def test_uppmaboss_remote(self):
sim = load(
"https://raw.githubusercontent.com/sysbio-curie/UPMaBoSS-docker/master/CellFate/CellFateModel_uppmaboss.bnd",
"https://raw.githubusercontent.com/sysbio-curie/UPMaBoSS-docker/master/CellFate/CellFateModel_uppmaboss.cfg"
)
uppmaboss_model = UpdatePopulation(
sim,
"https://github.com/sysbio-curie/UPMaBoSS-docker/blob/master/CellFate/CellFateModel_uppmaboss.upp"
)
uppmaboss_sim = uppmaboss_model.run('remote')
def test_uppmaboss_server(self):
sim = load(join(dirname(__file__), "CellFateModel.bnd"),
join(dirname(__file__), "CellFateModel_1h.cfg"))
uppmaboss_model = UpdatePopulation(
sim, join(dirname(__file__), "CellFate_1h.upp"))
uppmaboss_sim = uppmaboss_model.run(host='localhost', port=7777)
pop_ratios = uppmaboss_sim.get_population_ratios('WT').values.tolist()
expected_pop_ratios = [
1.0, 0.6907579999999945, 0.6341980442019741, 0.6126727283836865,
0.5992233366501704, 0.5788557354373725, 0.5473173595477481,
0.5081754112622799, 0.4654525962620004, 0.4247217704682538,
0.3886947462882363, 0.3581526679038661, 0.3328878624045683
]
for i, pop_ratio in enumerate(pop_ratios):
self.assertAlmostEqual(pop_ratio, expected_pop_ratios[i])
def test_uppmaboss_cmaboss(self):
sim = load(join(dirname(__file__), "CellFateModel.bnd"),
join(dirname(__file__), "CellFateModel_1h.cfg"))
uppmaboss_model = UpdatePopulation(
sim, join(dirname(__file__), "CellFate_1h.upp"))
uppmaboss_sim = uppmaboss_model.run('WT_cmaboss', cmaboss=True)
pop_ratios = uppmaboss_sim.get_population_ratios('WT').values.tolist()
expected_pop_ratios = [
1.0, 0.6907820416914479, 0.6341903631891185, 0.612996053462505,
0.5996083687781087, 0.5788914827739509, 0.5466795703259922,
0.5075723301828101, 0.46462393081796144, 0.4237712222056809,
0.388072085864841, 0.35730025864566073, 0.3320260202532354
]
for i, pop_ratio in enumerate(pop_ratios):
self.assertAlmostEqual(pop_ratio, expected_pop_ratios[i])
def test_uppmaboss_cmaboss_only_final_state(self):
sim = load(join(dirname(__file__), "CellFateModel.bnd"),
join(dirname(__file__), "CellFateModel_1h.cfg"))
uppmaboss_model = UpdatePopulation(
sim, join(dirname(__file__), "CellFate_1h.upp"))
uppmaboss_sim = uppmaboss_model.run('WT_cmaboss_final',
cmaboss=True,
only_final_state=True)
pop_ratios = uppmaboss_sim.get_population_ratios('WT').values.tolist()
expected_pop_ratios = [
1.0, 0.6778600000000088, 0.6279830611999899, 0.6097213137802712,
0.594362433886137, 0.5680084035675778, 0.5307981730498335,
0.4871453312981917, 0.4427225485370628, 0.4022798437281834,
0.367703891159712, 0.3393539211512898, 0.31562968852360135
]
for i, pop_ratio in enumerate(pop_ratios):
self.assertAlmostEqual(pop_ratio, expected_pop_ratios[i])
def test_uppmaboss_overwrite(self):
# Now again, but with a modified max_time, and with overwrite
# Results should be different if overwriting indeed works
sim = load(join(dirname(__file__), "CellFateModel.bnd"),
join(dirname(__file__), "CellFateModel_1h.cfg"))
sim.param["max_time"] = 2
expected_pop_ratios = [
1.0, 0.6323979999999877, 0.5972195964539613, 0.5413299949589563,
0.4570216375540166, 0.3810664694790497, 0.3280296382569338,
0.29096852169701004, 0.26290169809410047, 0.23962359303974,
0.2201920366329486, 0.2039266710788974, 0.19007637943255015
]
uppmaboss_model = UpdatePopulation(
sim, join(dirname(__file__), "CellFate_1h.upp"))
uppmaboss_sim = uppmaboss_model.run('WT', overwrite=True)
pop_ratios = uppmaboss_sim.get_population_ratios('WT').values.tolist()
for i, pop_ratio in enumerate(pop_ratios):
self.assertAlmostEqual(pop_ratio, expected_pop_ratios[i])
