diff --git a/doc/htmldoc/attribution-list.rst b/doc/htmldoc/attribution-list.rst index 10c3f23ab8..6a8c290501 100644 --- a/doc/htmldoc/attribution-list.rst +++ b/doc/htmldoc/attribution-list.rst @@ -19,7 +19,6 @@ For use in Forschungszentrum Juelich GmBH. Cite the author of the work if using. Icons provided by Flaticon -------------------------- - * Neuron icons created by Nadiinko - Flaticon * Neuron icons created by Freepik - Flaticon * Monitor icons created by Icongeek26 - Flaticon diff --git a/doc/htmldoc/get-started_index.rst b/doc/htmldoc/get-started_index.rst index 0508e39178..43ae7d9954 100644 --- a/doc/htmldoc/get-started_index.rst +++ b/doc/htmldoc/get-started_index.rst @@ -1,26 +1,232 @@ .. _tutorials_guides: -Tutorials and guides +Tutorials and Guides ==================== + +First steps: Learn how to use NEST +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + + +.. grid:: 1 1 3 3 + :gutter: 1 + + .. grid-item-card:: + :class-header: sd-d-flex-row sd-align-minor-center sd-bg-primary sd-text-white + + |start| PyNEST Tutorial + ^^^ + + A :ref:`step-by-step tutorial ` that introduces NEST concepts + and allows you to develop your first script. + + .. grid-item-card:: + :class-header: sd-d-flex-row sd-align-minor-center sd-bg-primary sd-text-white + + |write| A basic one neuron example + ^^^ + + :doc:`One neuron example `: A breakdown of a basic NEST script using one neuron, + to showcase the basic structure of a simulation. + + .. grid-item-card:: + :class-header: sd-d-flex-row sd-align-minor-center sd-bg-primary sd-text-white + + |interactive| Interactive graphical interface + ^^^ + + :doc:`NEST Desktop `: If you prefer a graphical approach, NEST Desktop offers an interactive graphical + format for creating neural networks. + +Next steps: Create your own network model +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. grid:: 1 1 3 3 + :gutter: 1 + + .. grid-item-card:: + :class-header: sd-d-flex-row sd-align-minor-center sd-bg-info sd-text-white + :columns: 4 + + |math| Create neurons, synapses, and devices + ^^^ + + * :ref:`modelsmain`: Discover the available models in NEST + or create and customize models with :doc:`NESTML ` + + + .. grid-item-card:: + :class-header: sd-d-flex-row sd-align-minor-center sd-bg-info sd-text-white + :columns: 4 + + |random| Connect neurons, synapses, and devices + ^^^ + + * :ref:`connection_management`: A guide to building connections in NEST + * :ref:`spatial_networks`: A deep dive into building 2D and 3D networks + + .. grid-item-card:: + :class-header: sd-d-flex-row sd-align-minor-center sd-bg-info sd-text-white + :columns: 4 + + |device| Device management + ^^^ + + * :ref:`stimulate_network`: An overview of how to stimulate the network + * :ref:`Get data from simulations `: How to record data from neurons + and synapses + + + .. grid-item-card:: + :class-header: sd-d-flex-row sd-align-minor-center sd-bg-dark sd-text-white + + |simulate| Simulate your network + ^^^ + + * :ref:`run_simulations`: A guide describing various factors in running simulations + * :ref:`random_numbers`: A guide to how random numbers are used in network simulations + + + .. grid-item-card:: + :class-header: sd-d-flex-row sd-align-minor-center sd-bg-dark sd-text-white + + |python| Handling nodes and connections + ^^^ + + * :ref:`Manipulating nodes (neurons and devices) `: understand basic functionality of nodes + * :ref:`Manipulating connections (synapses) `: understand basic functionality of connections + * :ref:`param_ex`: explore how to use parameter objects in NEST + + + + .. grid-item-card:: + :class-header: sd-d-flex-row sd-align-minor-center