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reprophylo

Reproducible Phylogenomics

https://github.com/hulluni-bioinformatics/reprophylo

Science Score: 28.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 8 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.7%) to scientific vocabulary
Last synced: 11 months ago · JSON representation ·

Repository

Reproducible Phylogenomics

Basic Info
Statistics
  • Stars: 22
  • Watchers: 6
  • Forks: 4
  • Open Issues: 24
  • Releases: 0
Created over 13 years ago · Last pushed about 10 years ago
Metadata Files
Readme Citation

README.md

ReproPhylo: Reproducible Phylogenomics

ReproPhylo is a reproducible phylogenomics pipeline written in python and making use of BioPython and other open tools. The main webpage is here http://hulluni-bioinformatics.github.io/ReproPhylo.

Licence

ReproPhylo is in the public domain under a CC0 licence. This is a 'no copyright' licence and you are free to use, modify and repurpose any part of our work as you see fit. Note that some dependencies might have more constricting licences. See manual for list of dependencies.

Documentation

Docs and guides are available in a public Google Doc, and you are encouraged to edit, extend and improve these docs if you wish.

Contributions

We welcome your additions and improvements, just fork the repository on GitHub and then send a pull request.

Sources

  1. This repository - active development of the python module and Galaxy tools as well as tutorials.
  2. The Dockerfile repository - contains the Dockerfile with its dependecies. You can use Docker to build a Docker image locally using this reporitory.
  3. The Galaxy distribution repository - A Galaxy distriution including the Galaxy ReproPhylo tools, their dependencies and an INSTALL file.
  4. The DockerHub reporitory - A Docker image of the python module in an IPython notebook environment.
  5. WinPython version with ReproPhylo, requires Git and Perl

CC0
To the extent possible under law, EvoHull has waived all copyright and related or neighboring rights to ReproPhylo.

Owner

  • Name: HullUni-bioinformatics
  • Login: HullUni-bioinformatics
  • Kind: organization
  • Location: Kingston-upon-Hull, UK

Citation (CITATION.TXT) 

Szitenberg A, John M, Blaxter ML, Lunt DH (2015) ReproPhylo: An Environment for Reproducible Phylogenomics. PLoS Comput Biol 11(9): e1004447. doi: 10.1371/journal.pcbi.1004447

@article{10.1371/journal.pcbi.1004447,
    author = {Szitenberg, Amir AND John, Max AND Blaxter, Mark L. AND Lunt, David H.},
    journal = {PLoS Comput Biol},
    publisher = {Public Library of Science},
    title = {ReproPhylo: An Environment for Reproducible Phylogenomics},
    year = {2015},
    month = {09},
    volume = {11},
    url = {http://dx.doi.org/10.1371%2Fjournal.pcbi.1004447},
    pages = {1-13},
    abstract = {<p>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.</p>},
    number = {9},
    doi = {10.1371/journal.pcbi.1004447}
}

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 196
  • Total Committers: 8
  • Avg Commits per committer: 24.5
  • Development Distribution Score (DDS): 0.352
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Amir Szitenberg s****g@g****m 127
Dave Lunt d****t@g****m 32
Dave Lunt d****t@g****m 15
Steve Moss g****l@g****m 6
Amir a****r@a****0 5
Amir Szitenberg a****6@g****m 5
aszitenberg A****g@h****k 4
root r****t@B****k 2
Committer Domains (Top 20 + Academic)
biopc2.hardy.hull.ac.uk: 1 hull.ac.uk: 1

Issues and Pull Requests

Last synced: almost 2 years ago

All Time
  • Total issues: 62
  • Total pull requests: 0
  • Average time to close issues: about 1 month
  • Average time to close pull requests: N/A
  • Total issue authors: 3
  • Total pull request authors: 0
  • Average comments per issue: 0.47
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • szitenberg (60)
  • kcranston (1)
  • yannisdim (1)
Pull Request Authors
Top Labels
Issue Labels
bug (15) enhancement (15) question (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 4 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 2
  • Total versions: 2
  • Total maintainers: 1
pypi.org: reprophylo

Reproducible phylogenetics pipeline

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 4 Last month
Rankings
Dependent packages count: 10.0%
Dependent repos count: 11.6%
Stargazers count: 13.1%
Forks count: 14.2%
Average: 21.0%
Downloads: 55.9%
Maintainers (1)
reprophylo
Last synced: 11 months ago