diff --git a/doc/htmldoc/examples/index.rst b/doc/htmldoc/examples/index.rst index cbd061272b..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 @@ -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 `_: 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) @@ -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 index af5fd66aa0..ade7f815e9 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/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 814f616189..1279f7765f 100644 --- 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_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 `. 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:: @@ -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 new file mode 100644 index 0000000000..c834d8e0d9 --- /dev/null +++ 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 `. + +We have a detailed guide on :ref:`spatially-structured 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 index 630fb67fcf..2c236824fa 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