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<a name="rfc"></a>
<h1>Documents</h1>
</div>
<h2>Requests for Comments (RFCs)</h2>
<p>Neurokernel's long-term development planning is conducted via the composition and revision of
Requests for Comments, or RFCs. First employed in the
<a href="http://www.ietf.org/rfc/rfc2026.txt">development of the
Internet</a>, RFCs are publicly accessible design proposals for
major new components or features of a complex computing system. A
new version of an RFC can supersede previous versions if it contains significant
differences that render the previous version obsolete. Anyone
can write and submit a Neurokernel RFC for consideration; see this <a
href="https://github.com/neurokernel/neurokernel/wiki/Requests-for-Comments">page</a>
on the project wiki for more information.</p>
<table class="table table-striped table-bordered table-hover">
<tr>
<th>Neurokernel RFC</th>
<th class="col-xs-4 col-sm-4 col-md-3 col-xs-4 col-lg-2">DOI</th>
<th>Information</th>
<th>Status</th>
<th>Code</th>
<th>Discussion</th>
</tr>
<tr>
<td><a href="./rfc/nk-rfc1.pdf">#1</a></td>
<td><a
href="http://dx.doi.org/10.5281/zenodo.11815"><img
class="img-responsive" style="min-width: 80px;"
src="https://zenodo.org/badge/DOI/10.5281/zenodo.11815.svg"
alt="10.5281/zenodo.11815"></a></td>
<td><b>Neurokernel: An Open Scalable Software Framework for
Emulation and Validation of Drosophila Brain Models on
Multiple GPUs</b>, Lev E. Givon, Aurel A. Lazar, February 2014</td>
<td>OBSOLETE</td>
<td>N.A.</td>
<td><a href="http://neurokernel.67426.x6.nabble.com/RFC-1-f4.html">Link</a></td>
</tr>
<tr>
<td><a href="./rfc/nk-rfc2.pdf">#2</a></td>
<td><a
href="http://dx.doi.org/10.5281/zenodo.11856"><img
class="img-responsive" style="min-width: 80px;"
src="https://zenodo.org/badge/DOI/10.5281/zenodo.11856.svg"
alt="10.5281/zenodo.11856"></a></td>
<td><b>The Cartridge: A Canonical Neural Circuit Abstraction of the Lamina Neuropil - Construction and Composition Rules</b>, Aurel A. Lazar, Nikul H. Ukani and Yiyin Zhou, January 2014</td>
<td>ACTIVE</td>
<td>
<a class="github" style="position:relative; float:left;"
href="https://github.com/neurokernel/lamina">
<img style="position:absolute; width:25px; height:25px;" src="img/github_purple.png">
</a>
</td>
<td><a href="http://neurokernel.67426.x6.nabble.com/RFC-2-f5.html">Link</a></td>
</tr>
<tr>
<td><a href="./rfc/nk-rfc3.pdf">#3</a></td>
<td><a
href="http://dx.doi.org/10.5281/zenodo.30036"><img
class="img-responsive" style="min-width: 80px;"
src="https://zenodo.org/badge/DOI/10.5281/zenodo.30036.svg"
alt="10.5281/zenodo.30036"></a></td>
<td><b>A Parallel Processing Model of the Drosophila Retina</b>, Aurel A. Lazar, Konstantinos Psychas, Nikul H. Ukani and Yiyin Zhou, August 2015</td>
<td>ACTIVE</td>
<td>
<a class="github" style="position:relative; float:left;"
href="https://github.com/neurokernel/retina">
<img style="position:absolute; width:25px; height:25px;" src="img/github_purple.png">
</a>
</td>
<td><a href="http://neurokernel.67426.x6.nabble.com/RFC-3-f34.html">Link</a></td>
</tr>
<tr>
<td><a href="./rfc/nk-rfc4.pdf">#4</a></td>
<td><a
href="http://dx.doi.org/10.5281/zenodo.31947"><img
class="img-responsive" style="min-width: 80px;"
src="https://zenodo.org/badge/DOI/10.5281/zenodo.31947.svg"
alt="10.5281/zenodo.31947"></a></td>
<td><b>Neurokernel: An Open Source Platform for
Emulating the Fruit Fly Brain</b>, Lev E. Givon, Aurel A. Lazar, October 2015</td>
<td>ACTIVE</td>
<td>
<a class="github" style="position:relative; float:left;"
href="https://github.com/neurokernel/neurokernel">
<img style="position:absolute; width:25px; height:25px;" src="img/github_purple.png">
</a>
</td>
<td><a href="http://neurokernel.67426.x6.nabble.com/RFC-4-f37.html">Link</a></td>
</tr>
<tr>
<td><a href="./rfc/nk-rfc5.pdf">#5</a></td>
<td><a
href="http://dx.doi.org/10.5281/zenodo.44225"><img
class="img-responsive" style="min-width: 80px;"
src="https://zenodo.org/badge/DOI/10.5281/zenodo.44225.svg"
alt="10.5281/zenodo.44225"></a></td>
<td><b>NeuroArch: A Graph dB for Querying and Executing Fruit Fly
Brain Circuits</b>, Lev E. Givon, Aurel A. Lazar, Nikul H.
