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update documentation organisation and landing page
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C.A.P. Linssen committed Jun 13, 2023
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265 changes: 134 additions & 131 deletions doc/htmldoc/templates/index.html
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<!--[if IE 8]> <html class="no-js lt-ie9"> <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js"> <!--<![endif]-->

<title>NEST documentation index </title>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="description" content="This is the documentation index for the NEST, a simulator for spiking neuronal networks.">
<meta name="keywords" content="">
<link rel="stylesheet" href="_static/stylesheets/application.css">
<link rel="stylesheet" href="_static/fonts/material-icons.css">
<link rel="stylesheet" href="_static/css/bootstrap/bootstrap.min.css">
<link rel="stylesheet" href="_static/css/normalize.css">
<link rel="stylesheet" href="_static/css/default.min.css">
<script src="_static/js/highlight.min.js"></script>
<script>hljs.highlightAll();</script>
<link rel="stylesheet" href="_static/js/flexslider/flexslider.css">
<link rel="stylesheet" href="_static/css/custom.css">
<script src="_static/js/modernizr-2.6.2.min.js"></script>
<script src="_static/javascripts/application.js"></script>
<title>NEST documentation index </title>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="description" content="This is the documentation index for the NEST, a simulator for spiking neuronal networks.">
<meta name="keywords" content="">
<link rel="stylesheet" href="_static/stylesheets/application.css">
<link rel="stylesheet" href="_static/fonts/material-icons.css">
<link rel="stylesheet" href="_static/css/bootstrap/bootstrap.min.css">
<link rel="stylesheet" href="_static/css/normalize.css">
<link rel="stylesheet" href="_static/css/default.min.css">
<script src="_static/js/highlight.min.js"></script>
<script>hljs.highlightAll();</script>
<link rel="stylesheet" href="_static/js/flexslider/flexslider.css">
<link rel="stylesheet" href="_static/css/custom.css">
<script src="_static/js/modernizr-2.6.2.min.js"></script>
<script src="_static/javascripts/application.js"></script>

<div role="main">

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<a href="#" id="gototop"><img src="{{ pathto('_static/img/arrow-up-circle.svg',1) }}"/></a>
<header id="header" class="wrapper clearfix">
<div id="background" class="particle-img">
<div id="banner">
<div id="logo">
<img src="{{ pathto('_static/img/nest_docs.png',1) }}" alt="logo"/>
<div id="banner">
<div id="logo">
<img src="{{ pathto('_static/img/nest_docs.png',1) }}" alt="logo"/>
</div>
</div>

<nav id="topnav" role="navigation">
<div class="menu-toggle">Menu</div>
<ul class="srt-menu" id="menu-main-navigation">
<li><a href="https://nest-simulator.org/">The NEST Homepage</a></li>
<li><a href="{{pathto('related_projects')}}">Related projects</a></li>
<li><a href="{{pathto('community')}}">Contact and support</a></li>
</ul>
</nav>
</div>
<nav id="topnav" role="navigation">
<div class="menu-toggle">Menu</div>
<ul class="srt-menu" id="menu-main-navigation">
<li><a href="https://nest-initiative.org/">The NEST Initiative</a></li>
<li><a href="https://nest-simulator.readthedocs.io/en/v3.4/related_projects.html">Related tools</a></li>
<li><a href="community.html">Contact and support</a></li>
</ul>
</nav>
</header>

<script src="_static/js/tsparticles.min.js"></script>
<script src="_static/js/particles-app.js"></script>

Expand All @@ -51,103 +54,99 @@
<div class="row">
<div class="grid_3">
<h1>Welcome to the NEST Simulator documentation!</h1>
<p>NEST is a simulator for spiking neural network models that focuses on the dynamics, size and structure of neural systems rather than on the exact morphology of individual neurons.</p>
<p>NEST is used in computational neuroscience to model and study behavior of large networks of neurons. The models describe single neuron and synapse behavior and their connections. Different mechanisms of plasticity can be used to investigate artificial learning and help to shed light on the fundamental principles of how the brain works.</p>
<p>NEST is ideal for networks of spiking neurons of any size, and scales flexibly from running on your laptop to high-performance computing systems involving hundreds of compute nodes.</p>
<p>It can be used to simulate small and large-scale models of information processing e.g. in the visual or auditory cortex of mammals, odels of network activity dynamics, e.g. laminar cortical networks or balanced random networks, and supports many models of learning and plasticity.</p>
</div>
<div class="grid_6">
<a href="installation/index.html" class="buttonlink">Install NEST</a>
<a href="get-started_index.html" class="buttonlink">Tutorials and examples</a>
<a href="ref_material/pynest_apis.html" class="buttonlink">PyNEST API</a>
<a href="models/index.html" class="buttonlink">Available models</a>
<a href="understand_index.html" class="buttonlink">How NEST works</a>
<a href="installation/index.html" class="buttonlink">Install NEST</a>
<a href="get-started_index.html" class="buttonlink">Tutorials and examples</a>
<a href="ref_material/pynest_apis.html" class="buttonlink">PyNEST API</a>
<a href="models/index.html" class="buttonlink">Available models</a>
<a href="understand_index.html" class="buttonlink">How NEST works</a>
</div>
</div>
</section>
<!-- XXX nesting here seems messed up. Run through W3C validator -->
</div>
</div>
</section>

