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paper.bib
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@article{smith2018,
title = {Journal of Open Source Software (JOSS): design and first-year review},
author = {Smith, Arfon M. and Niemeyer, Kyle E. and Katz, Daniel S. and Barba, Lorena A. and Githinji, George and Gymrek, Melissa and Huff, Kathryn D. and Madan, Christopher R. and Cabunoc Mayes, Abigail and Moerman, Kevin M. and Prins, Pjotr and Ram, Karthik and Rokem, Ariel and Teal, Tracy K. and Valls Guimera, Roman and Vanderplas, Jacob T.},
year = 2018,
month = feb,
keywords = {Research software, Code review, Computational research, Software citation, Open-source software, Scholarly publishing},
abstract = {
This article describes the motivation, design, and progress of the Journal of Open Source Software (JOSS). JOSS is a free and open-access journal that publishes articles describing research software. It has the dual goals of improving the quality of the software submitted and providing a mechanism for research software developers to receive credit. While designed to work within the current merit system of science, JOSS addresses the dearth of rewards for key contributions to science made in the form of software. JOSS publishes articles that encapsulate scholarship contained in the software itself, and its rigorous peer review targets the software components: functionality, documentation, tests, continuous integration, and the license. A JOSS article contains an abstract describing the purpose and functionality of the software, references, and a link to the software archive. The article is the entry point of a JOSS submission, which encompasses the full set of software artifacts. Submission and review proceed in the open, on GitHub. Editors, reviewers, and authors work collaboratively and openly. Unlike other journals, JOSS does not reject articles requiring major revision; while not yet accepted, articles remain visible and under review until the authors make adequate changes (or withdraw, if unable to meet requirements). Once an article is accepted, JOSS gives it a digital object identifier (DOI), deposits its metadata in Crossref, and the article can begin collecting citations on indexers like Google Scholar and other services. Authors retain copyright of their JOSS article, releasing it under a Creative Commons Attribution 4.0 International License. In its first year, starting in May 2016, JOSS published 111 articles, with more than 40 additional articles under review. JOSS is a sponsored project of the nonprofit organization NumFOCUS and is an affiliate of the Open Source Initiative (OSI).
},
volume = 4,
pages = {e147},
journal = {PeerJ Computer Science},
issn = {2376-5992},
url = {https://doi.org/10.7717/peerj-cs.147},
doi = {10.7717/peerj-cs.147}
}
@article{krewinkel2017,
title = {Formatting Open Science: agilely creating multiple document formats for academic manuscripts with Pandoc Scholar},
author = {Krewinkel, Albert and Winkler, Robert},
year = 2017,
month = may,
keywords = {Open science, Markdown, Latex, Publishing, Typesetting, Document formats},
abstract = {
The timely publication of scientific results is essential for dynamic advances in science. The ubiquitous availability of computers which are connected to a global network made the rapid and low-cost distribution of information through electronic channels possible. New concepts, such as Open Access publishing and preprint servers are currently changing the traditional print media business towards a community-driven peer production. However, the cost of scientific literature generation, which is either charged to readers, authors or sponsors, is still high. The main active participants in the authoring and evaluation of scientific manuscripts are volunteers, and the cost for online publishing infrastructure is close to negligible. A major time and cost factor is the formatting of manuscripts in the production stage. In this article we demonstrate the feasibility of writing scientific manuscripts in plain markdown (MD) text files, which can be easily converted into common publication formats, such as PDF, HTML or EPUB, using Pandoc. The simple syntax of Markdown assures the long-term readability of raw files and the development of software and workflows. We show the implementation of typical elements of scientific manuscripts—formulas, tables, code blocks and citations—and present tools for editing, collaborative writing and version control. We give an example on how to prepare a manuscript with distinct output formats, a DOCX file for submission to a journal, and a LATEX/PDF version for deposition as a PeerJ preprint. Further, we implemented new features for supporting ‘semantic web’ applications, such as the ‘journal article tag suite’—JATS, and the ‘citation typing ontology’—CiTO standard. Reducing the work spent on manuscript formatting translates directly to time and cost savings for writers, publishers, readers and sponsors. Therefore, the adoption of the MD format contributes to the agile production of open science literature. Pandoc Scholar is freely available from https://github.com/pandoc-scholar.
},
volume = 3,
pages = {e112},
journal = {PeerJ Computer Science},
issn = {2376-5992},
url = {https://doi.org/10.7717/peerj-cs.112},
doi = {10.7717/peerj-cs.112}
}
@book{Dominik2010,
author = {Carsten Dominik},
title = {The Org-Mode 7 Reference Manual: Organize
Your Life with GNU Emacs},
publisher = {Network Theory},
year = 2010,
address = {UK},
note = {with contributions by David O'Toole, Bastien Guerry,
Philip Rooke, Dan Davison, Eric Schulte, and Thomas
Dye}
}
@online{reStructuredText,
author = {David Goodger and others},
title = {reStructuredText},
date = {2022-04},
urldate = {2022-04-19},
url = {https://docutils.sourceforge.io/rst.html}
}
@inproceedings{johnston2016jatdown,
title = {Jatdown: A markdown language for writing JATS},
author = {Johnston, Paul},
booktitle = {Journal Article Tag Suite Conference (JATS-Con) Proceedings 2016 [Internet]},
year = {2016},
organization = {National Center for Biotechnology Information (US)}
}
@online{OfficialYAMLWeb,
title = {The {{Official YAML Web Site}}},
url = {https://yaml.org/},
keywords = {YAML},
date = {2022-04-19},
urldate = {2022-04-19},
}
@techreport{pdfa3,
type = {Standard},
key = {ISO 19005-3:2012},
date = {2012-10},
title = {Document management — Electronic document file format for long-term preservation — Part 3: Use of {ISO} 32000-1 with support for embedded files ({PDF/A-3})},
address = {Geneva, CH},
institution = {International Organization for Standardization}
}
@online{chatops,
title = {Chatops-driven publishing},
author = {Smith, Arfon},
url = {https://www.arfon.org/chatops-driven-publishing},
urldate = {2022-04-22},
keywords = {joss,whedon},
}
@software{quarto,
author = {Allaire, J.J. and Teague, Charles and Scheidegger, Carlos and Xie, Yihui and Dervieux, Christophe},
doi = {10.5281/zenodo.5960048},
month = {1},
title = {{Quarto}},
url = {https://github.com/quarto-dev/quarto-cli},
version = {0.3},
year = {2022}
}