ReScience C (rescience)

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@article{Rougier:2018,
  doi = {10.1038/d41586-018-04628-w},
  year = {2018},
  month = apr,
  publisher = {Springer Nature},
  volume = {556},
  number = {7701},
  pages = {309--309},
  author = {Rougier, Nicolas P. and Hinsen, Konrad},
  title = {Code reviewing puts extra demands on referees },
  journal = {Nature},
}

@article{Science:2018,
  doi = {10.1126/science.359.6377.725},
  author = {Hutson, Matthew},
  url = {http://science.sciencemag.org/content/359/6377/725},
  year = {2018},
  month = feb,
  volume = {359},
  number = {6377},
  title = {Artificial intelligence faces a replication crisis},
  journal = {Science},
}

@Misc{Roboto:2011,
  author =       {Christian Robertson},
  title =        {The Roboto family of fonts (Google)},
  url =          {https://github.com/google/roboto},
  year =         2011,
  note =         {Apache License, verison 2.0},
}

@Misc{SourceSerifPro:2014,
  author =       {Frank Grießhammer},
  title =        {Source Serif Pro (Adobe Systems)},
  url =          {https://github.com/adobe-fonts/source-serif-pro},
  year =         2014,
  note =         {SIL Open Font License, version 1.1},
}

@Misc{SourceCodePro:2012,
  author =       {Paul D. Hunt},
  title =        {Source Code Pro (Adobe Systems)},
  url =          {https://github.com/adobe-fonts/source-code-pro},
  year =         2012,
  note =         {SIL Open Font License, version 1.1},
}

@article{Topalidou:2015,
  author =       {Topalidou, Meropi and Rougier, Nicolas P.},
  title =        {{[Re] Interaction between cognitive and motor cortico-basal
                  ganglia loops during decision making: a computational study}},
  journal =      {ReScience},
  year =         2015,
  volume =       1,
  number =       1,
  doi =          {10.5281/zenodo.27944},
}

@article{Rougier:2017,
  doi =          {10.7717/peerj-cs.142},
  author =       {Nicolas P. Rougier and Konrad Hinsen and Frédéric Alexandre
                  and Thomas Arildsen and Lorena Barba and Fabien
                  C. Y. Benureau and C. Titus Brown and Pierre de Buyl and Ozan
                  Caglayan and Andrew P. Davison and Marc André Delsuc and
                  Georgios Detorakis and Alexandra K. Diem and Damien Drix and
                  Pierre Enel and Benoît Girard and Olivia Guest and Matt
                  G. Hall and Rafael Neto Henriques and Xavier Hinaut and Kamil
                  S Jaron and Mehdi Khamassi and Almar Klein and Tiina Manninen
                  and Pietro Marchesi and Dan McGlinn and Christoph Metzner and
                  Owen L. Petchey and Hans Ekkehard Plesser and Timothée Poisot
                  and Karthik Ram and Yoav Ram and Etienne Roesch and Cyrille
                  Rossant and Vahid Rostami and Aaron Shifman and Joseph
                  Stachelek and Marcel Stimberg and Frank Stollmeier and
                  Federico Vaggi and Guillaume Viejo and Julien Vitay and Anya
                  Vostinar and Roman Yurchak and Tiziano Zito},
  title =        {{Sustainable computational science: the ReScience
                  initiative}},
  journal =      {{PeerJ} Computer Science},
  month =        12,
  volume =       3,
  pages =        {e142},
  year =         2017,
  github =       {https://github.com/ReScience/ReScience-article-2},
  keywords =     {journal},
  tags =         {OS},
}

Three years, we launched ReScience, a new scientific journal aimed at publishing the
replication of existing computational research. Since ReScience published its first
article\supercite{Topalidou:2015}, things have been
going steadily. We are still alive, independent and without a budget. In the
meantime, we have published around 24 articles (mostly in computational
neuroscience \& computational ecology) and the initial
\href{https://rescience-c.github.io/board/}{editorial board} has grown from
around 10 to roughly 100 members (editors and reviewers), we have advertised
ReScience at several conferences worldwide, gave some
interviews\supercite{Science:2018}, and published an article introducing
ReScience in PeerJ~CS\supercite{Rougier:2017}. Based on our
experience\supercite{Rougier:2018} at managing the journal during these three
years, we think that time is ripe for some changes.

