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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>Building an Archive for Large-scale Neuroscience Data</title>
<meta name="description" content="Slides for a talk at LBL">
<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">
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<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>Building an Archive for Large-scale Neuroscience Data</h2>
<!-- <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>
<img style="width:200px; margin: 0px" data-src="pics/2023-lbl-building-dandi-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/2023-lbl-building-dandi.html">https://datasets.datalad.org/centerforopenneuroscience/talks/2023-lbl-building-dandi.html</a>
<br>
<small>
<a href="https://dandiarchive.org" target="_blank"> <img style="height:150px;margin:20px" data-src="pics/dandi-logo-square.svg"/></a>
<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://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>
<h1>Who am I?</h1>
<img style="height:400px" data-src="pics/borrowed/twitter-unsolicited-advice.png"/>
</section>
<section>
<h3>Brief Bio</h3>
<p>Born in Siberia (RSFSR, USSR), Grew up in Ukraine, Matured in U.S.A.</p>
<ul style="font-size:120%">
<li class="fragment"><b>-1994 Physics Mathematics Gymnasium #17 (Ukraine):</b><br>
<small> Regional&State Physics and Programming
competitions. MS-DOS. Borland Pascal</small></li>
<li class="fragment"><b>-1999 VSTU (Ukraine):
<span style="float:right;">Masters in Opto-Electronic Engineering</span></b><br>
<small> (@yarikoptic). State Physics and International ACM Programming
competitions. Spine diagnostic apparatus. Member of "Small Academy of Science of
Ukraine". SPIE. Soros Fellowship (twice). MS-DOS/Windows.
Borland Pascal, Delphi, VBA
</small></li>
<li class="fragment"><b>-2003 University of New Mexico:
<span style="float:right;">Masters in Computer Science</span></b><br>
<small><a href="http://www.bcl.hamilton.ie/~barak/">B.Pearlmutter</a>.
SOBI/JADE ICA for single trial MEG. Favorite course: Data structures
and algorithms.
<a href="https://debian.org">Debian GNU/Linux</a>.
C, Matlab, shell. CVS
</small></li>
<li class="fragment"><b>-2009 Rutgers-Newark/NJIT:
<span style="float:right;">Ph.D. in Computer Science</span></b><br>
<small><a href="http://rubic-web.rutgers.edu/people.html">S.Hanson</a>.
<a href="http://dx.doi.org/10.1162/neco.2007.09-06-340">fMRI decoding (RFE SVM)</a>.
<a href="https://link.springer.com/article/10.1385/NI:2:1:071?noAccess=true">RUMBA</a>.
HPC sysadmin (cfengine, PBS).
<a href="https://www.fz-juelich.de/SharedDocs/Personen/INM/INM-7/EN/Hanke_m.html">M.Hanke</a>.
Debian pkg-exppsy (for FSL and PyEPL).
<a href="https://nm.debian.org/person/yoh/">Official Debian developer</a>.
<a href="https://arxiv.org/abs/1307.2150">fMRI/EEG (TRANS)fusion</a>.
<a href="http://pymvpa.org">PyMVPA</a>.
C++, Python. SVN, GIT. 1 wife, 3 kids
</small></li>
<li class="fragment"><b>- NOW Dartmouth College, PBS Department: <br>
<span style="float:right;">Postdoc, Scientist, Research Assistant/Associate Professor</span></b><br>
<small><a href="https://haxbylab.dartmouth.edu/">J.Haxby</a>.
<a href="http://pymvpa.org">PyMVPA</a>
(<a href="http://dx.doi.org/10.1016/j.neuron.2011.08.026">Hyperalignment</a>,
...),
<a href="https://neuro.debian.net">NeuroDebian</a>,
<a href="https://datalad.org">DataLad</a>,
<a href="https://repronim.org">ReproNim</a>,
<a href="https://dandiarchive.org">DANDI</a>,
...
<a href="https://github.com/yarikoptic/coop">Chicken Coop</a>,
...
