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Improve discoverablility of network models in NEST docs #3428

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12 changes: 8 additions & 4 deletions doc/htmldoc/examples/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ PyNEST examples
===============

.. grid:: 1 1 2 3
:gutter: 1

.. grid-item-card:: Simple networks
:img-top: ../static/img/pynest/mc_neuron.png
Expand Down Expand Up @@ -76,11 +77,13 @@ PyNEST examples
* :doc:`../auto_examples/brunel_alpha_evolution_strategies`


.. grid-item-card:: Cortical microcircuit (Potjans)
:img-top: ../auto_examples/Potjans_2014/potjans_2014_raster_plot.png

* :doc:`../auto_examples/Potjans_2014/index`
.. grid-item-card:: Large scale cortical network models
:img-top: ../static/img/network_model_sketch_mesocircuit.png

* :doc:`../auto_examples/Potjans_2014/index` (Potjans and Diesmann 2014)
* `The mesocircuit model <https://mesocircuit-model.readthedocs.io/en/latest/>`_: A layered cortical network with distance-dependent connectivity
* `The multi-area model <https://inm-6.github.io/multi-area-model/>`_: A network model of the visual cortex of the macaque monkey
* `The HuMAM model <https://github.com/INM-6/human-multi-area-model>`_: Multi-Scale Spiking Network Model of Human Cerebral Cortex


.. grid-item-card:: EI clustered network (Rostami et al)
Expand Down Expand Up @@ -161,6 +164,7 @@ PyNEST examples

* :doc:`../auto_examples/wang_decision_making`


.. grid:: 1 1 2 3

.. grid-item-card:: Gap junctions
Expand Down
2 changes: 1 addition & 1 deletion doc/htmldoc/get-started_index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,7 @@ Next steps: Create your own network model
* :doc:`Brunel network </auto_examples/brunel_alpha_nest>`: A random balanced network
* :doc:`The microcircuit model <../auto_examples/Potjans_2014/index>`: A network model example based on Potjans and Diesman 2014
* `The mesocircuit model <https://mesocircuit-model.readthedocs.io/en/latest/>`_: A layered cortical network with distance-dependent connectivity
* The `multi-area model <https://inm-6.github.io/multi-area-model/>`_: A network model of the visual cortex of the macaque monkey
* `The multi-area model <https://inm-6.github.io/multi-area-model/>`_: A network model of the visual cortex of the macaque monkey



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18 changes: 8 additions & 10 deletions doc/htmldoc/index.rst
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Expand Up @@ -46,31 +46,29 @@ Welcome to the NEST Simulator documentation!
:data-bs-ride: carousel

.. figure:: static/img/network_model_sketch_mesocircuit.png
:target: networks/index.html


Create spatially structured networks

Create large network models

.. figure:: static/img/astrocyte_interaction.png

:target: auto_examples/astrocytes/index.html

Inspect neuron and astrocyte interactions


.. figure:: static/img/hpc_benchmark_connectivity.svg

:target: auto_examples/hpc_benchmark.html

Test perfomance and benchmarks

.. figure:: static/img/pong_sim.gif

:target: auto_examples/pong/run_simulations.html

Simulate a game of PONG with NEST

.. figure:: static/img/gapjunctions.png

.. figure:: static/img/pynest/eprop_supervised_classification_infrastructure.png
:target: auto_examples/eprop_plasticity/index.html

Explore synapse types like gap junctions
Explore eligibility propagation plasticity

.. grid-item::

Expand Down
40 changes: 38 additions & 2 deletions doc/htmldoc/models/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,34 @@ Model directory
===============


What type of model?
-------------------

NEST has over 100 models, choose an option for finding the one you need!


.. grid::

.. grid-item-card::
:columns: 4
:link: network_models
:link-type: ref

**Network Models**
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Lower-case "models"?




.. grid-item-card::
:columns: 4
:link: model_selector
:link-type: ref

**Neurons, synapses, and devices**
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Instead of these cards, I suggest to start the page with the section "What we mean by models" that is currently further down (https://nest-simulator--3428.org.readthedocs.build/en/3428/models/index.html#what-we-mean-by-models). This section should also mention devices.

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This was discussed before, and the decision was made that we want to see the model selector near the top, so this was pushed further down. but maybe we can add a link at the top of the page with the cards like 'what's the difference?'

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@jessica-mitchell I think for a new user it might be unclear that the model selector does not refer to network models after showing the cards of both. Yes, the "What's the difference?" already helps. In addition, I suggest to extend "Select a tag to display corresponding models." to "Select a tag to display corresponding neuron, synapse or device models."

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Maybe "Neuron, synapse, and device models"?

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Technically the devices are not 'models', at least how I understand we define them. I did add some text below in the 'what we mean by models' section to explain a bit more. Hopefully without confusing it more.


:ref:`What's the difference? <model_meaning>`



.. _model_selector:

Model selector
Expand Down Expand Up @@ -110,11 +136,16 @@ The term `models` in the context of NEST (and the field of computational neurosc
implementations of these conceptual entities. Most of the models in
NEST are based on either peer-reviewed publications or text books
like [1]_. This is what we mean for models in our model directory.
Note that **devices** are not models but are mechanisms to generate or read out
signals, like spikes. We list them together with neurons and synapses since they
are required to be able to produce and analyze neuron and synapse activity.

2. **Network models**. These models are created from individual neuron
and synapse models using the different commands provided by the
:ref:`PyNEST API <pynest_api>`. Examples for such network models
can be found :doc:`here </examples/index>`.
:ref:`PyNEST API <pynest_api>`. Network models have a defined population
and connectivity, with initial conditions, along with specific neuron and synapse models.
We have :doc:`a variety of examples for network models </examples/index>` and specifically,
:doc:`large scale networks examples </networks/index>`.

.. seealso::

Expand Down Expand Up @@ -149,3 +180,8 @@ References
{% for keys in model_dict %}
{{ keys | replace(".html", "") }}
{% endfor %}

.. toctree::
:hidden:

../networks/index
51 changes: 51 additions & 0 deletions doc/htmldoc/networks/index.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,51 @@
.. _network_models:

Network Models
==============

Here we have several examples of large-scale network models developed for NEST.

You can see how to build other networks for various neuron, synapse and device types in our
:doc:`examples gallery </examples/index>`.

We have a detailed guide on :ref:`spatially-structured networks <spatial_networks>` as well.



.. grid:: 1 2 3 4
:gutter: 1

.. grid-item-card:: Brunel Network
:columns: 4
:link: /auto_examples/brunel_alpha_nest
:link-type: doc

A random balanced network

.. grid-item-card:: Microcircuit Model
:columns: 4
:link: /auto_examples/Potjans_2014/index
:link-type: doc

A network model example based on Potjans and Diesman 2014


.. grid-item-card:: Mesocircuit Model
:columns: 4
:link: https://mesocircuit-model.readthedocs.io/en/latest/

A layered cortical network with distance-dependent connectivity


.. grid-item-card:: Multi-area Model
:columns: 4
:link: https://inm-6.github.io/multi-area-model/

A network model of the visual cortex of the macaque monkey


.. grid-item-card:: HuMAM model
:columns: 4
:link: https://github.com/INM-6/human-multi-area-model

Multi-Scale Spiking Network Model of Human Cerebral Cortex
2 changes: 1 addition & 1 deletion doc/htmldoc/static/img/excalidraw_nestconcept_horiz.svg
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