T2_5=352"]
simargs = ['(1 or 0) and (1 or 0) and (1 or 0) and (1 or 0)',
'(1 or 0) and (1 or 0) and (1 or 0) and (0 or 0)',
'(1 or 0) and (1 or 0) and (0 or 0) and (0 or 0)',
'(1 or 0) and (1 or 0) and (0 or 0) and (0 or 0)']
litr = [(15947.37, 55.33), (31894.74, 11.07), (34263.16, 5.79), (35052.63, 2.94)]
for (sim, arg, res) in zip(sims, simargs, litr):
pilstring = template(None)
simulation = sim
reporter = 'y'
metric = 'diagonal-crossing-time'
tmax = '36000'
cmax = '100'
current.add_system_simulation_setup(pilstring, simulation, reporter, metric,
':'.join([tmax, cmax]), res, simargs=arg)
current.pepperargs['default'] = current.pepperargs['Condensed'].copy()
current.pepperargs['default'].update(rates)
current.pepperargs['default'].update(seesaw)
if evaluate:
current.eval()
if verbose:
for df in current.get_dataframes():
print(df)
# SF30_OR = FigureData('Qian2011-SF30-OR')
# current = SF30_OR
# template = qian2011_SF30_OR
# sims = [ # Threshold = 320 * 1.1
# psim + h5l + " --pyplot-labels x1 x2 x3 x4 x5 x6 y1 y2 y3 y4 --p0 x1=90 x2=90 x3=10 x4=10 x5=10 x6=10",
# psim + h5l + " --pyplot-labels x1 x2 x3 x4 x5 x6 y1 y2 y3 y4 --p0 x1=90 x2=10 x3=10 x4=10 x5=10 x6=10",
# psim + h5l + " --pyplot-labels x1 x2 x3 x4 x5 x6 y1 y2 y3 y4 --p0 x1=10 x2=90 x3=10 x4=10 x5=10 x6=10",
# psim + h5l + " --pyplot-labels x1 x2 x3 x4 x5 x6 y1 y2 y3 y4 --p0 x1=10 x2=10 x3=10 x4=10 x5=10 x6=10"]
# litr = [('y1', [(4034.90, 0.61), (5387.92, 0.48), (5387.92, 0.48), (10413.42, 0.01)])]
# for (rep, results) in litr:
# for (sim, res) in zip(sims, results):
# pilstring = template(None)
# simulation = sim
# reporter = rep
# metric = 'diagonal-crossing-time'
# tmax = '10800'
# cmax = '1'
# current.add_system_simulation_setup(pilstring, simulation, reporter, metric,
# ':'.join([tmax, cmax]), res)
# current.pepperargs['default'] = current.pepperargs['CONDENSED'].copy()
# current.pepperargs['default'].update(rates)
# if evaluate:
# current.eval()
# if verbose:
# for df in current.get_dataframes():
# print(df)
return [SF22, SF23, F2C_OR, F2C_AND, SF26, SF27, SF28, SF29_OR, SF29_AND]#, SF30_OR]