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<!doctype html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no">
<!-- Edit me start! -->
<title>A challenge on the way to Neuroscience Nirvana</title>
<meta name="description" content="Slides for the https://neurosciencenetwork.org/ACNN_Workshop_2022.html">
<meta name="author" content=" Yaroslav O. Halchenko ">
<!-- Edit me end! -->
<link rel="stylesheet" href="reveal.js/dist/reset.css">
<link rel="stylesheet" href="reveal.js/dist/reveal.css">
<link rel="stylesheet" href="reveal.js/dist/theme/beige.css">
<!-- Theme used for syntax highlighted code -->
<link rel="stylesheet" href="reveal.js/plugin/highlight/monokai.css">
</head>
<body>
<div class="reveal">
<div class="slides">
<!-- Start of slides -->
<section>
<section>
<a href="http://centerforopenneuroscience.org/"><img data-src="pics/con-ccn-dartmouth-letterhead.svg"></a>
<h2>A challenge on the way to Neuroscience Nirvana:</h2>
<h1 class="fragment">WORKAROUNDS!</h1>
<!-- <a href="https://standforukraine.com/">
<img src="pics/Ukrainian_Blue-Yellow_ribbon.svg"
style="position:absolute; right:0%; top:70%; width:10%;
opacity:70%"/> -->
<div style="margin-top:1em;text-align:center">
<table style="border: none;">
<tr>
<td>
Yaroslav O. Halchenko<br><small><a href="https://twitter.com/yarikoptic" target="_blank">
<img data-src="pics/twitter.png" style="height:30px;margin:0px" />@yarikoptic</a></small>
</td>
<td></td>
</tr>
<tr>
<td>
<small><br><a href="http://centerforopenneuroscience.org/" target="_blank">Center for Open Neuroscience</a>
<br><a href="https://pbs.dartmouth.edu/" target="_blank">Department of Psychological and Brain Sciences</a>
<br><a href="https://www.dartmouth.edu/ccn/" target="_blank">Center for Cognitive Neuroscience</a><br>
<a href="http://www.dartmouth.edu" target="_blank">Dartmouth
College</a></small>
<!-- TODO <img style="width:200px; margin: 0px"
data-src="pics/2022-tx-big-neuroscience-qrcode.png"/> -->
</td>
<td>
</td>
</tr>
</table>
</div>
<!--
<p style="z-index: 100;position: fixed;background-color:#ede6d5;font-size:35px;box-shadow: 10px 10px 8px #888888;margin-top:0px;margin-bottom:100px;margin-left:1000px">
<img src="pics/QRcode_hhu.png" height="200">
</p>
<br><br><small>
Slides: <a href="https://doi.org/10.5281/zenodo.6346849" target="_blank">
DOI 10.5281/zenodo.6346849</a> (Scan the QR code)
<br>
</small>
-->
<small>
<!-- TODO place them there; Add QR code how in template -->
Live slides/<a href="https://datasets.datalad.org/centerforopenneuroscience/talks/.git">Sources</a>:
<a href="https://datasets.datalad.org/centerforopenneuroscience/talks/2025-ca-origami-retreat.html">https://datasets.datalad.org/centerforopenneuroscience/talks/2025-ca-origami-retreat.html</a>
<br>
<small>
<a href="http://pymvpa.org" target="_blank"> <img style="height:150px;margin:20px" data-src="pics/pymvpa_icon.png"/></a>
<a href="http://neuro.debian.net" target="_blank"> <img style="height:150px;margin:20px" data-src="pics/neurodebian.png"/></a>
<a href="http://repronim.org" target="_blank"> <img style="height:150px;margin:20px" data-src="pics/repronim-logo-vertical.svg"/></a>
<a href="https://open-brain-consent.readthedocs.io" target="_blank"> <img style="height:150px;margin:20px" data-src="pics/OBC_LogoCheck.svg"/></a>
<!-- <a href="https://bids.neuroimaging.io" target="_blank"> <img style="height:150px;margin:20px" data-src="pics/BIDS_Logo.png"/></a> -->
<a href="http://datalad.org" target="_blank"> <img style="height:150px;margin:20px" data-src="pics/datalad_logo_posters_banner.svg"/></a>
<a href="https://github.com/myyoda/myyoda" target="_blank"> <img style="height:150px;margin:20px" data-src="pics/yoda.svg"/></a>
<a href="https://dandiarchive.org" target="_blank"> <img style="height:150px;margin:20px" data-src="pics/dandi-logo-square.svg"/></a>
<a href="https://standforukraine.com/" target="_blank"> <img style="height:150px;margin:20px" data-src="pics/Ukrainian_Blue-Yellow_ribbon.svg"/></a>
</small>
</small>
</section>
</section>
<section data-transition-speed="zoom">
<!-- <a href="https://www.youtube.com/watch?v=uLx7-jrji9o"></a> -->
<section
data-background="pics/survive5+-whatisyour1.png" data-background-opacity="0.9" data-background-size="50%" data-background-position="top 10px left 10px">
