.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/astrocytes/astrocyte_single.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_astrocytes_astrocyte_single.py>`
        to download the full example code

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_astrocytes_astrocyte_single.py:


A model using a single astrocyte with calcium dynamics
-------------------------------------------------------

.. only:: html

----

 Run this example as a Jupyter notebook:

  .. card::
    :width: 25%
    :margin: 2
    :text-align: center
    :link: https://lab.ebrains.eu/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Fnest%2Fnest-simulator-examples&urlpath=lab%2Ftree%2Fnest-simulator-examples%2Fnotebooks%2Fnotebooks%2Fastrocytes%2Fastrocyte_single.ipynb&branch=main
    :link-alt: JupyterHub service

    .. image:: https://nest-simulator.org/TryItOnEBRAINS.png


.. grid:: 1 1 1 1
   :padding: 0 0 2 0

   .. grid-item::
     :class: sd-text-muted
     :margin: 0 0 3 0
     :padding: 0 0 3 0
     :columns: 4

     See :ref:`our guide <run_jupyter>` for more information and troubleshooting.

----


This script simulates an astrocyte with the model ``astrocyte_lr_1994``, which
implements the dynamics in the astrocyte based on [1]_, [2]_, and
[3]_. Recordings are made for two variables in the astrocyte,
inositol 1,4,5-trisphosphate (IP3) and cytosolic calcium. The astrocyte is driven
by a Poissonian spike train which induces the
generation of IP3 in the astrocyte, which in turn influences the calcium dynamics in
the astrocyte.

See Also
~~~~~~~~

:doc:`astrocyte_interaction`

References
~~~~~~~~~~

.. [1] Li, Y. X., & Rinzel, J. (1994). Equations for InsP3 receptor-mediated
       [Ca2+]i oscillations derived from a detailed kinetic model: a
       Hodgkin-Huxley like formalism. Journal of theoretical Biology, 166(4),
       461-473. DOI: https://doi.org/10.1006/jtbi.1994.1041

.. [2] De Young, G. W., & Keizer, J. (1992). A single-pool inositol
       1,4,5-trisphosphate-receptor-based model for agonist-stimulated
       oscillations in Ca2+ concentration. Proceedings of the National Academy
       of Sciences, 89(20), 9895-9899. DOI:
       https://doi.org/10.1073/pnas.89.20.9895

.. [3] Nadkarni, S., & Jung, P. (2003). Spontaneous oscillations of dressed
       neurons: a new mechanism for epilepsy?. Physical review letters, 91(26),
       268101. DOI: https://doi.org/10.1103/PhysRevLett.91.268101

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Import all necessary modules for simulation and plotting.

.. GENERATED FROM PYTHON SOURCE LINES 61-65

.. code-block:: Python


    import matplotlib.pyplot as plt
    import nest


.. GENERATED FROM PYTHON SOURCE LINES 66-67

Set parameters for the simulation.

.. GENERATED FROM PYTHON SOURCE LINES 67-76

.. code-block:: Python


    # simulation time
    sim_time = 60000
    # astrocyte parameters
    params_astro = {"IP3_0": 0.16}
    # Poisson input for the astrocyte
    poisson_rate = 1.0
    poisson_weight = 0.1


.. GENERATED FROM PYTHON SOURCE LINES 77-78

Create astrocyte and devices and connect them.

.. GENERATED FROM PYTHON SOURCE LINES 78-85

.. code-block:: Python


    astrocyte = nest.Create("astrocyte_lr_1994", params=params_astro)
    ps_astro = nest.Create("poisson_generator", params={"rate": poisson_rate})
    mm_astro = nest.Create("multimeter", params={"record_from": ["IP3", "Ca_astro"]})
    nest.Connect(ps_astro, astrocyte, syn_spec={"weight": poisson_weight})
    nest.Connect(mm_astro, astrocyte)


.. GENERATED FROM PYTHON SOURCE LINES 86-87

Run simulation and get results.

.. GENERATED FROM PYTHON SOURCE LINES 87-91

.. code-block:: Python


    nest.Simulate(sim_time)
    data = mm_astro.events


.. GENERATED FROM PYTHON SOURCE LINES 92-93

Create and show plots.

.. GENERATED FROM PYTHON SOURCE LINES 93-103

.. code-block:: Python


    fig, axes = plt.subplots(2, 1, sharex=True, figsize=(6.4, 4.8), dpi=100)
    axes[0].plot(data["times"], data["IP3"])
    axes[1].plot(data["times"], data["Ca_astro"])
    axes[0].set_ylabel(r"[IP$_{3}$] ($\mu$M)")
    axes[1].set_ylabel(r"[Ca$^{2+}$] ($\mu$M)")
    axes[1].set_xlabel("Time (ms)")
    plt.tight_layout()
    plt.show()
    plt.close()


.. _sphx_glr_download_auto_examples_astrocytes_astrocyte_single.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: astrocyte_single.ipynb <astrocyte_single.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: astrocyte_single.py <astrocyte_single.py>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_