sd-bg-dark sd-text-white + + |gallery| Example gallery + ^^^ + + * Explore our :ref:`PyNEST example networks ` that showcase the numerous features and models + in NEST + + .. grid-item-card:: + :class-header: sd-d-flex-row sd-align-minor-center sd-bg-success sd-text-white + + |network| Large network models + ^^^ + + Discover how to build large and more complex network models with these examples: + + * :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 + + + + .. grid-item-card:: + :class-header: sd-d-flex-row sd-align-minor-center sd-bg-success sd-text-white + + |parallel| Parallel computing + ^^^ + + * :ref:`parallel_computing`: How NEST handles thread parallel and distributed computing + +---- + +More topics +~~~~~~~~~~~ + + +.. grid:: 1 1 2 3 + :gutter: 1 + + .. grid-item-card:: + :class-header: sd-d-flex-row sd-align-minor-center sd-bg-info sd-text-white + + |neuron| More about neurons + ^^^ + + * :ref:`sim_precise_spike_times` + * :ref:`exact_integration` + + .. grid-item-card:: + :class-header: sd-d-flex-row sd-align-minor-center sd-bg-info sd-text-white + + |synapse| More about synapses + ^^^ + + + * :ref:`sim_gap_junctions` + * :ref:`weight_normalization` + + + + .. grid-item-card:: + :class-header: sd-d-flex-row sd-align-minor-center sd-bg-info sd-text-white + + |hpc| High performance computers (HPC) + ^^^ + + * :ref:`optimize_performance`: Guides to optimize NEST performance in large scale simulations + * :ref:`built_in_timers`: A guide to the various timers available in NEST + * :ref:`benchmark`: How to use the beNNch framework + + + + + +.. grid:: 1 1 2 3 + :gutter: 1 + + + + .. grid-item-card:: + :class-header: sd-d-flex-row sd-align-minor-center sd-bg-dark sd-text-white + + |connect| Connect to other tools + ^^^ + + * :ref:`nest_server`: A guide showcasing how to interact with NEST via a RESTful API + * :ref:`SONATA with NEST `: Guide to using the SONATA format + * :ref:`MUSIC Tutorial `: how to transmit data between applications + with the MUSIC interface, step-by-step + * :ref:`nest_music`: Additional guide for building scripts with MUSIC + + + .. grid-item-card:: + :class-header: sd-d-flex-row sd-align-minor-center sd-bg-dark sd-text-white + + + |refresh| Get the latest changes + ^^^ + + * :ref:`Update 2.X scripts to 3.X ` + * :ref:`See the latest changes ` + + .. toctree:: :maxdepth: 1 :hidden: tutorials/index + tutorials/pynest_tutorial/index -.. grid:: 1 1 2 2 - :gutter: 1 - - .. grid-item-card:: |nav| Tutorials: Introduction to PyNEST - :class-title: sd-d-flex-row sd-align-minor-center - :link: tutorials - :link-type: ref +.. toctree:: + :maxdepth: 1 + :hidden: - .. grid-item-card:: |example| Topical guides - :class-title: sd-d-flex-row sd-align-minor-center - :link: guides - :link-type: ref + Neurons + Synapses and connections + Devices + Spatially-structured networks + High performance computing + NEST models + NEST and SONATA + Simulation behavior + Randomness in NEST + Built-in timers + Connect NEST with other tools + From NEST 2.x to 3.x .. toctree:: :hidden: @@ -28,4 +234,32 @@ Tutorials and guides understand_index .. |nav| image:: static/img/GPS-Settings-256_nest.svg -.. |example| image:: static/img/Documents-02-256_nest.svg +.. |script| image:: static/img/script_white.svg + :scale: 20% +.. |start| image:: static/img/start_white.svg + :scale: 40% +.. |user| image:: static/img/020-user.svg +.. |teacher| image:: static/img/014-teacher.svg +.. |admin| image:: static/img/001-shuttle.svg +.. |dev| image:: static/img/dev_orange.svg +.. |nestml| image:: static/img/nestml-logo.png + :scale: 15% +.. |synapse| image:: static/img/synapse_white.svg +.. |neuron| image:: static/img/neuron_white.svg +.. |glossary| image:: static/img/glossary_white.svg +.. |git| image:: static/img/git_white.svg +.. |refresh| image:: static/img/refresh_white.svg +.. |hpc| image:: static/img/hpc_white.svg +.. |random| image:: static/img/random_white.svg +.. |math| image:: static/img/math_white.svg +.. |network| image:: static/img/network_brain_white.svg +.. |device| image:: static/img/device_white.svg +.. |connect| image:: static/img/connect_white.svg +.. |sonata| image:: static/img/sonata_white.svg +.. |write| image:: static/img/write_nest_white.svg + :scale: 60% +.. |parallel| image:: static/img/parallel_white.svg +.. |simulate| image:: static/img/simulate_white.svg +.. |interactive| image:: static/img/interactive_white.svg +.. |python| image:: static/img/python_white.svg +.. |gallery| image:: static/img/gallery_white.svg diff --git a/doc/htmldoc/index.rst b/doc/htmldoc/index.rst index 3833973da5..8071789531 100644 --- a/doc/htmldoc/index.rst +++ b/doc/htmldoc/index.rst @@ -23,7 +23,7 @@ Welcome to the NEST Simulator documentation :shadow: :color: primary - Get started with NEST + Start exploring NEST .. grid-item:: diff --git a/doc/htmldoc/static/css/custom.css b/doc/htmldoc/static/css/custom.css index 49b96cfaed..611dbdbc3e 100644 --- a/doc/htmldoc/static/css/custom.css +++ b/doc/htmldoc/static/css/custom.css @@ -20,6 +20,8 @@ --nest-dkblue: #072f42; --nest-brown: #4b210c; --sd-color-primary: var(--nest-orange); + --sd-color-secondary: #666; + --sd-color-warning: #f22; --sd-color-success: var(--nest-brown); --sd-color-dark: var(--nest-dkblue); --sd-color-primary-highlight: #e05a2d; @@ -222,7 +224,7 @@ 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diff --git a/doc/htmldoc/tutorials/index.rst b/doc/htmldoc/tutorials/index.rst index 153873dc4d..93bf132910 100644 --- a/doc/htmldoc/tutorials/index.rst +++ b/doc/htmldoc/tutorials/index.rst @@ -1,36 +1,28 @@ -.. _tutorials: - -Introduction to PyNEST - tutorial series -======================================== +.. _MUSIC_tutorials: +MUSIC Tutorials +=============== Learn step-by-step how to develop your PyNEST scripts and simulate your first networks! .. grid:: 1 1 1 1 - .. grid-item-card:: Introduction to PyNEST - * :ref:`pynest_tutorial_1` - * :ref:`pynest_tutorial_2` - * :ref:`pynest_tutorial_3` - * :ref:`pynest_tutorial_4` + .. grid-item-card:: MUSIC tutorial -.. grid:: + * :ref:`music_tutorial_1` + * :ref:`music_tutorial_2` + * :ref:`music_tutorial_3` + * :ref:`music_tutorial_4` + * :ref:`music_sli` + * :ref:`tips_music` - .. grid-item-card:: Video tutorial - :columns: 6 - :link: videos/index - :link-type: doc .. toctree:: :maxdepth: 1 :hidden: - pynest_tutorial/part_1_neurons_and_simple_neural_networks - pynest_tutorial/part_2_populations_of_neurons - pynest_tutorial/part_3_connecting_networks_with_synapses - pynest_tutorial/part_4_spatially_structured_networks music_tutorial/music_tutorial_1 music_tutorial/music_tutorial_2 music_tutorial/music_tutorial_sli diff --git a/doc/htmldoc/tutorials/pynest_tutorial/index.rst b/doc/htmldoc/tutorials/pynest_tutorial/index.rst new file mode 100644 index 0000000000..b05895d9f2 --- /dev/null +++ b/doc/htmldoc/tutorials/pynest_tutorial/index.rst @@ -0,0 +1,26 @@ +.. _pynest_tutorial: + +PyNEST tutorial +================ + + +The PyNEST tutorial series will guide you through the first steps to use the NEST +Simulator, from creating neurons and connections to developing spatially structured networks. + +.. grid:: 1 1 2 2 + + .. grid-item-card:: Introduction to PyNEST + + * :ref:`pynest_tutorial_1` + * :ref:`pynest_tutorial_2` + * :ref:`pynest_tutorial_3` + * :ref:`pynest_tutorial_4` + +.. toctree:: + :maxdepth: 