<a href="https://centerforopenneuroscience.org/">CON</a>:
</small>
</li>
</ul>
<aside class="notes"><ul>
<li>Russian Soviet Federative Socialist Republic</li>
</ul></aside>
</section>
<section>
<div class="r-stack">
<img 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"/>
-->
</div>
</section>
<section data-background-iframe="https://www.dandiarchive.org/team" data-background-interactive>
</section>
</section>
<section data-transition="slide">
<section data-background-gradient="radial-gradient(white, #f7dfd3)">
<h2>Challenge: Develop a BRAIN Initiative Archive</h2>
<br>
<a href="https://www.socialsciencespace.com/wp-content/uploads/625px-To_deposit_or_not_to_deposit_that_is_the_question_-_journal.pbio_.1001779.g001.png">
<img style="height:800px" data-src="pics/data-repository-submissions.png"/>
</a>
<br>
<small>
borrowed from <a href="https://www.socialsciencespace.com/wp-content/uploads/625px-To_deposit_or_not_to_deposit_that_is_the_question_-_journal.pbio_.1001779.g001.png">socialsciencespace.com</a></small>
</section>
<section data-transition="slide">
<a href="https://dandiarchive.org"> <img style="height:700px" data-src="pics/dandi-logo-square.svg"/></a>
<br/><br/>Born in 2019
</section>
<section>
<h2>What data is in DANDI</h2>
<img style="height:900px" data-src="pics/dandi-slide-modalities.svg"/></a>
</section>
<section data-transition="slide">
<h2> Ingredients needed to build an archive</h2>
<ul style="font-size:150%">
<li> People <span class="fragment"><b>(users are people too!)</b></span> </li>
<li> Standards </li>
<li> FOSS </li>
<li> Automations </li>
</ul>
<aside class="notes"><ul>
<li>Software needs to speak the languages</li>
<li>Automations to verify that everything speaks the same language</li>
</ul></aside>
</section>
</section>
<section data-transition="slide">
<section>
<img style="width:2000px" src="pics/DANDI-users-PI.svg" />
</section>
<section>
<img style="width:2000px" src="pics/DANDI-users-submitter.svg" />
</section>
<section>
<img style="width:2000px" src="pics/DANDI-users-researcher.svg" />
</section>
<section>
<img style="width:2000px" src="pics/DANDI-users-developer.svg" />
</section>
</section>
<section data-transition="slide">
<section>
<h2>Standards make DANDI FAIR for People</h2>
<img style="width:2000px" src="pics/DANDI-FAIR.svg" />
</section>
<section>
<h2>Standard for neurophysiology data (sessions): NWB</h2>
<img style="width:2000px" src="pics/NWB-datatypes.svg" />
<br/>
Just ask Oliver & Ryan around the corner: <a href="https://www.nwb.org/nwb-neurophysiology/">https://www.nwb.org/nwb-neurophysiology/ </a>
</section>
</section>
<section data-transition="slide">
<section>
<h2>Standard for neural datasets: BIDS</h2>
<img style="width:2000px" data-src="pics/bids-logo-wide.png"/>
<br>
<small>
<a href="https://www.nature.com/articles/sdata201644">
Gorgolewski, K. J., Auer, T., Calhoun, V. D., Craddock, R. C., Das, S., Duff,
E. P., Flandin, G., Ghosh, S. S., Glatard, T., <b>Halchenko, Y. O.</b>, Handwerker,
D. A., Hanke, M., Keator, D., Li, X., Michael, Z., Maumet, C., Nichols, B. N.,
Nichols, T. E., Pellman, J., Poline, J.-B., Rokem, A., Schaefer, G., Sochat, V.,
Triplett, W., Turner, J. A., Varoquaux, G., and Poldrack, R. A. (2016). The
brain imaging data structure, a format for organizing and describing outputs
of neuroimaging experiments. Scientific Data, 3:160044</a>
</small>
</section>
<section>
<h2>BIDS ...</h2>
<ul>
<li>standardizes at the level of the dataset</li>
<li><b>is intended to be boring: you have seen one BIDS dataset -- you have seen them
all!</b></li><ul>
<li>e.g., skim through <a href="https://github.com/OpenNeuroDatasets">https://github.com/OpenNeuroDatasets</a></li>
</ul>
<li>is both human- and machine- friendly</li>
<ul>
<li>From 1.7.0 WiP to make BIDS specification itself machine
readable!</li>
<li><b>In part inspired by the NWB schema</b>. Cross-standard work is ongoing</li>
<li>Schema avoids necessity for hard-coding BIDS in client software</li>
<li><b>Questions about schema/standards versioning and upgrades remain a taboo</b></li>
</ul>
<li>compliance could be automatically verified using
<a href="https://github.com/bids-standard/bids-validator">bids-validator</a>
BIDS-App</li>
<li>is enhanced through BIDS Enhancement Proposals (BEPs), <br>we participate in them to improve BIDS for DANDI archive
<ul>
<li>BEP028: Provenance (WiP)</li>