Ukani, December 2015</td>
<td>ACTIVE</td>
<td>
<a class="github" style="position:relative; float:left;"
href="https://github.com/neurokernel/neuroarch">
<img style="position:absolute; width:25px; height:25px;" src="img/github_purple.png">
</a>
</td>
<td><a href="http://neurokernel.67426.x6.nabble.com/RFC-5-f44.html">Link</a></td>
</tr>
<tr>
<td><a href="./rfc/nk-rfc6.pdf">#6</a></td>
<td><a href="http://dx.doi.org/10.1101/051318"><img
class="img-responsive" style="min-width: 80px;"
src="https://img.shields.io/badge/DOI-10.1101%2F051318-blue.svg"
alt="10.1101/051318"></a></td>
<td><b>Generating an Executable Model of the Drosophila Central
Complex</b>, L.E. Givon, A.A. Lazar, May 2016</td>
<td>ACTIVE</td>
<td>
<img style="position:absolute; width:25px; height:25px;" src="img/github_purple.png">
</td>
<td><a href="http://neurokernel.67426.x6.nabble.com/RFC-6-f50.html">Link</a></td>
</tr>
<tr>
<td><a href="http://biorxiv.org/content/biorxiv/early/2016/12/14/092288.full.pdf">#7</a></td>
<td><a href="http://dx.doi.org/10.1101/092288"><img
class="img-responsive" style="min-width: 80px;"
src="https://img.shields.io/badge/DOI-10.1101%2F092288-blue.svg"
alt="10.1101/051318"></a></td>
<td><b>The Fruit Fly Brain Observatory: From Structure to Function</b>, Nikul H. Ukani, Chung-Heng Yeh, Adam Tomkins, Yiyin Zhou, Dorian Florescu, Carlos Luna Ortiz, Yu-Chi Huang, Cheng-Te Wang, Paul Richmond, Chung-Chuan Lo, Daniel Coca, Ann-Shyn Chiang, Aurel A. Lazar, December 2016</td>
<td>ACTIVE</td>
<td>
<a class="github" style="position:relative; float:left;"
href="https://github.com/fruitflybrain">
<img style="position:absolute; width:25px; height:25px;" src="img/github_purple.png">
</a>
</td>
<td><a href="http://neurokernel.67426.x6.nabble.com/RFC-7-f51.html">Link</a></td>
</tr>
<tr>
<td><a href="http://biorxiv.org/content/biorxiv/early/2016/12/14/092429.full.pdf">#8</a></td>
<td><a href="http://dx.doi.org/10.1101/092429"><img
class="img-responsive" style="min-width: 80px;"
src="https://img.shields.io/badge/DOI-10.1101%2F092429-blue.svg"
alt="10.1101/051318"></a></td>
<td><b>NeuroNLP: A Natural Language Portal for Aggregated Fruit Fly Brain Data</b>, Nikul H. Ukani, Adam Tomkins, Chung-Heng Yeh, Wesley Bruning, Allison L Fenichel, Yiyin Zhou, Yu-Chi Huang, Dorian Florescu, Carlos Luna Ortiz, Paul Richmond, Chung-Chuan Lo, Daniel Coca, Ann-Shyn Chiang, Aurel A. Lazar, December 2016</td>
<td>ACTIVE</td>
<td>
<a class="github" style="position:relative; float:left;"
href="https://github.com/fruitflybrain/neuronlp">
<img style="position:absolute; width:25px; height:25px;" src="img/github_purple.png">
</a>
</td>
<td><a href="http://neurokernel.67426.x6.nabble.com/RFC-8-f52.html">Link</a></td>
</tr>
<tr>
<td><a href="http://biorxiv.org/content/biorxiv/early/2017/02/12/092437.full.pdf">#9</a></td>
<td><a href="http://dx.doi.org/10.1101/092437"><img
class="img-responsive" style="min-width: 80px;"
src="https://img.shields.io/badge/DOI-10.1101%2F092437-blue.svg"
alt="10.1101/051318"></a></td>
<td><b>NeuroGFX: A Graphical Functional Explorer for Fruit Fly Brain Circuits</b>, Chung-Heng Yeh, Yiyin Zhou, Nikul H. Ukani, Aurel A. Lazar, December 2016</td>
<td>ACTIVE</td>
<td>
<a class="github" style="position:relative; float:left;"
href="https://github.com/fruitflybrain/neurogfx">
<img style="position:absolute; width:25px; height:25px;" src="img/github_purple.png">
</a>
</td>
<td><a href="http://neurokernel.67426.x6.nabble.com/RFC-9-f53.html">Link</a></td>
</tr>
<tr>
<td><a href="http://biorxiv.org/content/biorxiv/early/2017/12/21/237669.full.pdf">#10</a></td>
<td><a href="http://dx.doi.org/10.1101/237669"><img
class="img-responsive" style="min-width: 80px;"
src="https://img.shields.io/badge/DOI-10.1101%2F237669-blue.svg"
alt="10.1101/237669"></a></td>
<td><b>A Parallel Processing Model of <i>Drosophila</i> Olfactory Sensory Neurons and Its Biological Validation</b>, Aurel A. Lazar, Chung-Heng Yeh, December 2017</td>
<td>ACTIVE</td>
<td>
<img style="position:absolute; width:25px; height:25px;" src="img/github_purple.png">
</td>
<td><a href="http://neurokernel.67426.x6.nabble.com/RFC-10-f54.html">Link</a></td>
</tr>
<tr>
<td>#11</td>
<td>coming soon</td>
<td><b>The Channel: A Canonical Neural Circuit Abstraction of the
Fruit Fly Antennal Lobe Construction and Composition Rules</b>,
A.A. Lazar, Chung-Heng Yeh</td>
<td>pending</td>
<td>
<img style="position:absolute; width:25px; height:25px;" src="img/github_purple.png">
</td>
<td>N.A</td>
</tr>
</table>
<a name="rfc_template"></a>
<h3>RFC template</h3>
<p>A <span class="latex">L<sup>A</sup>T<sub>E</sub>X</span> template
for the Neurokernel RFC can be found here: <a
href="./rfc/nk_rfc.tex">nk_rfc.tex</a>.
