An Overview of Platforms for Reproducible Research and Augmented Publications

There exist several dissemination repositories, computation platforms, and online tools that might be used to implement Reproducible Research. In this paper, we discuss the strengths and weaknesses, or better, the adequacy of each of them for this purpose. Specifically, we present aspects such as the freely availability of contents for the scientific community, the languages which are accepted, or how the platform solves the problem of dependency to specific library versions. We discuss if articles and codes are peer-reviewed or if they are simply spread through a dissemination platform, and if changes are allowed after publication. The most popular platforms and tools are presented with the perspective to highlight new ways for scientific communication.

[1]  Pascal Monasse,et al.  IPOL: A new journal for fully reproducible research; analysis of four years development , 2015, NTMS.

[2]  Daniel J. Blankenberg,et al.  Galaxy: a platform for interactive large-scale genome analysis. , 2005, Genome research.

[3]  et al.,et al.  Jupyter Notebooks - a publishing format for reproducible computational workflows , 2016, ELPUB.

[4]  Marco Loog,et al.  Reproducible Pattern Recognition Research: The Case of Optimistic SSL , 2016, RRPR@ICPR.

[5]  Roberto Di Cosmo,et al.  Software Heritage: Why and How to Preserve Software Source Code , 2017, iPRES.

[6]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[7]  Pascal Monasse,et al.  Reproducible Research in Pattern Recognition - First International Workshop, RRPR@ICPR 2016, Cancún, Mexico, December 4, 2016, Revised Selected Papers , 2017, RRPR@ICPR.

[8]  Arian Maleki,et al.  Reproducible Research in Computational Harmonic Analysis , 2009, Computing in Science & Engineering.

[9]  Jon F. Claerbout,et al.  Electronic documents give reproducible research a new meaning: 62nd Ann , 1992 .

[10]  Daniel S. Katz,et al.  Journal of Open Source Software (JOSS): design and first-year review , 2017, PeerJ Comput. Sci..

[11]  Konrad Hinsen,et al.  ReScience C: A Journal for Reproducible Replications in Computational Science , 2018, RRPR.

[12]  Brian B. Avants,et al.  N4ITK: Improved N3 Bias Correction , 2010, IEEE Transactions on Medical Imaging.

[13]  M. Baker 1,500 scientists lift the lid on reproducibility , 2016, Nature.

[14]  Rafael Grompone von Gioi,et al.  LSD: A Fast Line Segment Detector with a False Detection Control , 2010, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[15]  David L. Donoho,et al.  WaveLab and Reproducible Research , 1995 .

[16]  Pierre Baruch,et al.  Open access developments in France: the HAL Open Archives System , 2007, Learn. Publ..

[17]  Prasad Patil,et al.  A statistical definition for reproducibility and replicability , 2016, bioRxiv.

[18]  John Chilton,et al.  The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update , 2016, Nucleic Acids Res..

[19]  Pascal Monasse,et al.  The IPOL Demo System: A Scalable Architecture of Microservices for Reproducible Research , 2016, RRPR@ICPR.

[20]  Daniel P. Lopresti,et al.  The DAE Platform: A Framework for Reproducible Research in Document Image Analysis , 2016, RRPR@ICPR.

[21]  Brian E. Granger,et al.  IPython: A System for Interactive Scientific Computing , 2007, Computing in Science & Engineering.