\subsubsection{ReScience C \& ReScience X}

The biggest and most visible change we would like to propose is to change the
name of the journal ``ReScience'' in favor of ``ReScience C'' where the C
stands for (c)omputational. This change would be necessary to have consistent
naming with the upcoming creation of the ``ReScience X'' journal that will be
dedicated to e(x)perimental replications and co-directed by E.Roesch
(University of Reading) and N.Rougier (University of Bordeaux). The name
``ReScience'' would then be used for the name of a non-profit organization
(that is yet to be created) for the two journals as well as future journals
(such as the utopian CoScience\supercite{Rougier:2017} or a future and
tentative ``ReScience T'' for theoretical science).


\subsubsection{A new submission process}

The current submission process requires authors to fork, clone and branch the
submission repository in order to write their article and to place code and
data at the relevant places in the forked repository. Once done, authors have
to push their changes and to make a pull request that is considered as a
submission. This process is cumbersome for authors and has induced many
troubles for editors as well once the article is accepted and ready to be
published, mostly because of the complexity of the editing procedure. In order
to make life easier for everyone, we greatly simplified the submission process
for ReScience C and X. Authors are now responsible for getting a DOI for their
code \& data and only have to submit a PDF and a metadata file in a GitHub
issue.
We also provide Python programs that largely automate the subsequent editing
process. We will still archive the submission on Zenodo but this archive will
be made for the final PDF only. However, both the PDF and the Zenodo entry will
contain all associated DOIs (data and code).


\subsubsection{A simplified publishing process}

In ReScience, we have been using a combination of
\href{https://daringfireball.net/projects/markdown/syntax}{markdown} and
\href{http://pandoc.org/}{pandoc} for producing both the draft and the final
version of all the published articles. This had worked reasonably well until it
started to cause all kind of problems for both authors and editors, especially
with the reference and citation plugins. Consequently, articles will be now
submitted directly in PDF with accompanying metadata in a separate file using
the \href{https://en.wikipedia.org/wiki/YAML}{YAML} format (they were
previously embedded in the markdown file). Once an article has been accepted,
authors will be responsible for updating the metadata and for rebuilding the PDF if
necessary. We could also consider using the
\href{https://github.com/openjournals/whedon}{Whedon} API that helps with automating
most of the editorial tasks for \href{http://joss.theoj.org/}{JOSS} and
\href{http://jose.theoj.org/}{JOSE}. This will most probably require some
tweaking because our publishing pipeline is a bit different.


\subsubsection{A new design}

The combination of markdown and pandoc has also severely limited the layout and
style possibilities for the article template and since we are switching to
\LaTeX, this is the opportunity to propose a new design based on a more elegant
style, using a new font stack\supercite{SourceSerifPro:2014, Roboto:2011,
  SourceCodePro:2012} (you are currently reading it). The goal is to have a
subtle but strong identity with enhanced readability. Considering that articles
will be mostly read on screen (as opposed to printed), we can benefit from a
more ethereal style. If a \TeX~expert is ready to help review
the template (and possibly rewrite it as a class), their help would be much
welcome and appreciated. The same holds for LibreOffice, Word or Pages, any
template is welcome, just contact us beforehand such that we can coordinate
efforts.


\subsubsection{Editorials, letters and special issues}

ReScience C remains dedicated to the publication of computational replications
but we (i.e., the editorial team) would like to have the opportunity to
publish \emph{editorials} when deemed necessary and to give anyone the
opportunity to write \emph{letters} to the community on a specific topic
related to reproducibility. Both editorials and letters are expected to be 1 or
2 pages long (but no hard limit will be enforced), will be (quickly) peer reviewed,
and will be assigned a DOI. Furthermore, with the advent of reproducibility
hackathons worldwide, we will host {\em special issues} with guest editors (such
as, for example, the organizers of a hackathon) in order to publish the results
and to enhance their discoverability. Each entry will have to go through the
regular open peer-reviewed pipeline.\\


We hope that most readers will agree on the proposed changes such that we can
commit to them in the next few weeks. The review for this editorial is open (as
usual) and anyone can comment on and/or oppose any of the proposed changes. New
ideas are also welcome.