<section id="intro" class="vertical-padding">
<section id="intro" class="vertical-padding">
<div id="main" class="blueelement wrapper clearfix">
<div class="row vertical-padding">
<div class="grid_12">
<h2 id="nest-sample"> Here is a sample NEST script. Click each section and discover related topics!</h2>
</div>


<div class="accordion"> <img id="pulse" src="_static/img/pulse.svg" style="position:relative" />
<pre><code class="language-python">
import nest
</code></pre>
<div>
<ul>
<li><a href="installation/index.html">Get and install NEST</a></li>
<li><a href="ref_material/pynest_apis.html">Access PyNEST APIs</a></li>
<li><a href= "release_notes/v3.0/refguide_nest2_nest3.html">Convert script from NEST 2.x to 3.x</a></li>
</ul>
</div>


<pre><code class="language-python">
neurons = nest.Create("iaf_psc_alpha", 10000, {
"V_m": nest.random.normal(-5.0),
"I_e": 1000.0
})
</code></pre>

<div>
<ul>
<li><a href="neurons/node_handles.html">Learn about creating neurons</a></li>
<li><a href= "neurons/parametrization.html">Discover parameterization possibilities</a></li>
<li><a href="models/index_neuron.html">Want a different neuron model? Find them all here!</a></li>
<li><a href="nest_behavior/random_numbers.html">Learn how we do randomness in NEST</a></li>
<li><a href="ref_material/pynest_apis.html#module-nest.lib.hl_api_nodes">Get API docs for Create</a></li>
</ul>
</div>
<pre><code class="language-python">
input = nest.Create("noise_generator", params={
"amplitude": 500.0
})
nest.Connect(input, neurons, syn_spec={'synapse_model': 'stdp_synapse'})
</code></pre>
<div>
<ul>
<li><a href="devices/stimulate_the_network.html">Learn about stimulating the network</a></li>
<li><a href="models/index_generator.html">Explore the stimulators in our model directory</a></li>
<li><a href="synapses/handling_connections.html">Find out more about synapse creation in NEST</a></li>
<li><a href="synapses/connection_management.html">Find out how to manage connections in NEST</a></li>
</ul>
</div>

<pre><code class="language-python">
spikes = nest.Create("spike_recorder", params={
'record_to': 'ascii',
'label': 'excitatory_spikes'
})
nest.Connect(neurons, spikes)
</code></pre>
<div>
<ul>
<li><a href="devices/record_from_simulations.html">Get more info on recording from simulations</a></li>
<li><a href="models/index_recorder.html">See our recording devices in our model directory</a></li>
<li><a href="ref_material/pynest_apis.html#module-nest.lib.hl_api_connections">Get API docs for Connect</a></li>
</ul>
<div class="grid_12">
<h2 id="nest-sample"> Here is a sample NEST script. Click each section and discover related topics!</h2>
</div>

<pre><code class="language-python">
nest.Simulate(100.0)
nest.raster_plot.from_device(spikes, hist=True)
plt.show()
</code></pre>
<div>
<ul>
<li><a href="nest_behavior/running_simulations.html">Check out our guide how to run simulations</a></li>
<li><a href="ref_material/pynest_apis.html#nest.lib.hl_api_simulation.Simulate">Get API docs for Simulate</a></li>
</ul>
<div class="accordion"> <img id="pulse" src="_static/img/pulse.svg" style="position:relative" />
<pre><code class="language-python">
import nest
</code></pre>
<div>
<ul>
<li><a href="installation/index.html">Get and install NEST</a></li>
<li><a href="ref_material/pynest_apis.html">Access PyNEST APIs</a></li>
<li><a href= "release_notes/v3.0/refguide_nest2_nest3.html">Convert script from NEST 2.x to 3.x</a></li>
</ul>
</div>

