330 lines
13 KiB
HTML
330 lines
13 KiB
HTML
<!doctype html>
|
|
<html lang="en">
|
|
|
|
<head>
|
|
<title>VAMP it up!</title>
|
|
<meta name="description" content=" some description ">
|
|
<meta name="author" content="Michael Hanke">
|
|
|
|
<meta charset="utf-8">
|
|
<meta name="apple-mobile-web-app-capable" content="yes" />
|
|
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
|
|
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no, minimal-ui">
|
|
<link rel="stylesheet" href="../css/main.css" id="theme">
|
|
<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">
|
|
<link rel="stylesheet" href="../css/main.css">
|
|
<!-- Theme used for syntax highlighted code -->
|
|
<link rel="stylesheet" href="../reveal.js/plugin/highlight/monokai.css">
|
|
</head>
|
|
<body>
|
|
|
|
<div class="reveal">
|
|
|
|
<!-- Any section element inside of this container is displayed as a slide -->
|
|
<div class="slides">
|
|
<section>
|
|
<h2>VAMP it up!<br><small>A pragmatic approach to reusable research outputs</small></h2>
|
|
|
|
<p>Michael Hanke</p>
|
|
<p>
|
|
<small>Institute of Neuroscience and Medicine, Brain & Behavior (INM-7),
|
|
Research Center Jülich</small><br>
|
|
<small>Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf</small></br>
|
|
<a href="http://psychoinformatics.de">http://psychoinformatics.de</a></p>
|
|
<p style="margin-top:50px"><img style="height:100px;margin-right:100px" data-src="../pics/fzj_logo.svg" />
|
|
<img style="height:100px" data-src="../pics/hhu_logo.svg" /></p>
|
|
</section>
|
|
|
|
<section>
|
|
<section data-markdown data-transition="none"><script type="text/template">
|
|
|
|
|
|
<note><a href="http://pymvpa.org">http://pymvpa.org</a></note>
|
|
Note:
|
|
open-source neuroimaging ML toolbox, In my Phd
|
|
</script></section>
|
|
|
|
<section data-markdown data-transition="none"><script type="text/template">
|
|
|
|
|
|
<note><a href="http://neuro.debian.org">http://neuro.debian.org</a></note>
|
|
Note:
|
|
largest repository of readily usable open-source neuro-software
|
|
</script></section>
|
|
|
|
<section>
|
|
<h2 style="font-size:150%"><em>Open</em>, "naturalistic" data: studyforrest.org</h2>
|
|
<img style="width:45%" data-src="../pics/forrest_gump_xlg.jpg" />
|
|
<img style="margin-bottom:8%" data-src="../pics/forrest_data_records.png" />
|
|
<note>Hanke, Baumgartner, Ibe, Kaule, Pollmann, Speck, Zinke, & Stadler (2014)
|
|
<em>A high-resolution 7-Tesla fMRI dataset from complex natural stimulation with an audio movie</em>. Scientific Data, 1:140003.
|
|
<a href="http://www.nature.com/articles/sdata20143">http://www.nature.com/articles/sdata20143</a>
|
|
</note>
|
|
<aside class="notes">
|
|
ongoing open-data experiment
|
|
</aside>
|
|
</section>
|
|
</section>
|
|
|
|
<section>
|
|
<section>
|
|
<ul style="list-style-type:none">
|
|
<li><h1 style="display:inline">F</h1>indable</li>
|
|
<li><h1 style="display:inline">A</h1>ccessible</li>
|
|
<li><h1 style="display:inline">I</h1>nteroperable</li>
|
|
<li><h1 style="display:inline">R</h1>eusable</li>
|
|
</ul>
|
|
<note><a href="https://www.go-fair.org/fair-principles">https://www.go-fair.org/fair-principles</a></note>
|
|
<aside class="notes">
|
|
since 2016 (five years), no way around it, declared "done"
|
|
</aside>
|
|
</section>
|
|
|
|
<section>
|
|
<ul style="list-style-type:none">
|
|
<li><h1 style="display:inline">F?</h1> I already have it, it's right here!</li>
|
|
<li><h1 style="display:inline">A?</h1> I am working with it already, I made it!</li>
|
|
<li><h1 style="display:inline">I?</h1> With what?</li>
|
|
<li><h1 style="display:inline">R?</h1> First let me finish this PhD and then we talk, OK?</li>
|
|
</ul>
|
|
<aside class="notes">
|
|
individual/limited perspective less clear, tendency to delay and make expensive
|
|
</aside>
|
|
</section>
|
|
|
|
<section data-markdown data-transition="none"><script type="text/template">
|
|
<!-- .element: height="1000px" -->
|
|
<imgcredit>Divebomb Records</imgcredit>
|
|
|
|
Note:
|
|
My proposal: Let's think about VAMP instead
|
|
</script></section>
|
|
|
|
<section>
|
|
<ul style="list-style-type:none">
|
|
<li><h1 style="display:inline">V</h1>ersion-controlled</li>
|
|
<li><h1 style="display:inline">A</h1>ctionable metadata</li>
|
|
<li><h1 style="display:inline">M</h1>odular</li>
|
|
<li><h1 style="display:inline">P</h1>portable</li>
|
|
</ul>
|
|
<aside class="notes">
|
|
not the band, but...