%% ----------------------------------------------------------------------------
%% ReScience article template
%% Copyright (c) 2018 N.P. Rougier,
%% Released under a Creative Commons Attribution 4.0 International license.
%% ----------------------------------------------------------------------------

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%% --- Abstract ---------------------------------------------------------------
%% \ifdefempty{\articleABSTRACT}{}{
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%% --- Replication ------------------------------------------------------------
%% \ifdefempty{\replicationBIB}{}{
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\def \reviewURL{}
\def \articleABSTRACT{Three years have passed since ReScience published its first article and since September 2015, things have been going steadily. We're still alive, independent and without a budget. In the meantime, we have published around 20 articles (mostly in computational neuroscience \& computational ecology) and the initial has grown from around 10 to roughly 100 members (editors and reviewers), we have advertised ReScience at several conferences worldwide, gave some interviews and we published an article introducing ReScience in PeerJ. Based on our experience at managing the journal during these three years, we think the time is ripe for proposing some changes.}
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\def \contactNAME{Nicolas P. Rougier}
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\def \authorsFULL{Konrad Hinsen and Nicolas P. Rougier}
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\def \authorsSHORT{Hinsen and Rougier}
\title{\articleTITLE}
\date{}
\author[1,2,\orcid{0000-0003-0330-9428}]{Konrad Hinsen}
\author[3,4,5,\orcid{0000-0002-6972-589X}]{Nicolas P. Rougier}
\affil[1]{Centre de Biophysique Moléculaire, CNRS UPR4301, Orléans, France}
\affil[2]{Synchrotron SOLEIL, Division Expériences, Gif sur Yvette, France}
\affil[3]{INRIA Bordeaux Sud-Ouest, Bordeaux, France}
\affil[4]{LaBRI, Université de Bordeaux, Institut Polytechnique de Bordeaux, Centre National de la Recherche Scientifique, UMR 5800, Talence, France}
\affil[5]{Institut des Maladies Neurodégénératives, Université  de Bordeaux, Centre National de la Recherche Scientifique, UMR 5293, Bordeaux, France}

%% ----------------------------------------------------------------------------
%% ReScience article template
%% Copyright (c) 2018 N.P. Rougier,
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%% ============================================================================

Font data copyright Google 2012

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Copyright 2010, 2012 Adobe Systems Incorporated (http://www.adobe.com/), with Reserved Font Name 'Source'. All Rights Reserved. Source is a trademark of Adobe Systems Incorporated in the United States and/or other countries.

This Font Software is licensed under the SIL Open Font License, Version 1.1.
This license is copied below, and is also available with a FAQ at: http://scripts.sil.org/OFL

-----------------------------------------------------------
SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007
-----------------------------------------------------------

PREAMBLE
The goals of the Open Font License (OFL) are to stimulate worldwide development of collaborative font projects, to support the font creation efforts of academic and linguistic communities, and to provide a free and open framework in which fonts may be shared and improved in partnership with others.

The OFL allows the licensed fonts to be used, studied, modified and redistributed freely as long as they are not sold by themselves. The fonts, including any derivative works, can be bundled, embedded, redistributed and/or sold with any software provided that any reserved names are not used by derivative works. The fonts and derivatives, however, cannot be released under any other type of license. The requirement for fonts to remain under this license does not apply to any document created using the fonts or their derivatives.

DEFINITIONS
"Font Software" refers to the set of files released by the Copyright Holder(s) under this license and clearly marked as such. This may include source files, build scripts and documentation.

"Reserved Font Name" refers to any names specified as such after the copyright statement(s).

"Original Version" refers to the collection of Font Software components as distributed by the Copyright Holder(s).

"Modified Version" refers to any derivative made by adding to, deleting, or substituting -- in part or in whole -- any of the components of the Original Version, by changing formats or by porting the Font Software to a new environment.

"Author" refers to any designer, engineer, programmer, technical writer or other person who contributed to the Font Software.

PERMISSION & CONDITIONS
Permission is hereby granted, free of charge, to any person obtaining a copy of the Font Software, to use, study, copy, merge, embed, modify, redistribute, and sell modified and unmodified copies of the Font Software, subject to the following conditions:

1) Neither the Font Software nor any of its individual components, in Original or Modified Versions, may be sold by itself.

2) Original or Modified Versions of the Font Software may be bundled, redistributed and/or sold with any software, provided that each copy contains the above copyright notice and this license. These can be included either as stand-alone text files, human-readable headers or in the appropriate machine-readable metadata fields within text or binary files as long as those fields can be easily viewed by the user.

