Submitting a paper to JOSS

If you’ve already developed a fully featured research code, released it under an OSI-approved license, and written good documentation and tests, then we expect that it should take perhaps an hour or two to prepare and submit your paper to JOSS. But please read these instructions carefully for a streamlined submission.

Submission requirements

  • The software should be open source as per the OSI definition.
  • The software should have an obvious research application.
  • You should be a major contributor to the software you are submitting.
  • The software should be a significant contribution to the available open source software that either enables some new research challenges to be addressed or makes addressing research challenges significantly better (e.g., faster, easier, simpler).
  • The software should be feature-complete (no half-baked solutions) and designed for maintainable extension (not one-off modifications). Minor ‘utility’ packages, including ‘thin’ API clients, are not acceptable.
  • Your paper (paper.md and BibTeX files, plus any figures) must be hosted in a Git-based repository, ideally together with your software.

In addition, the software associated with your submission must:

  • Be stored in a repository that can be cloned without registration.
  • Be stored in a repository that is browsable online without registration.
  • Have an issue tracker that is readable without registration.
  • Permit individuals to create issues/file tickets against your repository.

JOSS publishes articles about research software. This definition includes software that: solves complex modeling problems in a scientific context (physics, mathematics, biology, medicine, social science, neuroscience, engineering); supports the functioning of research instruments or the execution of research experiments; extracts knowledge from large data sets; offers a mathematical library, or similar.

Typical paper submission flow

Before you submit, you should:

  • Make your software available in an open repository (GitHub, Bitbucket, etc.) and include an OSI approved open source license.
  • Make sure that the software complies with the JOSS review criteria. In particular, your software should be full-featured, well-documented, and contain procedures (such as automated tests) for checking correctness.
  • Write a short paper in Markdown format using paper.md as file name, including a title, summary, author names, affiliations, and key references. See our example paper to follow the correct format.
  • (Optional) create a metadata file describing your software and include it in your repository. We provide a script that automates the generation of this metadata.

What should my paper contain?

Important

Begin your paper with a summary of the high-level functionality of your software for a non-specialist reader. Avoid jargon in this section.

JOSS welcomes submissions from broadly diverse research areas. For this reason, we require that authors include in the paper some sentences that explain the software functionality and domain of use to a non-specialist reader. We also require that authors explain the research applications of the software. The paper should be between 250-1000 words.

Your paper should include:

  • A list of the authors of the software and their affiliations, using the correct format (see the example below).
  • A summary describing the high-level functionality and purpose of the software for a diverse, non-specialist audience.
  • A clear Statement of Need that illustrates the research purpose of the software.
  • A list of key references, including to other software addressing related needs.
  • Mention (if applicable) of any past or ongoing research projects using the software and recent scholarly publications enabled by it.
  • Acknowledgement of any financial support.

As this short list shows, JOSS papers are only expected to contain a limited set of metadata (see example below), a Statement of Need, Summary, Acknowledgements, and References sections. You can look at an example accepted paper. Given this format, a “full length” paper is not permitted, and software documentation such as API (Application Programming Interface) functionality should not be in the paper and instead should be outlined in the software documentation.

Important

Your paper will be reviewed by two or more reviewers in a public GitHub issue. Take a look at the review checklist and review criteria to better understand how your submission will be reviewed.

Example paper and bibliography

This example paper.md is adapted from Gala: A Python package for galactic dynamics by Adrian M. Price-Whelan http://doi.org/10.21105/joss.00388:

---
title: 'Gala: A Python package for galactic dynamics'
tags:
  - Python
  - astronomy
  - dynamics
  - galactic dynamics
  - milky way
authors:
  - name: Adrian M. Price-Whelan
    orcid: 0000-0003-0872-7098
    affiliation: "1, 2" # (Multiple affiliations must be quoted)
  - name: Author Without ORCID
    affiliation: 2
affiliations:
 - name: Lyman Spitzer, Jr. Fellow, Princeton University
   index: 1
 - name: Institution 2
   index: 2
date: 13 August 2017
bibliography: paper.bib

