9 Matching Annotations
  1. Aug 2018
  2. Jun 2018
    1. Acero F., Ackermann M., Ajello M. et al (Fermi-LAT) 2015 arXiv:1501.02003Preprint

      Starting in 2014-2015, AAS/IOP started linking to preprints in reference lists if they were the version cited by the author and an accepted manuscript did not at that time exist.

      Thus we now have built in "categories" for references, which could be expanded to include data/software sections.

    2. The most up-to-date version of the open-source package NPTFit may be found at https://github.com/bsafdi/NPTFit and the latest documentation at http://nptfit.readthedocs.io. In addition, the version used in this paper has been archived at https://zenodo.org/record/380469#.WN_pSFPyvMV.

      This is an example of incorrect software citation per the AAS Journal's policy. The Zenodo metadata should have been added to the reference list as a 1st class citation.

      It is also an example of an incorrectly typeset URL. URLs that come from DOIs should be typeset using the DOI string not the resolved URL. It should have read, "version used in this paper has been archived at https://doi.org/10.5281/zenodo.380469"

    3. Foreman-Mackey D., Vousden W., Price-Whelan A. et al 2016 corner.py: corner.py v2.0.0, doi:10.5281/zenodo.53155

      corner.py is one of the more interesting examples of software citations. there are at least 3 different formal references in the wild:

      https://doi.org/10.5281/zenodo.11020 https://doi.org/10.5281/zenodo.53155 https://doi.org/10.21105/joss.00024

      with different versions and author lists.

    1. Barbary K. 2014 sncosmo Zenodo, 10.5281/zenodo.11938

      This software citation losts its version information. We will have to work on our typsetting and production rules, as well as develop formal JATS/NLM XML schema to contain versioning information.

    2. https://doi.org/10.5281/zenodo.11938

      This DOI software archive is also in the Reference list per our Journal's software policy.

    3. Software: hotpants, PostgreSQL, realbogus (Bloom et al. 2012) scamp (Bertin 2006), sextractor (Bertin & Arnouts 1996), sncosmo (Barbary 2014), swarp (Bertin et al. 2002), matplotlib (Hunter 2007), numpy (Van Der Walt et al. 2011).

      The AASJournals now highlight software using a paragraph trailing the acknowledgements that lists all software used in the paper's analysis. The software doesn't need to be mentioned in the main text; context-free mentions can be placed here.

      The format is a 2 item tuple containing the short/common name of the software, and a citation or URL for the software.

      In principle this section could be data mined. At the moment it is just a free paragraph in the XML, but could be given more explicit markup to aide in data mining reuse and indexing.

    1. Software: Juypter notebook (http://jupyter.org), Jupyterlab (https://github.com/jupyterlab), VOspace (http://www.canfar.net/en/docs/storage), vos (https://pypi.python.org/pypi/vos), VirtualBox (https://www.virtualbox.org), JupyterHub      (https://jupyterhub.readthedocs.io/en/latest/), ipywidgets (https://ipywidgets.readthedocs.io), NuPyCEE (http://nugrid.github.io/NuPyCEE), NuGridSetExplorer (https://github.com/NuGrid/WENDI), hdf5 (https://www.hdfgroup.org), Cyberlaboratories cyberhubs (https://github.com/cyberlaboratories/cyberhubs), Cyberlaboratories astrohubs        (https://github.com/cyberlaboratories/astrohubs), Cyberhubs Docker repository (https://hub.docker.com/u/cyberhubs), Docker (https://www.docker.com), NOAO data lab (http://datalab.noao.edu), ansible (https://www.ansible.com), puppet (https://puppet.com), mesa_h5 (https://github.com/NuGrid/mesa_h5), Python (https://www.python.org), MESA (http://mesa.sourceforge.net), WENDI (http://wendi.nugridstars.org), OpenMP (http://www.openmp.org), MESA-SDK (http://www.astro.wisc.edu/~townsend/static.php?ref=mesasdk), MPI (https://www.open-mpi.org), gfortran (https://gcc.gnu.org/fortran), SuperLU (http://crd-legacy.lbl.gov/~xiaoye/SuperLU), OpenBLAS (http://www.openblas.net), mencoder (http://www.mplayerhq.hu).

      It would be better to see some of these going to bibliographic references instead of URLs though many of them do not list preferred citations.

  3. Sep 2017