<a name="docs">
</a>
<h2>Online Documentation</h2>
<p>Neurokernel's API documentation is available <a
href="http://neurokernel.rtfd.io">here</a>.
</p>
<a name="ipynb">
</a><h2>IPython Notebooks</h2>
<p>Demonstrations of how to use Neurokernel are available as <a
href="http://ipython.org/notebook.html">notebooks</a> for the IPython
interactive computing environment. All notebooks can be downloaded as
part of Neurokernel's <a
href="https://github.com/neurokernel/neurokernel">source code</a>. The notebooks below hosted
in various branches of the source code (see the
project <a
href="https://github.com/neurokernel/neurokernel/wiki/Neurokernel-Code-Organization">Wiki</a>
for more information about each branch).</p>
<table class="table table-striped table-bordered table-hover">
<tr>
<th class="col-sm-3">Demo</th>
<th>Information</th>
</tr>
<tr>
<tr>
<td><a
href="http://nbviewer.ipython.org/github/neurokernel/neurokernel/blob/master/notebooks/ec2.ipynb">Running Neurokernel on Amazon EC2</a></td>
<td>How to run Neurokernel on GPU instances of the Amazon Elastic Compute Cloud (Amazon EC2). An Amazon Machine Image is provided for ease of use.</td>
</tr>
<td><a
href="http://nbviewer.ipython.org/github/neurokernel/neurokernel/blob/master/notebooks/JetsonTK1.ipynb">Running Neurokernel on NVIDIA Jetson Embedded Platform</a></td>
<td>How to run Neurokernel on the Jetson TK1/TX1 Embedded Development Kit.</td>
</tr>
<td><a
href="http://nbviewer.ipython.org/github/neurokernel/neurodriver/blob/master/notebooks/intro.ipynb">How to use Neurokernel's API</a></td>
<td>Introduction to using Neurokernel's API.</td>
</tr>
<tr>
<td><a
href="http://nbviewer.ipython.org/github/neurokernel/neurodriver/blob/master/notebooks/multi.ipynb">Mapping a Network of LPUs onto Multiple GPUs</a></td>
<td>How to connect and execute several generic LPUs on multiple GPUs.</td>
</tr>
<tr>
<td ><a href="http://nbviewer.ipython.org/github/neurokernel/olfaction/blob/master/notebooks/olfaction.ipynb">Olfaction Model</a></td>
<td>The response of a Drosophila antennal lobe circuit to a basic olfactory concentration stimulus.</td>
</tr>
<tr>
<td><a
href="http://nbviewer.ipython.org/github/neurokernel/vision/blob/master/notebooks/vision.ipynb">Vision Model</a></td>
<td>The response of graded potential neurons of a Drosophila vision circuit to a basic visual input stimulus.</td>
</tr>
<tr>
<td><a
href="http://nbviewer.ipython.org/github/neurokernel/sensory_int/blob/master/notebooks/sensory_int.ipynb">Sensory Integration</a></td>
<td>How to integrate Drosophila's olfactory and vision circuits into a multisensory coincidence detector.</td>
</tr>
<tr>
<td><a
href="http://nbviewer.ipython.org/github/neurokernel/retina-lamina/blob/master/notebooks/IntegrationDemo.ipynb">Interfacing Retina and Lamina LPUs</a></td>
<td>How to interface a retina LPU and a lamina LPU using
Neurokernel's API.</td>
</tr>
</table>
<h2>References</h2>
<p>All the references associated with Neurokernel development
are listed on
<a href="http://www.bibsonomy.org/group/neurokernel">BibSonomy</a>.
</div>
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