3 Matching Annotations
  1. Jul 2018
  2. journals.plos.org journals.plos.org
    Reconciling species diversity in a tropical plant clade (Canarium, Burseraceae)
    1
    1. npscience 19 Jul 2018
      Fully reproducible code is available in the form of jupyter notebooks (https://jupyter.org) with instructions to install all necessary software, download sequence data, assemble it, and run genomic analyses (https://github.com/dereneaton/Canarium-GBS) (DOI 10.5281/zenodo.1273357). For all genomic analyses in this study we used the ipyrad Python API and the ipyrad-analysis toolkit (https://github.com/dereneaton/ipyrad) which provides a set of wrappers around common genomic analysis tools to run highly parallelized analyses using simple Python scripts.

      Example of author sharing all code via jupyter notebooks in a github repo. They have archived to Zenodo and include both URLs in the text. Their analysis relies on an existing toolkit - it is not obvious from the manuscript whether this toolkit has been deposited anywhere.

      Journal: PLOS ONE Subject area: plant biology, ecology (check?)

      software-deposit
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    journals.plos.org/plosone/article
  3. elifesciences.org elifesciences.org
    CRISPR-based herd immunity can limit phage epidemics in bacterial populations
    2
    1. npscience 19 Jul 2018
      Source code of the model presented here is available on GitHub (https://github.com/lukasgeyrhofer/phagegrowth) (Payne et al., 2018) and its archived version is accessible through Zenodo: https://dx.doi.org/10.5281/zenodo.1038582 and https://github.com/elifesciences-publications/phagegrowth.

      Example of authors archiving their own code. The eLife process is to fork the author's repo to the eLife github repo to save a snapshot of the repo at the time of acceptance. The authors here have also chosen to archive to Zenodo (via the Github release --> Zenodo mechanism?). Both the Zenodo DOI and the eLife fork are included in the text as archive/snapshot copies of the original (also cited).

      Note the author's original repo is included in the references.

      Journal: eLife Subject area: ecology, evolutionary biology

      software-deposit
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    URL

    elifesciences.org/articles/32035