From 17813dc973c88626d6884fd7c5d16e82c3bfa327 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Wed, 19 Mar 2025 22:54:13 +0100 Subject: [PATCH 1/6] better illustrate network models --- doc/htmldoc/examples/index.rst | 10 ++++---- doc/htmldoc/get-started_index.rst | 2 +- doc/htmldoc/models/index.rst | 29 ++++++++++++++++++++++ doc/htmldoc/networks/index.rst | 40 +++++++++++++++++++++++++++++++ 4 files changed, 76 insertions(+), 5 deletions(-) create mode 100644 doc/htmldoc/networks/index.rst diff --git a/doc/htmldoc/examples/index.rst b/doc/htmldoc/examples/index.rst index dba7539b99..bec79a5694 100644 --- a/doc/htmldoc/examples/index.rst +++ b/doc/htmldoc/examples/index.rst @@ -76,11 +76,12 @@ 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 `_: A layered cortical network with distance-dependent connectivity + * `The multi-area model `_: A network model of the visual cortex of the macaque monkey .. grid-item-card:: EI clustered network (Rostami et al) @@ -161,6 +162,7 @@ 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 index 47330b633e..1ee245bf88 100644 --- 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 `: 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 `_: A layered cortical network with distance-dependent connectivity - * The `multi-area model `_: A network model of the visual cortex of the macaque monkey + * `The multi-area model `_: A network model of the visual cortex of the macaque monkey diff --git a/doc/htmldoc/models/index.rst b/doc/htmldoc/models/index.rst index 749a41ac40..5a716bb996 100644 --- a/doc/htmldoc/models/index.rst +++ b/doc/htmldoc/models/index.rst @@ -5,8 +5,32 @@ 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** + + + + .. _model_selector: Model selector @@ -153,3 +177,8 @@ 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 new file mode 100644 index 0000000000..7e4b4be0a6 --- /dev/null +++ b/doc/htmldoc/networks/index.rst @@ -0,0 +1,40 @@ +.. _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 `. + + +.. grid:: + :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 From 6d2611c94ba71983cf3f8238a4bd51aa4f7cbc02 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Thu, 20 Mar 2025 13:14:09 +0100 Subject: [PATCH 2/6] add humam --- doc/htmldoc/networks/index.rst | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/doc/htmldoc/networks/index.rst b/doc/htmldoc/networks/index.rst index 7e4b4be0a6..28c81d414c 100644 --- a/doc/htmldoc/networks/index.rst +++ b/doc/htmldoc/networks/index.rst @@ -38,3 +38,10 @@ You can see how to build other networks for various neuron, synapse and device t :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 From df06cc0114d4e5530c01ecc8c9e831c6345cd09d Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Thu, 20 Mar 2025 15:37:54 +0100 Subject: [PATCH 3/6] update link in svg and add HuMAM to examples --- doc/htmldoc/examples/index.rst | 1 + doc/htmldoc/static/img/excalidraw_nestconcept_horiz.svg | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/htmldoc/examples/index.rst b/doc/htmldoc/examples/index.rst index bec79a5694..fe95cd1edf 100644 --- a/doc/htmldoc/examples/index.rst +++ b/doc/htmldoc/examples/index.rst @@ -82,6 +82,7 @@ PyNEST examples * :doc:`../auto_examples/Potjans_2014/index` (Potjans and Diesmann 2014) * `The mesocircuit model `_: A layered cortical network with distance-dependent connectivity * `The multi-area model `_: A network model of the visual cortex of the macaque monkey + * `The HuMAM model `_: Multi-Scale Spiking Network Model of Human Cerebral Cortex .. grid-item-card:: EI clustered network (Rostami et al) diff --git a/doc/htmldoc/static/img/excalidraw_nestconcept_horiz.svg b/doc/htmldoc/static/img/excalidraw_nestconcept_horiz.svg index 6c8d09d8cd..5b0043c39a 100644 --- a/doc/htmldoc/static/img/excalidraw_nestconcept_horiz.svg +++ b/doc/htmldoc/static/img/excalidraw_nestconcept_horiz.svg @@ -18,4 +18,4 @@ - Experimental ProtocolsNeuron ModelsNetwork ModelsSynapse ModelsRecording DevicesStimulation DevicesData AnalysisConnection Rules + Experimental ProtocolsNeuron ModelsNetwork ModelsSynapse ModelsRecording DevicesStimulation DevicesData AnalysisConnection Rules From 0d118a68d2b59b09cbf1390b62310562b81e8feb Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Fri, 21 Mar 2025 08:59:42 +0100 Subject: [PATCH 4/6] fix grid --- doc/htmldoc/examples/index.rst | 1 + doc/htmldoc/networks/index.rst | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/htmldoc/examples/index.rst b/doc/htmldoc/examples/index.rst index ed372826b1..0ff124e048 100644 --- 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 diff --git a/doc/htmldoc/networks/index.rst b/doc/htmldoc/networks/index.rst index 28c81d414c..e53cce0e70 100644 --- a/doc/htmldoc/networks/index.rst +++ b/doc/htmldoc/networks/index.rst @@ -8,7 +8,7 @@ You can see how to build other networks for various neuron, synapse and device t :doc:`examples gallery `. -.. grid:: +.. grid:: 1 2 3 4 :gutter: 1 .. grid-item-card:: Brunel Network From 77acc5393316edc6e63204822bbe9351eb645ed7 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Tue, 19 Aug 2025 10:05:28 +0200 Subject: [PATCH 5/6] improve network model text, add links --- doc/htmldoc/index.rst | 18 ++++++++---------- doc/htmldoc/models/index.rst | 11 +++++++++-- doc/htmldoc/networks/index.rst | 4 ++++ 3 files changed, 21 insertions(+), 12 deletions(-) diff --git a/doc/htmldoc/index.rst b/doc/htmldoc/index.rst index a0a227d31a..7eb1ababea 100644 --- 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 index 4ace4ee0e5..c4b9ed0bb7 100644 --- a/doc/htmldoc/models/index.rst +++ b/doc/htmldoc/models/index.rst @@ -10,6 +10,7 @@ What type of model? NEST has over 100 models, choose an option for finding the one you need! + .. grid:: .. grid-item-card:: @@ -28,6 +29,7 @@ NEST has over 100 models, choose an option for finding the one you need! **Neurons, synapses, and devices** +:ref:`What's the difference? ` @@ -134,11 +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 `. Examples for such network models - can be found :doc:`here `. + :ref:`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 ` and specifically, + :doc:`large scale networks examples `. .. seealso:: diff --git a/doc/htmldoc/networks/index.rst b/doc/htmldoc/networks/index.rst index e53cce0e70..c834d8e0d9 100644 --- a/doc/htmldoc/networks/index.rst +++ b/doc/htmldoc/networks/index.rst @@ -4,9 +4,13 @@ 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 `. +We have a detailed guide on :ref:`spatially-structured networks ` as well. + + .. grid:: 1 2 3 4 :gutter: 1 From ff1166e8cc8724e3f914636a2e4884ab968bdb20 Mon Sep 17 00:00:00 2001 From: jessica-mitchell Date: Tue, 19 Aug 2025 12:09:55 +0200 Subject: [PATCH 6/6] Update doc/htmldoc/models/index.rst --- doc/htmldoc/models/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/htmldoc/models/index.rst b/doc/htmldoc/models/index.rst index c4b9ed0bb7..1279f7765f 100644 --- a/doc/htmldoc/models/index.rst +++ b/doc/htmldoc/models/index.rst @@ -18,7 +18,7 @@ NEST has over 100 models, choose an option for finding the one you need! :link: network_models :link-type: ref - **Network Models** + **Network models**