<div dir="ltr"><div class="gmail_quote"><div dir="ltr"><div>Have any of us come across ActivePapers? It combines code, data and documentation into an HDF5 file to be uploaded as supplementary info for a journal article. It looks like it focuses more on the storage and reusability than the presentation and interactivity of IPython notebooks - so there could be interesting opportunities for integration, such as an IPython notebook backed by code and data stored in this form.<br>
<br><a href="https://bitbucket.org/khinsen/active_papers_py/wiki/Home" target="_blank">https://bitbucket.org/khinsen/active_papers_py/wiki/Home</a><span class="HOEnZb"><font color="#888888"><br><br></font></span></div><span class="HOEnZb"><font color="#888888">Thomas</font></span><div>
<div class="h5"><br><div><div><br><div class="gmail_quote">---------- Forwarded message ----------<br>
From: <b class="gmail_sendername">Konrad Hinsen</b> <span dir="ltr"><<a href="mailto:konrad.hinsen@fastmail.net" target="_blank">konrad.hinsen@fastmail.net</a>></span><br>Date: 24 October 2013 01:16<br>Subject: [SciTech] ActivePapers Python edition<br>
To: <a href="mailto:scitech@hackingscience.org" target="_blank">scitech@hackingscience.org</a><br><br><br>Hi everyone,<br>
<br>
The Python port of my ActivePapers project has advanced to the point<br>
that I make a public announcement. For an overview, see<br>
<br>
<a href="http://bitbucket.org/khinsen/active_papers_py/wiki/Home" target="_blank">http://bitbucket.org/khinsen/active_papers_py/wiki/Home</a><br>
<br>
For more details and a practical example, see the tutorial:<br>
<br>
<a href="http://bitbucket.org/khinsen/active_papers_py/wiki/Tutorial" target="_blank">http://bitbucket.org/khinsen/active_papers_py/wiki/Tutorial</a><br>
<br>
For two recent publications that come with an ActivePaper as<br>
supplementary material, see<br>
<br>
<a href="http://dx.doi.org/10.1063/1.4821598" target="_blank">http://dx.doi.org/10.1063/1.4821598</a><br>
<a href="http://dx.doi.org/10.1063/1.4823996" target="_blank">http://dx.doi.org/10.1063/1.4823996</a><br>
<br>
<br>
In brief, ActivePapers is a framework for doing and publishing<br>
reproducible computational science that addresses three key points<br>
that weren't covered by existing tools:<br>
<br>
- potentially large binary datasets<br>
- computations spread over multiple machines (desktop, cluster, computing centre, ...)<br>
- installation-free use and re-use of published code<br>
<br>
The first two points were a requirement for much of my own work, so<br>
the main motivation for ActivePapers was to allow me to not only<br>
preach, but also practice reproducible research.<br>
<br>
An ActivePaper is a single file containing any combination of data and<br>
code. It can re-use previously published data and code by references<br>
to other ActivePapers through a DOI. References are downloaded<br>
automatically (for now this works only with Figshare).<br>
<br>
The original ActivePapers project<br>
(<a href="https://bitbucket.org/khinsen/active_papers" target="_blank">https://bitbucket.org/khinsen/active_papers</a>) was a proof of concept<br>
for implementing as many desirable features as possible in a single<br>
framework for reproducible research. It used JVM bytecode for code<br>
storage, for reasons of longevity, universality, and secure<br>
execution. For this reason, it was of little practical interest to<br>
most of today's computational science practitioners because most<br>
existing scientific software is not based on the JVM. The Python port<br>
had to remove some of the features of the original project, but is<br>
usable right now with many widely used software packages.<br>
<br>
Konrad.<br>
--<br>
---------------------------------------------------------------------<br>
Konrad Hinsen<br>
Centre de Biophysique Moléculaire, CNRS Orléans<br>
Synchrotron Soleil - Division Expériences<br>
Saint Aubin - BP 48<br>
91192 Gif sur Yvette Cedex, France<br>
Tel. <a href="tel:%2B33-1%2069%2035%2097%2015" value="+33169359715" target="_blank">+33-1 69 35 97 15</a><br>
E-Mail: research AT khinsen DOT fastmail DOT net<br>
<a href="http://dirac.cnrs-orleans.fr/~hinsen/" target="_blank">http://dirac.cnrs-orleans.fr/~hinsen/</a><br>
ORCID: <a href="http://orcid.org/0000-0003-0330-9428" target="_blank">http://orcid.org/0000-0003-0330-9428</a><br>
Twitter: @khinsen<br>
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