overhaul experimental conditions notebook (#1460)

* overhaul experimental conditions notebook * fix kernel * Apply suggestions from code review Co-authored-by: Daniel Weindl <[email protected]> * update and rerun notebook * fix kernel Co-authored-by: Daniel Weindl <[email protected]>
AMICI-dev · Mar 15, 2021 · 9d36032 · 9d36032
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diff --git a/documentation/ExampleExperimentalConditions.ipynb b/documentation/ExampleExperimentalConditions.ipynb
@@ -0,0 +1 @@
+../python/examples/example_presimulation/ExampleExperimentalConditions.ipynb
diff --git a/documentation/GettingStarted.ipynb b/documentation/GettingStarted.ipynb
@@ -185,7 +185,7 @@
  "cell_type": "markdown",
  "metadata": {},
  "source": [
- "This notebook only explains the basics of AMICI simulations. In general, AMICI simulations are highly customizable and can also be used to simulate sensitivities. The [ExampleSteadystate](https://amici.readthedocs.io/en/latest/ExampleSteadystate.html) notebook in this folder gives more detail about the model employed here and goes into the basics of sensitivity analysis. The [ExampleEquilibrationLogic](https://amici.readthedocs.io/en/latest/ExampleEquilibrationLogic.html) notebook, builds on this by using a modified version of this model to give detailed insights into the methods and options to compute steady states before and after simulations, as well as respective sensitivities. The [Presimulation example](https://amici.readthedocs.io/en/latest/model_presimulation.html) notebook, goes into the details of how even more complex experimental setups, such as addition of drugs at predefined timepoints, can be simulated in AMICI. Finally, the [petab](https://amici.readthedocs.io/en/latest/petab.html) notebook explains how standardized definitions of experimental data and conditions in the [PEtab](https:/PEtab-dev/PEtab) format can be imported in AMICI."
+ "This notebook only explains the basics of AMICI simulations. In general, AMICI simulations are highly customizable and can also be used to simulate sensitivities. The [ExampleSteadystate](https://amici.readthedocs.io/en/latest/ExampleSteadystate.html) notebook in this folder gives more detail about the model employed here and goes into the basics of sensitivity analysis. The [ExampleEquilibrationLogic](https://amici.readthedocs.io/en/latest/ExampleEquilibrationLogic.html) notebook, builds on this by using a modified version of this model to give detailed insights into the methods and options to compute steady states before and after simulations, as well as respective sensitivities. The [ExampleExperimentalConditions example](https://amici.readthedocs.io/en/latest/ExampleExperimentalConditions.html) notebook, goes into the details of how even more complex experimental setups, such as addition of drugs at predefined timepoints, can be simulated in AMICI. Finally, the [petab](https://amici.readthedocs.io/en/latest/petab.html) notebook explains how standardized definitions of experimental data and conditions in the [PEtab](https:/PEtab-dev/PEtab) format can be imported in AMICI."
  ]
  }
  ],

diff --git a/documentation/model_presimulation.ipynb b/documentation/model_presimulation.ipynb
diff --git a/documentation/python_interface.rst b/documentation/python_interface.rst
@@ -125,7 +125,7 @@ Examples
  GettingStarted.ipynb
  ExampleSteadystate.ipynb
  petab.ipynb
- model_presimulation.ipynb
+ ExampleExperimentalConditions.ipynb
  ExampleEquilibrationLogic.ipynb
 
 

diff --git a/python/examples/example_presimulation/ExampleExperimentalConditions.ipynb b/python/examples/example_presimulation/ExampleExperimentalConditions.ipynb
diff --git a/python/examples/example_presimulation/model_presimulation.ipynb b/python/examples/example_presimulation/model_presimulation.ipynb