|
|
</aside>
|
|
</section>
|
|
</section>
|
|
|
|
|
|
<section>
|
|
<section data-markdown data-transition="none"><script type="text/template">
|
|
## Exhaustive tracking of research components
|
|
<!-- .element: width="100%" -->
|
|
Well-structured datasets (using community standards), and portable computational environments — and their evolution — are the precondition for reproducibility
|
|
|
|
Note:
|
|
your community could be really small (your lab), when data are precious resources
|
|
will be spent to understand it, but information must be capture to make this possible
|
|
</script></section>
|
|
|
|
<section data-markdown data-transition="none"><script type="text/template">
|
|
## Capture computational provenance
|
|
<!-- .element: width="100%" -->
|
|
Which data was needed at which version, as input into which code, running with what parameterization in which
|
|
computional environment, to generate an outcome?
|
|
|
|
Note:
|
|
The missing link: even when everything is shared, we still don't know how to start.
|
|
README is minimum, but executable prov-records are much better.
|
|
</script></section>
|
|
|
|
<section data-markdown data-transition="none"><script type="text/template">
|
|
## Exhaustive capture enables portability
|
|
<!-- .element: width="100%" -->
|
|
Precise identification of data and computational environments, combined for provenance records form a comprehensive and portable data structure, capturing all aspects of an investigation.
|
|
|
|
Note:
|
|
Does it fly? Can you give it to someone? Or can you take it with you to your new lab?
|
|
</script></section>
|
|
|
|
<section data-markdown data-transition="none"><script type="text/template">
|
|
## Reproducibility strengthens trust
|
|
<!-- .element: width="100%" -->
|
|
Outcomes of computational transformations can be validated by authorized 3rd-parties. This enables audits, promotes accountability, and streamlines automated "upgrades" of outputs
|
|
|
|
Note:
|
|
Goal is automated reproducibility, enables assessment of robustness and benchmarking algorithmic developments
|
|
</script></section>
|
|
|
|
<section data-markdown data-transition="none"><script type="text/template">
|
|
## Ultimate goal: (re-)usability
|
|
<!-- .element: width="100%" -->
|
|
Verifiable, portable, self-contained data structures that track all aspects of an investigation exhaustively can be (re-)used as modular components in larger contexts — propagating their traits
|
|
|
|
Note:
|
|
With these in place, re-usability is a small(er) step
|
|
</script></section>
|
|
</section>
|
|
|
|
|
|
<section>
|
|
<section data-markdown><script type="text/template">
|
|
## DataLad: manage evolution of digital objects
|
|
<!-- .element: width="1000" style="margin-bottom:-50px" -->
|
|
|
|
Consume, create, curate, analyze, publish, and query data with full provenance capture and "universal" metadata support.
|
|
<p style="font-size:80%">
|
|
DataLad is free and open source (MIT-licensed).
|
|
</p>
|
|
http://datalad.org
|
|
|
|
Note:
|
|
DataLad implements al these features. Go get it at URL
|
|
</script></section>
|
|
|
|
|
|
<section data-markdown data-transition="none"><script type="text/template">
|
|
## Advantages of the VAMP attitude
|
|
|
|
- *Overlay data structure* hides away peculiarities of (current) environment choices for storage and computation<br>
|
|
— focus on content, not infrastructure
|
|
|
|
- Self-contained units that are *valid and complete without any external services*<br>
|
|
— federation-ready for improved resilience
|
|
|
|
- Metadata plurality puts *focus on metadata validity* (for your own work) without becoming a problem for global standardization efforts<br>
|
|
— ability to verify detailed metadata is more useful than today's
|
|
choice of terminology and minimal description standard
|
|
|
|
- Promotes *long-term curation and stewardship* for flexibly reusable unit<br>
|
|
— yields proven and trusted resources for incremental science
|
|
|
|
</script></section>
|
|
|
|
<section data-markdown data-transition="none"><script type="text/template">
|
|
### "Automatic" interoperability with 3rd-party solutions
|
|
<!-- .element: width="600px" style="margin-bottom:-30px;margin-top:-10px"-->
|
|
|
|
- Technology directly used by OpenNeuro, CBRAIN platform, BrainLife.io,
|
|
and compatible with AWS/S3, GIN, Dropbox, etc. (optional strong encryption)
|
|
|
|
- 100+TB of research data, homogenously accessible regardless of hosting choices
|
|
(datasets.datalad.org)
|
|
|
|
Note:
|
|
Interoperability is now an orthogonal aspect that can be improved collaboratively
|
|
</script></section>
|
|
|
|
|
|
<section data-markdown><script type="text/template">
|
|
## Reproducible paper - a Magic trick?
|
|
|
|
<!-- .element: width="1000" -->
|
|
- See for yourself: https://youtu.be/_I3JFhJJtW0?t=861
|
|
|
|
- Get step-by-step instructions: http://handbook.datalad.org/usecases/reproducible-paper.html
|
|
|
|
Note:
|
|
No time to explain, see for yourself
|
|
</script></section>
|
|
|
|
|
|
<section data-markdown><script type="text/template">
|
|
## Open science education
|
|
<!-- .element: class="ackimg" -->
|
|
<!-- .element: width="950" style="margin-top:-20px;margin-bottom:-10px" -->
|
|
|
|
http://handbook.datalad.org
|
|
|
|
- **educational materials** on technologies — **targeting scientists**, not developers (executable paper,
|
|
student surpervisor workflow, ...)
