[IPython-dev] Fwd: [SciTech] ActivePapers Python edition

[Thomas Kluyver]

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.

https://bitbucket.org/khinsen/active_papers_py/wiki/Home

Thomas


---------- Forwarded message ----------
From: Konrad Hinsen <konrad.hinsen at fastmail.net>
Date: 24 October 2013 01:16
Subject: [SciTech] ActivePapers Python edition
To: scitech at hackingscience.org


Hi everyone,

The Python port of my ActivePapers project has advanced to the point
that I make a public announcement. For an overview, see

   http://bitbucket.org/khinsen/active_papers_py/wiki/Home

For more details and a practical example, see the tutorial:

    http://bitbucket.org/khinsen/active_papers_py/wiki/Tutorial

For two recent publications that come with an ActivePaper as
supplementary material, see

    http://dx.doi.org/10.1063/1.4821598
    http://dx.doi.org/10.1063/1.4823996


In brief, ActivePapers is a framework for doing and publishing
reproducible computational science that addresses three key points
that weren't covered by existing tools:

 - potentially large binary datasets
 - computations spread over multiple machines (desktop, cluster, computing
centre, ...)
 - installation-free use and re-use of published code

The first two points were a requirement for much of my own work, so
the main motivation for ActivePapers was to allow me to not only
preach, but also practice reproducible research.

An ActivePaper is a single file containing any combination of data and
code. It can re-use previously published data and code by references
to other ActivePapers through a DOI. References are downloaded
automatically (for now this works only with Figshare).

The original ActivePapers project
(https://bitbucket.org/khinsen/active_papers) was a proof of concept
for implementing as many desirable features as possible in a single
framework for reproducible research. It used JVM bytecode for code
storage, for reasons of longevity, universality, and secure
execution. For this reason, it was of little practical interest to
most of today's computational science practitioners because most
existing scientific software is not based on the JVM. The Python port
had to remove some of the features of the original project, but is
usable right now with many widely used software packages.

Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
http://dirac.cnrs-orleans.fr/~hinsen/
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen
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