<pre><code class="language-python">
neurons = nest.Create("iaf_psc_alpha", 10000, {
"V_m": nest.random.normal(-5.0),
"I_e": 1000.0
})
</code></pre>
<div>
<ul>
<li><a href="neurons/node_handles.html">Learn about creating neurons</a></li>
<li><a href= "neurons/parametrization.html">Discover parameterization possibilities</a></li>
<li><a href="models/index_neuron.html">Want a different neuron model? Find them all here!</a></li>
<li><a href="nest_behavior/random_numbers.html">Learn how we do randomness in NEST</a></li>
<li><a href="ref_material/pynest_apis.html#module-nest.lib.hl_api_nodes">Get API docs for Create</a></li>
</ul>
</div>

<pre><code class="language-python">
input = nest.Create("noise_generator", params={
"amplitude": 500.0
})
nest.Connect(input, neurons, syn_spec={'synapse_model': 'stdp_synapse'})
</code></pre>
<div>
<ul>
<li><a href="devices/stimulate_the_network.html">Learn about stimulating the network</a></li>
<li><a href="models/index_generator.html">Explore the stimulators in our model directory</a></li>
<li><a href="synapses/handling_connections.html">Find out more about synapse creation in NEST</a></li>
<li><a href="synapses/connection_management.html">Find out how to manage connections in NEST</a></li>
</ul>
</div>

<pre><code class="language-python">
spikes = nest.Create("spike_recorder", params={
'record_to': 'ascii',
'label': 'excitatory_spikes'
})
nest.Connect(neurons, spikes)
</code></pre>
<div>
<ul>
<li><a href="devices/record_from_simulations.html">Get more info on recording from simulations</a></li>
<li><a href="models/index_recorder.html">See our recording devices in our model directory</a></li>
<li><a href="ref_material/pynest_apis.html#module-nest.lib.hl_api_connections">Get API docs for Connect</a></li>
</ul>
</div>

<pre><code class="language-python">
nest.Simulate(100.0)
nest.raster_plot.from_device(spikes, hist=True)
plt.show()
</code></pre>
<div>
<ul>
<li><a href="nest_behavior/running_simulations.html">Check out our guide how to run simulations</a></li>
<li><a href="ref_material/pynest_apis.html#nest.lib.hl_api_simulation.Simulate">Get API docs for Simulate</a></li>
</ul>
</div>
</div>
</div>
</div>

</div>
</section>

<section id="topics" class="vertical-padding">
Expand Down Expand Up @@ -189,6 +188,7 @@ <h2 id="nest-sample"> Here is a sample NEST script. Click each section and disco
</div>
</div>
</section>

<section id="backmatter" class="greenelement vertical-padding">
<div class="wrapper clearfix">
<h1>Related projects</h1>
Expand All @@ -214,34 +214,37 @@ <h1>Developer space</h1>
code is rock solid at all times. If you want the gritty details
and find out how it's done
come to the dark side! See our <a href="developer_space/index.html">developer facing documentation.</a>
</p>
</p>
</div>
</section>

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<img class="icon" src="_static/img/eu_logo.png" />
</div>
<div class="grid_4 narrow">
<h2><a href="https://github.com/nest/nest-simulator/blob/master/ACKNOWLEDGMENTS.md">Acknowledgments</a></h2>
<div class="grid_4 narrow">
<img class="icon" src="_static/img/3_HBP + EBRAINS logo_Color+White.png" />
</div>
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</div>
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<h2><a href="https://github.com/nest/nest-simulator/blob/master/ACKNOWLEDGMENTS.md">Acknowledgments</a></h2>
<p>NEST is grateful for the support from numerous organizations and individuals.</p> <br>
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6 changes: 3 additions & 3 deletions doc/htmldoc/templates/layout.html
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<nav id="topnav" role="navigation">
<div class="menu-toggle">Menu</div>
<ul class="srt-menu" id="menu-main-navigation">
<li><a href="https://www.nest-simulator.org">NEST Homepage</a></li>
<li><a href="{{pathto('related_projects')}}">Related projects</a></li>
<li><a href="{{pathto('community')}}">Contact us</a></li>
<li><a href="https://nest-simulator.org/">The NEST Homepage</a></li>
<li><a href="{{pathto('related_projects')}}">Related projects</a></li>
<li><a href="{{pathto('community')}}">Contact and support</a></li>
</ul>
</nav>
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