|
|
- handbook with 400+ pages on concepts, workflows, and use cases (work in progress, led by Adina Wagner)
|
|
|
|
Note:
|
|
RDM Education is key. Handbook helps people be more productive, yielding more FAIR resources as an outcome, but not as the main goal.
|
|
</script></section>
|
|
|
|
|
|
</section>
|
|
|
|
<section>
|
|
<h2>Acknowledgements</h2>
|
|
<table>
|
|
<tr style="vertical-align:middle">
|
|
<td style="vertical-align:middle">
|
|
<ul style="font-size:80%">
|
|
<li>Yaroslav Halchenko</li>
|
|
<li>Benjamin Poldrack</li>
|
|
<li>Kyle Meyer</li>
|
|
<li>Adina Wagner</li>
|
|
<li>30+ Datalad contributors</li>
|
|
</ul>
|
|
</td>
|
|
<td style="vertical-align:middle">
|
|
<img style="height:150px;margin-right:50px" data-src="../pics/nsf.png" />
|
|
<img style="height:150px;margin-right:50pxi;margin-left:50px" data-src="../pics/binc.png" />
|
|
<img style="height:150px;margin-left:50px" data-src="../pics/bmbf.png" />
|
|
<br />
|
|
<img style="height:80px;margin-top:-40px;margin-left:auto;margin-right:auto;width:100%" data-src="../pics/fzj_logo.svg" />
|
|
<div style="margin-top:-20px">
|
|
<img style="height:60px;margin-right:200px" data-src="../pics/erdf.png" />
|
|
<img style="height:60px" data-src="../pics/LSA-Logo.png" />
|
|
</div>
|
|
<div style="margin-top:-20px">
|
|
<img style="height:100px;margin:20px" data-src="../pics/hbp_logo.png" />
|
|
<img style="height:100px;margin:20px" data-src="../pics/conp_logo.png" />
|
|
<img style="height:100px;margin:20px" data-src="../pics/vbc_logo.png" />
|
|
</div>
|
|
<div style="margin-top:-40px">
|
|
<img style="height:120px;margin:20px" data-src="../pics/openneuro_logo.png" />
|
|
<img style="height:120px;margin:20px" data-src="../pics/cbrain_logo.png" />
|
|
<img style="height:140px;margin:20px" data-src="../pics/brainlife_logo.png" />
|
|
</div>
|
|
</td>
|
|
</tr>
|
|
</table>
|
|
<p>Website: <a href="http://datalad.org">http://datalad.org</a><br />
|
|
Documentation: <a href="http://handbook.datalad.org">http://handbook.datalad.org</a><br />
|
|
Open data: <a href="http://datasets.datalad.org">http://datasets.datalad.org</a></p>
|
|
</section>
|
|
|
|
|
|
|
|
<script src="../reveal.js/js/reveal.js"></script>
|
|
|
|
<script>
|
|
// Full list of configuration options available at:
|
|
// https://github.com/hakimel/reveal.js#configuration
|
|
Reveal.initialize({
|
|
// The "normal" size of the presentation, aspect ratio will be preserved
|
|
// when the presentation is scaled to fit different resolutions. Can be
|
|
// specified using percentage units.
|
|
width: 1280,
|
|
height: 1024,
|
|
|
|
// Factor of the display size that should remain empty around the content
|
|
margin: 0.1,
|
|
|
|
// Bounds for smallest/largest possible scale to apply to content
|
|
minScale: 0.2,
|
|
maxScale: 1.0,
|
|
|
|
controls: false,
|
|
progress: true,
|
|
history: true,
|
|
center: true,
|
|
|
|
transition: 'slide', // none/fade/slide/convex/concave/zoom
|
|
|
|
// Optional reveal.js plugins
|
|
dependencies: [
|
|
{ src: '../reveal.js/plugin/highlight/highlight.js', async: true, condition: function() { return !!document.querySelector( 'pre code' ); }, callback: function() { hljs.initHighlightingOnLoad(); } },
|
|
{ src: '../reveal.js/plugin/markdown/marked.js', condition: function() { return !!document.querySelector( '[data-markdown]' ); } },
|
|
{ src: '../reveal.js/plugin/markdown/markdown.js', condition: function() { return !!document.querySelector( '[data-markdown]' ); } },
|
|
{ src: '../reveal.js/plugin/zoom-js/zoom.js', async: true },
|
|
{ src: '../reveal.js/plugin/notes/notes.js', async: true }
|
|
]
|
|
});
|
|
</script>
|
|
</body>
|
|
</html>
|