1 + :hidden: + + part_1_neurons_and_simple_neural_networks + part_2_populations_of_neurons + part_3_connecting_networks_with_synapses + part_4_spatially_structured_networks diff --git a/doc/htmldoc/understand_index.rst b/doc/htmldoc/understand_index.rst deleted file mode 100644 index 104266db96..0000000000 --- a/doc/htmldoc/understand_index.rst +++ /dev/null @@ -1,137 +0,0 @@ -.. _guides: - -Guides -======= - -Here you can dive into various topics about NEST. - -.. grid:: 1 1 2 3 - - .. grid-item-card:: |neuron| All about neurons - :class-title: sd-d-flex-row sd-align-minor-center - - * :ref:`node_handles` - - * :ref:`param_ex` - - * :ref:`sim_precise_spike_times` - - * :ref:`exact_integration` - - .. grid-item-card:: |synapse| All about synapses and connections - :class-title: sd-d-flex-row sd-align-minor-center - - * :ref:`connection_management` - - * :ref:`handling_connections` - - * :ref:`sim_gap_junctions` - - * :ref:`weight_normalization` - - - .. grid-item-card:: |device| All about devices - :class-title: sd-d-flex-row sd-align-minor-center - - * :ref:`record_simulations` - - * :ref:`stimulate_network` - -.. grid:: 1 1 2 3 - - .. grid-item-card:: |network| Spatially-structured networks - :class-title: sd-d-flex-row sd-align-minor-center - :link: spatial_networks - :link-type: ref - - - .. grid-item-card:: |math| Models in NEST - :class-title: sd-d-flex-row sd-align-minor-center - :link: modelsmain - :link-type: ref - - - .. grid-item-card:: |sonata| NEST SONATA guide - :class-title: sd-d-flex-row sd-align-minor-center - :link: nest_sonata - :link-type: ref - - -.. grid:: 1 1 2 3 - - .. grid-item-card:: |random| NEST behavior - :class-title: sd-d-flex-row sd-align-minor-center - - * :ref:`built_in_timers` - - * :ref:`random_numbers` - - * :ref:`run_simulations` - - .. grid-item-card:: |connect| Connect to other tools - :class-title: sd-d-flex-row sd-align-minor-center - - * :ref:`nest_server` - - * :ref:`nest_music` - - - .. grid-item-card:: |hpc| High performance computers (HPC) - :class-title: sd-d-flex-row sd-align-minor-center - - * :ref:`optimize_performance` - * :ref:`parallel_computing` - * :ref:`benchmark` - -.. grid:: 1 1 2 3 - - .. grid-item-card:: |refresh| Convert NEST 2.X scripts to 3.X - :class-title: sd-d-flex-row sd-align-minor-center - :link: refguide_2_3 - :link-type: ref - - .. grid-item-card:: |git| What's new? - :class-title: sd-d-flex-row sd-align-minor-center - :link: whats_new - :link-type: ref - - .. grid-item-card:: |glossary| Glossary - :class-title: sd-d-flex-row sd-align-minor-center - :link: glossary - :link-type: ref - - - -.. toctree:: - :hidden: - - - What's new? - Neurons - Synapses and connections - Devices - Spatially-structured networks - NEST models - High performance computing - NEST models - NEST and SONATA - Simulation behavior - Randomness in NEST - Built-in timers - Connect NEST with other tools - From NEST 2.x to 3.x - Glossary - - -.. |synapse| image:: static/img/synapse_orange128.svg -.. |neuron| image:: static/img/neuron_orange.svg -.. |glossary| image:: static/img/glossary_orange128.svg -.. |git| image:: static/img/version-control_orange128.svg -.. |refresh| image:: static/img/refresh_orange128.svg -.. |hpc| image:: static/img/hpc_orange128.svg -.. |random| image:: static/img/random_orange128.svg -.. |math| image:: static/img/math_orange128.svg -.. |network| image:: static/img/brainnetwork_orange128.svg -.. |device| image:: static/img/device_orange128.svg -.. |connect| image:: static/img/connect_orange128.svg -.. |sonata| image:: static/img/nestsonata.svg