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Doc: Rename 'steadystate example'
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New title + some minor updates

Closes #1990
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dweindl committed Sep 19, 2023
1 parent a321e0f commit 6366406
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Showing 2 changed files with 11 additions and 10 deletions.
2 changes: 1 addition & 1 deletion binder/overview.ipynb
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"\n",
" Brief intro to AMICI for first-time users.\n",
"\n",
"* [Example \"steadystate\"](../python/examples/example_steadystate/ExampleSteadystate.ipynb)\n",
"* [SBML import, observation model, sensitivity analysis, data export and visualization](../python/examples/example_steadystate/ExampleSteadystate.ipynb)\n",
"\n",
" A more detailed introduction to the AMICI interface, demonstrating sensitivity analysis, various options, finite difference checks, ...\n",
"\n",
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19 changes: 10 additions & 9 deletions python/examples/example_steadystate/ExampleSteadystate.ipynb
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Expand Up @@ -4,9 +4,14 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# AMICI Python example \"steadystate\"\n",
"# SBML import, observation model, sensitivity analysis, data export and visualization\n",
"\n",
"This is an example using the [model_steadystate_scaled.sbml] model to demonstrate and test SBML import and AMICI Python interface."
"This is an example using the [model_steadystate_scaled.sbml] model to demonstrate:\n",
"\n",
"* SBML import\n",
"* specifying the observation model\n",
"* performing sensitivity analysis\n",
"* exporting and visualizing simulation results"
]
},
{
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"model_output_dir = model_name\n",
"\n",
"import libsbml\n",
"import importlib\n",
"import amici\n",
"import os\n",
"import sys\n",
"import numpy as np\n",
"import matplotlib.pyplot as plt"
]
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"metadata": {},
"outputs": [],
"source": [
"constantParameters = [\"k0\"]"
"constant_parameters = [\"k0\"]"
]
},
{
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" model_output_dir,\n",
" verbose=logging.INFO,\n",
" observables=observables,\n",
" constant_parameters=constantParameters,\n",
" constant_parameters=constant_parameters,\n",
" sigmas=sigmas,\n",
")"
]
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"metadata": {},
"outputs": [],
"source": [
"sys.path.insert(0, os.path.abspath(model_output_dir))\n",
"model_module = importlib.import_module(model_name)"
"model_module = amici.import_model_module(model_name, model_output_dir)"
]
},
{
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