Exemplos de Model em Python

Exemplo n.º 1

Arquivo: test_tgfb_smad.py Projeto: okadalabipr/biomass

import os
import shutil

import numpy as np

from biomass import Model, run_simulation
from biomass.models import tgfb_smad

model = Model(tgfb_smad.__package__).create()

for dir in ["figure", "simulation_data"]:
    if os.path.isdir(os.path.join(model.path, dir)):
        shutil.rmtree(os.path.join(model.path, dir))


def test_simulate_successful():
    x = model.pval()
    y0 = model.ival()
    assert model.problem.simulate(x, y0) is None


def test_run_simulation():
    run_simulation(model)
    simulated_value = np.load(
        os.path.join(
            model.path,
            "simulation_data",
            "simulations_original.npy",
        ))
    assert np.isfinite(simulated_value).all()

Exemplo n.º 2

import os
import shutil

import matplotlib.pyplot as plt
import numpy as np

from biomass import Model, run_simulation
from biomass.models import nfkb_pathway

model = Model(nfkb_pathway.__package__).create()

for dir in ["figure", "simulation_data"]:
    if os.path.isdir(os.path.join(model.path, dir)):
        shutil.rmtree(os.path.join(model.path, dir))


def test_simulate_successful():
    x = model.pval()
    y0 = model.ival()
    assert model.problem.simulate(x, y0) is None


def test_example_plot():
    assert run_simulation(model, viz_type="original") is None
    res = np.load(
        os.path.join(model.path, "simulation_data",
                     "simulations_original.npy"))

    fig = plt.figure(figsize=(9, 9))
    plt.rcParams["font.family"] = "Arial"
    plt.rcParams["font.size"] = 18

Exemplo n.º 3

import os
import shutil

import numpy as np

from biomass import (
    Model,
    OptimizationResults,
    optimize,
    optimize_continue,
    run_analysis,
    run_simulation,
)
from biomass.models import mapk_cascade

model = Model(mapk_cascade.__package__).create()

for dir in [
    "figure",
    "simulation_data",
    "sensitivity_coefficients",
    "optimization_results",
]:
    if os.path.isdir(os.path.join(model.path, dir)):
        shutil.rmtree(os.path.join(model.path, dir))


def test_simulate_successful():
    x = model.pval()
    y0 = model.ival()
    assert model.problem.simulate(x, y0) is None

Exemplo n.º 4

import os
import shutil

import matplotlib.pyplot as plt
import numpy as np

from biomass import Model, run_simulation
from biomass.models import insulin_signaling

model = Model(insulin_signaling.__package__).create()

for dir in ["figure", "simulation_data"]:
    if os.path.isdir(os.path.join(model.path, dir)):
        shutil.rmtree(os.path.join(model.path, dir))


def test_simulate_successful():
    x = model.pval()
    y0 = model.ival()
    assert model.problem.simulate(x, y0) is None


def test_example_plot():
    assert run_simulation(model) is None
    res = np.load(
        os.path.join(model.path, "simulation_data",
                     "simulations_original.npy"))

    plt.figure(figsize=(8, 8))
    plt.rcParams["font.family"] = "Arial"
    plt.rcParams["xtick.direction"] = "in"

Exemplo n.º 5

import os
import shutil
from distutils.dir_util import copy_tree

import numpy as np
import pytest
from scipy.optimize import OptimizeResult, differential_evolution

from biomass import Model, OptimizationResults, optimize, run_analysis, run_simulation
from biomass.estimation import ExternalOptimizer
from biomass.models import Nakakuki_Cell_2010

# from biomass import run_analysis

model = Model(Nakakuki_Cell_2010.__package__).create()


def test_initialization():
    for dir in [
            "figure", "out", "simulation_data", "sensitivity_coefficients"
    ]:
        if os.path.isdir(os.path.join(model.path, dir)):
            shutil.rmtree(os.path.join(model.path, dir))
    os.mkdir(os.path.join("biomass", "models", "Nakakuki_Cell_2010", "out"))
    copy_tree(
        os.path.join("tests", "out"),
        os.path.join("biomass", "models", "Nakakuki_Cell_2010", "out"),
    )


def test_run_simulation():

Exemplo n.º 6

import os
import shutil

import matplotlib.pyplot as plt
import numpy as np

from biomass import Model, run_simulation
from biomass.models import circadian_clock

model = Model(circadian_clock.__package__).create()

for dir in ["figure", "simulation_data"]:
    if os.path.isdir(os.path.join(model.path, dir)):
        shutil.rmtree(os.path.join(model.path, dir))


def test_simulate_successful():
    x = model.pval()
    y0 = model.ival()
    assert model.problem.simulate(x, y0) is None


def test_example_plot():
    assert run_simulation(model, viz_type="original") is None
    res = np.load(
        os.path.join(model.path, "simulation_data",
                     "simulations_original.npy"))

    plt.rcParams["font.size"] = 16
    fig, ax1 = plt.subplots(figsize=(6, 4))
    ax2 = ax1.twinx()