from maboss import load, UpdatePopulation
from os.path import exists, splitext
if __name__ == "__main__":
if len(argv) < 4:
print("Usage:\n")
print("UpMaBoSS.py <file.bnd> <file.cfg> <file.upp>")
exit(1)
bnd_file = argv[1]
cfg_file = argv[2]
upp_file = argv[3]
if not exists(bnd_file):
print("Cannot find .bnd file")
exit(1)
if not exists(cfg_file):
print("Cannot find .cfg file")
exit(1)
if not exists(upp_file):
print("Cannot find .upp file")
exit(1)
workdir = splitext(cfg_file)[0]
maboss_model = load(bnd_file, cfg_file)
simulation = UpdatePopulation(maboss_model, upp_file, verbose=True)
result = simulation.run(workdir=workdir)
result.save(workdir)
def test_uppmaboss_restore(self):
# Now again, but with save results (from the overwrite run)
expected_pop_ratios = [
1.0, 0.6323979999999877, 0.5972195964539613, 0.5413299949589563,
0.4570216375540166, 0.3810664694790497, 0.3280296382569338,
0.29096852169701004, 0.26290169809410047, 0.23962359303974,
0.2201920366329486, 0.2039266710788974, 0.19007637943255015
]
sim = load(join(dirname(__file__), "CellFateModel.bnd"),
join(dirname(__file__), "CellFateModel_1h.cfg"))
uppmaboss_model = UpdatePopulation(
sim, join(dirname(__file__), "CellFate_1h.upp"))
uppmaboss_sim = uppmaboss_model.run('WT')
pop_ratios = uppmaboss_sim.get_population_ratios('WT').values.tolist()
for i, pop_ratio in enumerate(pop_ratios):
self.assertAlmostEqual(pop_ratio, expected_pop_ratios[i])
uppmaboss_sim.save('results')
uppmaboss_sim.results[0].plot_piechart()
expected_state_tnf = [
1.7e-05,
0.e+00,
0.e+00,
0.e+00,
5.0e-06,
0.e+00,
0.e+00,
0.e+00,
0.e+00,
0.e+00,
0.e+00,
0.e+00,
0.e+00,
]
for i, val in enumerate(
uppmaboss_sim.get_stepwise_probability_distribution(
).loc[:, "TNF"].values):
self.assertAlmostEqual(val, expected_state_tnf[i])
expected_node_tnf = [
0.736098, 0.542901, 0.507657, 0.541154, 0.555409, 0.562324,
0.576159, 0.598795, 0.622031, 0.644684, 0.666123, 0.688512, 0.70853
]
for i, val in enumerate(
uppmaboss_sim.get_nodes_stepwise_probability_distribution(
nodes=["TNF"]).loc[:, "TNF"].values):
self.assertAlmostEqual(val, expected_node_tnf[i])
expected_sum = [
0.719123,
0.446561,
0.37057,
0.405835,
0.425728,
0.41935,
0.412577,
0.413467,
0.414721,
0.412329,
0.405407,
0.396948,
0.384865,
]
for i, val in enumerate(
uppmaboss_sim.get_stepwise_probability_distribution(
include=["TNF"], exclude=["NFkB"]).sum(axis=1).values):
self.assertAlmostEqual(val, expected_sum[i])
following_sim = UpdatePopulation(sim,
join(dirname(__file__),
"CellFate_1h.upp"),
previous_run=uppmaboss_sim)
following_sim.run()
def test_uppmaboss_write(self):
sim = load(
"https://raw.githubusercontent.com/sysbio-curie/UPMaBoSS-docker/master/CellFate/CellFateModel_uppmaboss.bnd",
"https://raw.githubusercontent.com/sysbio-curie/UPMaBoSS-docker/master/CellFate/CellFateModel_uppmaboss.cfg"
)
uppmaboss_model = UpdatePopulation(sim)
uppmaboss_model.setDivisionNode("Division")
uppmaboss_model.setDeathNode("Death")
uppmaboss_model.setExternalVariable(
"$TNF_induc", "$ProdTNF_NFkB*p[(NFkB,Death) = (1,0)]")
uppmaboss_model.setStepNumber(12)
uppmaboss_sim = uppmaboss_model.run('defined')
expected_pop_ratios = [
1.0, 0.9218339999999924, 0.8467423241939606, 0.8180987248510877,
0.7990468417467085, 0.7717098511967935, 0.7300537251389624,
0.677575273214723, 0.6208988119113313, 0.5665235984581267,
0.5183656934475426, 0.4771136331972621, 0.4430243412189205
]
pop_ratios = uppmaboss_sim.get_population_ratios('WT').values.tolist()
for i, pop_ratio in enumerate(pop_ratios):
self.assertAlmostEqual(pop_ratio, expected_pop_ratios[i])