<li>BEP031: Microscopy (done)</li>
<li>BEP032: Animal electrophysiology (WiP)</li>
</ul>
</li>
</ul>
</section>
<section>
<!-- <h2>BIDS is "meta"standard</h2> -->
<!-- <img class="fragment current-visible" data-fragment-index="2" src="pics/bg.png"
style="position:absolute; left:10%; top:0%; width:80%; opacity: 90%"/>
<img class="fragment current-visible" data-fragment-index="2" src="pics/BIDS-minder.svg"
style="position:absolute; left:0%; top:0%; width:100%;"/> -->
<img src="pics/BIDS-minder.svg"/>
</section>
</section>
</section>
<section data-transition="slide">
<section >
<h2>One more "Standard": DANDI schema</h2>
<img data-src="pics/20210421-INCF-dandischema.svg"/>
</section>
<section>
<h2>Overall: Standards ...</h2>
<ul style="font-size:150%">
<li>are needed for FAIR archives</li>
<li>are a common language for users and computers</li>
<li>can compose of other standards</li>
<li>are evolving</li>
</ul>
</section>
</section>
<section data-transition="slide">
<section>
<h2>DANDI is a FOSS platform</h2>
<img src="pics/DANDI-shot-and-interactions.svg"/>
</section>
<section>
<h2>DANDI integrates with external resources</h2>
<img style="width:2000px" data-src="pics/DANDI-ecosystem.svg"/>
</section>
<!-- <section>
<h2>DANDI for a developer:</h2>
<img style="width:2000px" data-src="pics/20220630-BRAIN-IWG-Developer.svg"/>
</section>
-->
</section>
<section data-transition="slide">
<section>
<h2>How do we ensure correct operation?</h2>
<h3>Collaborate and automate!</h3>
<ul style="font-size:120%">
<li>Delegate data validation to standards</li>
<ul><li>work with standards developers/communities</li></ul>
<li>Impose additional requirements through harmonized schema</li>
<!-- <ul><li></li></ul> -->
</ul>
</section>
<section>
<h2>Unit- and integration- test software components</h2>
<ul>
<li>an entire archive can be instantiated on any machine with docker-compose</li>
<li>Releases and deployment of the components are automated on GitHub</li>
</ul>
<img data-src="pics/dandi-cli-pr-ci-tests.png"/>
</section>
<section>
<h2>con/tinuous archives all the logs and builds</h2>
<img style="height:400px" data-src="pics/con-tinuous-github.png"/>
<img style="height:400px" data-src="pics/con-tinuous-term-dandi-cli.png"/>
</section>
<section>
<h2>Dandisets are converted into DataLad datasets and pushed to GitHub</h2>
<ul>
<li>data resides on S3 (and some institutional backups)</li>
<li>provides aggressive testing of API and data access</li>
</ul>
<img data-src="pics/github-dandisets.png"/>
</section>
<section>
<h2>Webshots of all dandisets for timing and smoke testing</h2>
<h3>Trivia: this setup was used to quickly troubleshoot OHBM 2021 online conference deficiencies</h3>
<img style="height:1400px" data-src="pics/dandiarchive-webshots.png"/>
</section>
<section>
<h2>Testing trivial IO across all dandisets</h2>
<img style="height:1400px" data-src="pics/dandisets-healthstatus.png"/>
</section>
</section>
<section data-transition="slide">
<h2>DANDI ...</h2>
<b>to accommodate growing width (different data types) and size of neural data</b>
<ul style="font-size:120%">
<li><b>provides range of interfaces for data contribution and access:</b>
<br>API, Python CLI client/library, direct S3, FSSPEC, DataLad / git-annex </li>
<li><b>heavily relies on, and contributes to the development of various standards:</b>
<br>NWB, BIDS, OME-Zarr, etc</li>
<li><b>has modular architecture to reuse and contribute to various FOSS projects:</b>
<br>(used to: girder,) h5py, git-annex, DataLad, con/tinuous, pyout, etc.</li>
<li><b>integrates with external services:</b> <br>MetaCell NWB Exporer, bioimagesuiteweb </li>
<li><b>is adopting novel technologies to account for data growth:</b><br> IPFS/Filecoin </li>
<li><b>pays special attention to automated software testing and data QC</b></li>
</ul>
</section>
<section data-transition="slide">
<section> <img src="pics/2022-INCF-help.svg" /> </section>
</section>
<section data-transition-speed="zoom">
<H1>Thank you!</H1>
<h2>Questions?</h2>
</section>
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<section data-background="pics/con-ccn-dartmouth-letterhead.svg" data-background-opacity="100%" data-background-size="95%" data-background-position="top">
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</div>
</div>
<script src="reveal.js/dist/reveal.js"></script>
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