<img class="fragment" style="height:800px" data-src="pics/yarik-goal.svg"/>
</section>
</section>
<section data-background="pics/digits-budda.svg" data-background-opacity="0.9" data-background-size="80%" data-background-position="top 10px center 10px">
<section>
<!-- <h1>Nirvana?</h1> -->
<pre style="font-size:100%" class="fragment">
From WordNet (r) 3.0 (2006) [wn]:
nirvana
n 1: (Hinduism and Buddhism) the beatitude that <mark>transcends the</mark>
<mark>cycle of reincarnation</mark>; characterized by the extinction of
desire and suffering and individual consciousness [syn:
{nirvana}, {enlightenment}]
2: <mark>any place of complete bliss and delight and peace</mark> [syn:
{Eden}, {paradise}, {nirvana}, {heaven}, {promised land},
{Shangri-la}]
</pre>
</section>
<section>
<h2>Q: Where data go to die?</h2>
<h3 class="fragment">Data archive</h3>
<h2 class="fragment">Q: How data are reincarnated?</h2>
<h3 class="fragment">Re-used from archive(s)</h3>
<aside class="notes"><ul>
<li>Distributed data has to transcend the cycle of reincarnation upon
reaching an archive.</li>
<li> Data must not die having been deposited to public archive, it should
start its next cycle of life, ideally even richer and more fulfilling.</li>
</ul></aside>
</section>
<section>
<img style="height:800px" data-src="pics/yarik-goal.svg"/>
<h3>... by helping data to transcend the data archive(s)</h3>
</section>
<section>
<h2>Q: How to get to a state <mark>of complete bliss and delight and
peace</mark> while working with (big) data?</h2>
<div class="r-stack">
<img class="fragment" style="width:2000px" data-src="pics/con-webshot-20150812-front-up.png"/>
<!-- TODO update this compilation! prepend with proper Ack-->
<!-- <img class="fragment" style="width:1000px" data-src="pics/con-ack-bmbf.png"/>
<img class="fragment" data-src="pics/borrowed/con-webshot-20150812-front-down.png"/> -->
<img class="fragment" style="width:2000px" data-src="pics/con-principles.png"/>
<!-- TODO: Extend this one and with DANDI accent etc
<img class="fragment" style="width:2000px"
data-src="pics/con-ack-joeybenetc-extended.svg"/>
-->
<h3 class="fragment">Make re-use convenient</h3>
</div>
</section>
</section>
<section>
<section>
<h2>What makes data
re-use <span style="color:red">IN</span>convenient?</h2>
<img src="pics/digits-bug.svg"
style="position:absolute; left:20%; top:10%; width:100%; opacity:70%"/>
<ul>
<li>Data bugs<span class="fragment" data-fragment-index="1">. Possible origins:</span>
<ul class="fragment" data-fragment-index="1">
<li>Human entry
<span class="fragment"
data-fragment-index="2"><br><b>Solution</b> -
minimize:
<ul>
<li>pre-scribe
(standardize): <a href="https://reproin.repronim.org/">ReproIn</a>,
BIDS, Nipoppy, ...</li>
<li>automate: <a href="https://heudiconv.repronim.org/">HeuDiConv</a>,
ReproStim,
ReproEvents,...</li>
</ul>
</span>
<li>Software (human code)
<span class="fragment" data-fragment-index="2"><br><b>Solution</b> avoid
creating new, re-use (needs standardized interfaces),<br/>
automate and standardize! testing.</span></li>
<li>Hardware (made by humans)
<span class="fragment"
data-fragment-index="2"><br><b>Solution</b>:
<ul>
<li> automate
detection - write
software to auto-detect
(QA/QC. Join <a href="https://incf.github.io/niQC/">INCF
niQC</a>)</li>
<li> engage with manufacturers and their standards
(DICOM):<br/> WiP to
join <a href="https://www.ihe-europe.net/IHE_SHARAZONE">IHE
SHARAZONE</a>.</span></li>
</ul>
</ul>
</li>
</ul>
</section>
<section>
<h2>What makes data
re-use <span style="color:red">IN</span>convenient?</h2>
<img src="pics/digits-feedme.svg"
style="position:absolute; left:20%; top:10%; width:100%; opacity:80%"/>
<ul>
<li>Ad-hoc data access<br>
<span class="fragment"
data-fragment-index="3"><b>Solution</b>:
<ul>
<li>standardize (HTTP 401/403, OAuth, etc),</li>
<li>abstract behind common interface
(<a href="https://filesystem-spec.readthedocs.io/">fsspec</a>,
DataLad) </li>
<li>think about both
humans (UI) and bots (API)</span></li>
</ul>
<li>Crafty data format/organization
<span class="fragment"
data-fragment-index="3"><br><b>Solution</b>:
standardize, simplify and automate organization
(<a href="">ReproNim/ReproIn</a> )</span></li>
<li>Opinionated software
<span class="fragment"
data-fragment-index="3"><br><b>Solution</b>:
