Merge pull request #3428 from jessica-mitchell/network-docs

jessica-mitchell · web-flow · commit 86f5e379372d · 2025-08-21T09:20:21.000+02:00
Improve discoverablility of network models in NEST docs
diff --git a/doc/htmldoc/examples/index.rst b/doc/htmldoc/examples/index.rst
@@ -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
@@ -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)
@@ -161,6 +164,7 @@ PyNEST examples
 
            * :doc:`../auto_examples/wang_decision_making`
 
+
 .. grid:: 1 1 2 3
 
     .. grid-item-card:: Gap junctions
diff --git a/doc/htmldoc/get-started_index.rst b/doc/htmldoc/get-started_index.rst
@@ -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
 
 
 
diff --git a/doc/htmldoc/index.rst b/doc/htmldoc/index.rst
@@ -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::
 
diff --git a/doc/htmldoc/models/index.rst b/doc/htmldoc/models/index.rst
@@ -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**
+
+
+
+   .. grid-item-card::
+      :columns: 4
+      :link: model_selector
+      :link-type: ref
+
+      **Neurons, synapses, and devices**
+
+:ref:`What's the difference? <model_meaning>`
+
+
+
 .. _model_selector:
 
 Model selector
@@ -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::
 
@@ -149,3 +180,8 @@ References
     {% for keys in model_dict %}
     {{ keys | replace(".html", "") }}
     {% endfor %}
+
+.. toctree::
+   :hidden:
+
+   ../networks/index
diff --git a/doc/htmldoc/networks/index.rst b/doc/htmldoc/networks/index.rst
@@ -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
diff --git a/doc/htmldoc/static/img/excalidraw_nestconcept_horiz.svg b/doc/htmldoc/static/img/excalidraw_nestconcept_horiz.svg