# Optional fields if submitting to a AAS journal too, see this blog post:
# https://blog.joss.theoj.org/2018/12/a-new-collaboration-with-aas-publishing
aas-doi: 10.3847/xxxxx <- update this with the DOI from AAS once you know it.
aas-journal: Astrophysical Journal <- The name of the AAS journal.
---

# Summary

The forces on stars, galaxies, and dark matter under external gravitational
fields lead to the dynamical evolution of structures in the universe. The orbits
of these bodies are therefore key to understanding the formation, history, and
future state of galaxies. The field of "galactic dynamics," which aims to model
the gravitating components of galaxies to study their structure and evolution,
is now well-established, commonly taught, and frequently used in astronomy.
Aside from toy problems and demonstrations, the majority of problems require
efficient numerical tools, many of which require the same base code (e.g., for
performing numerical orbit integration).

``Gala`` is an Astropy-affiliated Python package for galactic dynamics. Python
enables wrapping low-level languages (e.g., C) for speed without losing
flexibility or ease-of-use in the user-interface. The API for ``Gala`` was
designed to provide a class-based and user-friendly interface to fast (C or
Cython-optimized) implementations of common operations such as gravitational
potential and force evaluation, orbit integration, dynamical transformations,
and chaos indicators for nonlinear dynamics. ``Gala`` also relies heavily on and
interfaces well with the implementations of physical units and astronomical
coordinate systems in the ``Astropy`` package [@astropy] (``astropy.units`` and
``astropy.coordinates``).

``Gala`` was designed to be used by both astronomical researchers and by
students in courses on gravitational dynamics or astronomy. It has already been
used in a number of scientific publications [@Pearson:2017] and has also been
used in graduate courses on Galactic dynamics to, e.g., provide interactive
visualizations of textbook material [@Binney:2008]. The combination of speed,
design, and support for Astropy functionality in ``Gala`` will enable exciting
scientific explorations of forthcoming data releases from the *Gaia* mission
[@gaia] by students and experts alike.

# Mathematics

Single dollars ($) are required for inline mathematics e.g. $f(x) = e^{\pi/x}$

Double dollars make self-standing equations:

$$\Theta(x) = \left\{\begin{array}{l}
0\textrm{ if } x < 0\cr
1\textrm{ else}
\end{array}\right.$$


# Citations

Citations to entries in paper.bib should be in
[rMarkdown](http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html)
format.

For a quick reference, the following citation commands can be used:
- `@author:2001`  ->  "Author et al. (2001)"
- `[@author:2001]` -> "(Author et al., 2001)"
- `[@author1:2001; @author2:2001]` -> "(Author1 et al., 2001; Author2 et al., 2002)"

# Figures

Figures can be included like this: ![Example figure.](figure.png)

# Acknowledgements

We acknowledge contributions from Brigitta Sipocz, Syrtis Major, and Semyeong
Oh, and support from Kathryn Johnston during the genesis of this project.

# References

Example paper.bib file:

@article{Pearson:2017,
  	Adsnote = {Provided by the SAO/NASA Astrophysics Data System},
  	Adsurl = {http://adsabs.harvard.edu/abs/2017arXiv170304627P},
  	Archiveprefix = {arXiv},
  	Author = {{Pearson}, S. and {Price-Whelan}, A.~M. and {Johnston}, K.~V.},
  	Eprint = {1703.04627},
  	Journal = {ArXiv e-prints},
  	Keywords = {Astrophysics - Astrophysics of Galaxies},
  	Month = mar,
  	Title = {{Gaps in Globular Cluster Streams: Pal 5 and the Galactic Bar}},
  	Year = 2017
}

