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ReproPhylo: An Environment for Reproducible Phylogenomics

The reproducibility of experiments is key to the scientific process, and particularly necessary for accurate reporting of analyses in data-rich fields such as phylogenomics. We present ReproPhylo, a phylogenomic analysis environment developed to ensure experimental reproducibility, to facilitate the...

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Detalles Bibliográficos
Autores principales: Szitenberg, Amir, John, Max, Blaxter, Mark L., Lunt, David H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4559436/
https://www.ncbi.nlm.nih.gov/pubmed/26335558
http://dx.doi.org/10.1371/journal.pcbi.1004447
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author Szitenberg, Amir
John, Max
Blaxter, Mark L.
Lunt, David H.
author_facet Szitenberg, Amir
John, Max
Blaxter, Mark L.
Lunt, David H.
author_sort Szitenberg, Amir
collection PubMed
description The reproducibility of experiments is key to the scientific process, and particularly necessary for accurate reporting of analyses in data-rich fields such as phylogenomics. We present ReproPhylo, a phylogenomic analysis environment developed to ensure experimental reproducibility, to facilitate the handling of large-scale data, and to assist methodological experimentation. Reproducibility, and instantaneous repeatability, is built in to the ReproPhylo system and does not require user intervention or configuration because it stores the experimental workflow as a single, serialized Python object containing explicit provenance and environment information. This ‘single file’ approach ensures the persistence of provenance across iterations of the analysis, with changes automatically managed by the version control program Git. This file, along with a Git repository, are the primary reproducibility outputs of the program. In addition, ReproPhylo produces an extensive human-readable report and generates a comprehensive experimental archive file, both of which are suitable for submission with publications. The system facilitates thorough experimental exploration of both parameters and data. ReproPhylo is a platform independent CC0 Python module and is easily installed as a Docker image or a WinPython self-sufficient package, with a Jupyter Notebook GUI, or as a slimmer version in a Galaxy distribution.
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spelling pubmed-45594362015-09-10 ReproPhylo: An Environment for Reproducible Phylogenomics Szitenberg, Amir John, Max Blaxter, Mark L. Lunt, David H. PLoS Comput Biol Research Article The reproducibility of experiments is key to the scientific process, and particularly necessary for accurate reporting of analyses in data-rich fields such as phylogenomics. We present ReproPhylo, a phylogenomic analysis environment developed to ensure experimental reproducibility, to facilitate the handling of large-scale data, and to assist methodological experimentation. Reproducibility, and instantaneous repeatability, is built in to the ReproPhylo system and does not require user intervention or configuration because it stores the experimental workflow as a single, serialized Python object containing explicit provenance and environment information. This ‘single file’ approach ensures the persistence of provenance across iterations of the analysis, with changes automatically managed by the version control program Git. This file, along with a Git repository, are the primary reproducibility outputs of the program. In addition, ReproPhylo produces an extensive human-readable report and generates a comprehensive experimental archive file, both of which are suitable for submission with publications. The system facilitates thorough experimental exploration of both parameters and data. ReproPhylo is a platform independent CC0 Python module and is easily installed as a Docker image or a WinPython self-sufficient package, with a Jupyter Notebook GUI, or as a slimmer version in a Galaxy distribution. Public Library of Science 2015-09-03 /pmc/articles/PMC4559436/ /pubmed/26335558 http://dx.doi.org/10.1371/journal.pcbi.1004447 Text en © 2015 Szitenberg et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Szitenberg, Amir
John, Max
Blaxter, Mark L.
Lunt, David H.
ReproPhylo: An Environment for Reproducible Phylogenomics
title ReproPhylo: An Environment for Reproducible Phylogenomics
title_full ReproPhylo: An Environment for Reproducible Phylogenomics
title_fullStr ReproPhylo: An Environment for Reproducible Phylogenomics
title_full_unstemmed ReproPhylo: An Environment for Reproducible Phylogenomics
title_short ReproPhylo: An Environment for Reproducible Phylogenomics
title_sort reprophylo: an environment for reproducible phylogenomics
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4559436/
https://www.ncbi.nlm.nih.gov/pubmed/26335558
http://dx.doi.org/10.1371/journal.pcbi.1004447
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