avoid creating new; IO and interfaces
ideally should <br>use standards (e.g., Boutiques, BIDS/BIDS-Apps,
BrainLife ABCD)</span>
</li>
</ul>
</section>
<section>
<h2>What allows to make data re-use convenient?</h2>
<img src="pics/digits-budda.svg"
style="position:absolute; left:30%; top:10%; width:100%; opacity:80%"/>
<ul>
<li>Standards
<ul class="fragment" data-fragment-index="1">
<li>The language(s) for humans and/or computers</li>
<li>Multilingual support</li>
</ul>
</li>
<li>Validation
<ul class="fragment" data-fragment-index="2">
<li>To make sure that you & others can understand the data</li>
</ul>
</li>
</ul>
</section>
<section>
<h2>What allows to make data re-use convenient?</h2>
<img src="pics/digits-budda.svg"
style="position:absolute; left:30%; top:10%; width:100%; opacity:80%"/>
<h3 class="fragment" data-fragment-index="1">Standards: BIDS</h3>
<ul class="fragment" data-fragment-index="1">
<li><a href="https://en.wikipedia.org/wiki/Unix_philosophy">UNIX
Philosophy #1</a>: "Make each program do one thing
well" applies </li>
<img class="fragment current-visible" data-fragment-index="2" src="pics/bg.png"
style="position:absolute; left:10%; top:11%; width:80%; opacity: 90%"/>
<img class="fragment current-visible" data-fragment-index="2" src="pics/BIDS-minder.svg"
style="position:absolute; left:0%; top:11%; width:100%;"/>
<li class="fragment" data-fragment-index="3">Reuse/improve/adapt/convert/... instead of
re-implement!</li>
<li class="fragment" data-fragment-index="3">Accompany with
tools to manipulate
<ul><li>desperately still needed for BIDS</li></ul>
</li>
<li class="fragment" data-fragment-index="3">Accompany with tools to validate</li>
<li class="fragment" data-fragment-index="3">Accompany with
tools to operate on (BIDS-Apps)</li>
</ul>
</section>
<section>
<h2>What allows to make data re-use convenient?</h2>
<img src="pics/digits-budda.svg"
style="position:absolute; left:30%; top:10%; width:100%; opacity:80%"/>
<h3 class="fragment" data-fragment-index="1">Validation: BIDS</h3>
<ul class="fragment" data-fragment-index="1">
<li>Huge part comes "for free" from standardization
<ul>
<li>contemporary "standard practices" for
software development <br>(CI, containerization, distributions)
</ul>
</li>
<li>Data "quality" is a separate (niQC!) topic</li>
<li>Dialog started to harmonize & potentially standardize
validation results,<br/>
join
at <a href="https://github.com/con/validation/">con/validation</a>
& its
<a href="https://github.com/con/validation/issues/1">issue#1</a>
</li>
</ul>
</section>
<section>
<h2>What if standard does not (yet) "fill the bill"?</h2>
<h3 class="fragment" data-fragment-index="1">Standards: BIDS</h3>
<ul class="fragment" data-fragment-index="1">
<li><a href="https://en.wikipedia.org/wiki/Unix_philosophy">UNIX
Philosophy #1</a>: "Make each program do one thing
well" applies </li>
<img class="fragment current-visible" data-fragment-index="2" src="pics/bg.png"
style="position:absolute; left:10%; top:11%; width:80%; opacity: 90%"/>
<img class="fragment current-visible" data-fragment-index="2" src="pics/BIDS-minder.svg"
style="position:absolute; left:0%; top:11%; width:100%;"/>
<li class="fragment" data-fragment-index="3">Reuse/improve/adapt/convert/... instead of
re-implement!</li>
<li class="fragment" data-fragment-index="3">Accompany with
tools to manipulate
<ul><li>desperately still needed for BIDS</li></ul>
</li>
<li class="fragment" data-fragment-index="3">Accompany with tools to validate</li>
<li class="fragment" data-fragment-index="3">Accompany with
tools to operate on (BIDS-Apps)</li>
</ul>
</section>
</section>
<section data-background="pics/digits-budda.svg" data-background-opacity="0.9" data-background-size="80%" data-background-position="top 10px center 10px">
<h2>In Nirvana we are in a complete bliss and delight and
peace of being to "talk in BIDS"!</h2>
</section>
</section>
<section data-transition-speed="zoom">
<H1>Thank you!</H1>
<h2>Questions?</h2>
</section>
<!-- background slide , Needs tune up of config below
<section data-background="pics/con-ccn-dartmouth-letterhead.svg" data-background-opacity="100%" data-background-size="95%" data-background-position="top">
</section>
-->
<!-- End of slides -->
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