@book{Binney:2008,
  	Adsnote = {Provided by the SAO/NASA Astrophysics Data System},
  	Adsurl = {http://adsabs.harvard.edu/abs/2008gady.book.....B},
  	Author = {{Binney}, J. and {Tremaine}, S.},
  	Booktitle = {Galactic Dynamics: Second Edition, by James Binney and Scott Tremaine.~ISBN 978-0-691-13026-2 (HB).~Published by Princeton University Press, Princeton, NJ USA, 2008.},
  	Publisher = {Princeton University Press},
  	Title = {{Galactic Dynamics: Second Edition}},
  	Year = 2008
}

@article{gaia,
    author = {{Gaia Collaboration}},
    title = "{The Gaia mission}",
    journal = {\aap},
    archivePrefix = "arXiv",
    eprint = {1609.04153},
    primaryClass = "astro-ph.IM",
    keywords = {space vehicles: instruments, Galaxy: structure, astrometry, parallaxes, proper motions, telescopes},
    year = 2016,
    month = nov,
    volume = 595,
    doi = {10.1051/0004-6361/201629272},
    adsurl = {http://adsabs.harvard.edu/abs/2016A%26A...595A...1G},
}

@article{astropy,
    author = {{Astropy Collaboration}},
    title = "{Astropy: A community Python package for astronomy}",
    journal = {\aap},
    archivePrefix = "arXiv",
    eprint = {1307.6212},
    primaryClass = "astro-ph.IM",
    keywords = {methods: data analysis, methods: miscellaneous, virtual observatory tools},
    year = 2013,
    month = oct,
    volume = 558,
    doi = {10.1051/0004-6361/201322068},
    adsurl = {http://adsabs.harvard.edu/abs/2013A%26A...558A..33A}
}

Note that the paper ends with a References heading, and the references are built automatically from the content in the .bib file. You should enter in-text citations in the paper body following correct Markdown citation syntax.

Checking that your paper compiles

JOSS uses Pandoc to compile papers from their Markdown form into a PDF. You can test that your paper is properly structured using the JOSS paper preview service.

Submitting your paper

Submission is as simple as:

  • Filling in the short submission form
  • Waiting for the managing editor to start a pre-review issue over in the JOSS reviews repository: https://github.com/openjournals/joss-reviews

No submission fees

There are no fees for submitting or publishing in JOSS. You can read more about our cost and sustainability model.

Preprint Policy

Authors are welcome to submit their papers to a preprint server (arXiv, bioRxiv, SocArXiv, PsyArXiv etc.) at any point during the submission and review process.

Submission to a preprint server is not considered a previous publication.

Authorship

Purely financial (such as being named on an award) and organizational (such as general supervision of a research group) contributions are not considered sufficient for co-authorship of JOSS submissions, but active project direction and other forms of non-code contributions are. The authors themselves assume responsibility for deciding who should be credited with co-authorship, and co-authors must always agree to be listed. In addition, co-authors agree to be accountable for all aspects of the work, and to notify JOSS if any retraction or correction of mistakes are needed after publication.

Submissions using proprietary languages/dev environments

We strongly prefer software that doesn’t rely upon proprietary (paid for) development environments/programming languages. However, provided your submission meets our requirements (including having a valid open source license) then we will consider your submission for review. Should your submission be accepted for review, we may ask you, the submitting author, to help us find reviewers who already have the required development environment installed.

The review process

After submission:

  • An Associate Editor-in-Chief will carry out an initial check of your submission, and proceed to assign a handling editor.
  • The handling editor will assign two or more JOSS reviewers, and the review will be carried out in the JOSS reviews repository.
  • Authors will respond to reviewer-raised issues (if any are raised) on the submission repository’s issue tracker. Reviewer and editor contributions, like any other contributions, should be acknowledged in the repository.
  • Upon successful completion of the review, authors will make a tagged release of the software, and deposit a copy of the repository with a data-archiving service such as Zenodo or figshare, get a DOI for the archive, and update the review issue thread with the version number and DOI.
  • After we assign a DOI for your accepted JOSS paper, its metadata is deposited with CrossRef and listed on the JOSS website.
  • The review issue will be closed, and an automatic tweet from @JOSS_TheOJ will announce it!

If you want to learn more details about the review process, take a look at the reviewer guidelines.