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In [1]:
import tellurium as te, tempfile, os
te.setDefaultPlottingEngine('matplotlib')
%matplotlib inline
antimony_str = '''
model myModel
S1 -> S2; k1*S1
S1 = 10; S2 = 0
k1 = 1
end
'''
phrasedml_str = '''
model1 = model "myModel"
sim1 = simulate uniform(0, 5, 100)
task1 = run sim1 on model1
plot "Figure 1" time vs S1, S2
'''
# create an inline OMEX (inline representation of a COMBINE archive)
# from the antimony and phrasedml strings
inline_omex = '\n'.join([antimony_str, phrasedml_str])
# execute the inline OMEX
te.executeInlineOmex(inline_omex)
# export to a COMBINE archive
workingDir = tempfile.mkdtemp(suffix="_omex")
te.exportInlineOmex(inline_omex, os.path.join(workingDir, 'archive.omex'))
In [2]:
te.executeCombineArchive(os.path.join(workingDir, 'archive.omex'))
Out[2]:
{'c:\\users\\kirich~1\\appdata\\local\\temp\\tmpbllk1j\\main.xml': {'code': u'r"""\n####################################################################################################\n tellurium 2.0.12\n-+++++++++++++++++- Python Environment for Modeling and Simulating Biological Systems\n .+++++++++++++++.\n .+++++++++++++. Homepage: http://tellurium.analogmachine.org/\n-//++++++++++++/. -:/-` Documentation: https://tellurium.readthedocs.io/en/latest/index.html\n.----:+++++++/.++ .++++/ Forum: https://groups.google.com/forum/#!forum/tellurium-discuss\n :+++++: .+:` .--++ Bug reports: https://github.com/sys-bio/tellurium/issues\n -+++- ./+:-://. Repository: https://github.com/sys-bio/tellurium\n .+. `...`\n\nSED-ML simulation experiments: http://www.sed-ml.org/\n sedmlDoc: L1V2 \n inputType: \'SEDML_FILE\'\n workingDir: \'c:\\users\\kirich~1\\appdata\\local\\temp\\tmpbllk1j\'\n saveOutputs: \'False\'\n outputDir: \'None\'\n plottingEngine: \'<MatplotlibEngine>\'\n\nWindows-7-6.1.7601-SP1\npython 2.7.13 (v2.7.13:a06454b1afa1, Dec 17 2016, 20:53:40) [MSC v.1500 64 bit (AMD64)]\n####################################################################################################\n"""\nimport tellurium as te\nfrom roadrunner import Config\nfrom tellurium.sedml.mathml import *\nfrom tellurium.sedml.tesedml import process_trace, terminate_trace, fix_endpoints\n\nimport numpy as np\nimport matplotlib.pyplot as plt\nimport mpl_toolkits.mplot3d\ntry:\n import tesedml as libsedml\nexcept ImportError:\n import libsedml\nimport pandas\nimport os.path\nConfig.LOADSBMLOPTIONS_RECOMPILE = True\n\nworkingDir = r\'c:\\users\\kirich~1\\appdata\\local\\temp\\tmpbllk1j\'\n\n# --------------------------------------------------------\n# Models\n# --------------------------------------------------------\n# Model <model1>\nmodel1 = te.loadSBMLModel(os.path.join(workingDir, \'myModel.xml\'))\n\n\n\n\n# --------------------------------------------------------\n# Tasks\n# --------------------------------------------------------\n# Task <task1>\n# Task: <task1>\ntask1 = [None]\nmodel1.setIntegrator(\'cvode\')\nif model1.conservedMoietyAnalysis == True: model1.conservedMoietyAnalysis = False\nmodel1.timeCourseSelections = [\'[S1]\', \'[S2]\', \'time\']\nmodel1.reset()\ntask1[0] = model1.simulate(start=0.0, end=5.0, steps=100)\n\n# --------------------------------------------------------\n# DataGenerators\n# --------------------------------------------------------\n# DataGenerator <plot_0_0_0>\n__var__time = np.concatenate([sim[\'time\'] for sim in task1])\nif len(__var__time.shape) == 1:\n __var__time.shape += (1,)\nplot_0_0_0 = __var__time\n# DataGenerator <plot_0_0_1>\n__var__S1 = np.concatenate([sim[\'[S1]\'] for sim in task1])\nif len(__var__S1.shape) == 1:\n __var__S1.shape += (1,)\nplot_0_0_1 = __var__S1\n# DataGenerator <plot_0_1_1>\n__var__S2 = np.concatenate([sim[\'[S2]\'] for sim in task1])\nif len(__var__S2.shape) == 1:\n __var__S2.shape += (1,)\nplot_0_1_1 = __var__S2\n\n# --------------------------------------------------------\n# Outputs\n# --------------------------------------------------------\n# Output <plot_0>\n_engine = te.getPlottingEngine()\ntefig = _engine.newFigure(title=\'Figure 1\', xtitle=\'time\')\n\nfor k in range(plot_0_0_0.shape[1]):\n extra_args = {}\n if k == 0:\n extra_args[\'name\'] = \'S1\'\n tefig.addXYDataset(plot_0_0_0[:,k], plot_0_0_1[:,k], color=\'C0\', tag=\'tag0\', **extra_args)\nfor k in range(plot_0_0_0.shape[1]):\n extra_args = {}\n if k == 0:\n extra_args[\'name\'] = \'S2\'\n tefig.addXYDataset(plot_0_0_0[:,k], plot_0_1_1[:,k], color=\'C1\', tag=\'tag1\', **extra_args)\nfig = tefig.render()\n\n####################################################################################################',
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In [ ]:
Content source: sys-bio/tellurium
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