3) No Modified Version of the Font Software may use the Reserved Font Name(s) unless explicit written permission is granted by the corresponding Copyright Holder. This restriction only applies to the primary font name as presented to the users.

4) The name(s) of the Copyright Holder(s) or the Author(s) of the Font Software shall not be used to promote, endorse or advertise any Modified Version, except to acknowledge the contribution(s) of the Copyright Holder(s) and the Author(s) or with their explicit written permission.

5) The Font Software, modified or unmodified, in part or in whole, must be distributed entirely under this license, and must not be distributed under any other license. The requirement for fonts to remain under this license does not apply to any document created using the Font Software.

TERMINATION
This license becomes null and void if any of the above conditions are not met.

DISCLAIMER
THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT OF COPYRIGHT, PATENT, TRADEMARK, OR OTHER RIGHT. IN NO EVENT SHALL THE COPYRIGHT HOLDER BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, INCLUDING ANY GENERAL, SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF THE USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM OTHER DEALINGS IN THE FONT SOFTWARE.

Copyright 2014 Adobe Systems Incorporated (http://www.adobe.com/), with Reserved Font Name 'Source'. All Rights Reserved. Source is a trademark of Adobe Systems Incorporated in the United States and/or other countries.

This Font Software is licensed under the SIL Open Font License, Version 1.1.
This license is copied below, and is also available with a FAQ at: http://scripts.sil.org/OFL

-----------------------------------------------------------
SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007
-----------------------------------------------------------

PREAMBLE
The goals of the Open Font License (OFL) are to stimulate worldwide development of collaborative font projects, to support the font creation efforts of academic and linguistic communities, and to provide a free and open framework in which fonts may be shared and improved in partnership with others.

The OFL allows the licensed fonts to be used, studied, modified and redistributed freely as long as they are not sold by themselves. The fonts, including any derivative works, can be bundled, embedded, redistributed and/or sold with any software provided that any reserved names are not used by derivative works. The fonts and derivatives, however, cannot be released under any other type of license. The requirement for fonts to remain under this license does not apply to any document created using the fonts or their derivatives.

DEFINITIONS
"Font Software" refers to the set of files released by the Copyright Holder(s) under this license and clearly marked as such. This may include source files, build scripts and documentation.

"Reserved Font Name" refers to any names specified as such after the copyright statement(s).

"Original Version" refers to the collection of Font Software components as distributed by the Copyright Holder(s).

"Modified Version" refers to any derivative made by adding to, deleting, or substituting -- in part or in whole -- any of the components of the Original Version, by changing formats or by porting the Font Software to a new environment.

"Author" refers to any designer, engineer, programmer, technical writer or other person who contributed to the Font Software.

PERMISSION & CONDITIONS
Permission is hereby granted, free of charge, to any person obtaining a copy of the Font Software, to use, study, copy, merge, embed, modify, redistribute, and sell modified and unmodified copies of the Font Software, subject to the following conditions:

1) Neither the Font Software nor any of its individual components, in Original or Modified Versions, may be sold by itself.

2) Original or Modified Versions of the Font Software may be bundled, redistributed and/or sold with any software, provided that each copy contains the above copyright notice and this license. These can be included either as stand-alone text files, human-readable headers or in the appropriate machine-readable metadata fields within text or binary files as long as those fields can be easily viewed by the user.

3) No Modified Version of the Font Software may use the Reserved Font Name(s) unless explicit written permission is granted by the corresponding Copyright Holder. This restriction only applies to the primary font name as presented to the users.

4) The name(s) of the Copyright Holder(s) or the Author(s) of the Font Software shall not be used to promote, endorse or advertise any Modified Version, except to acknowledge the contribution(s) of the Copyright Holder(s) and the Author(s) or with their explicit written permission.

5) The Font Software, modified or unmodified, in part or in whole, must be distributed entirely under this license, and must not be distributed under any other license. The requirement for fonts to remain under this license does not apply to any document created using the Font Software.

TERMINATION
This license becomes null and void if any of the above conditions are not met.

DISCLAIMER
THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT OF COPYRIGHT, PATENT, TRADEMARK, OR OTHER RIGHT. IN NO EVENT SHALL THE COPYRIGHT HOLDER BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, INCLUDING ANY GENERAL, SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF THE USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM OTHER DEALINGS IN THE FONT SOFTWARE.