paper.bib

@article{bradford1976,
  title = {A Rapid and Sensitive Method for the Quantitation of Microgram
                  Quantities of Protein Utilizing the Principle of Protein-Dye
                  Binding},
  author = {Bradford, Marion M.},
  date = {1976},
  journaltitle = {Analytical Biochemistry},
  volume = {72},
  number = {1},
  pages = {248--254},
  issn = {0003-2697},
  doi = {10.1016/0003-2697(76)90527-3},
  url = {https://www.sciencedirect.com/science/article/pii/0003269776905273},
  abstract = {A protein determination method which involves the binding of
                  Coomassie Brilliant Blue G-250 to protein is described. The
                  binding of the dye to protein causes a shift in the absorption
                  maximum of the dye from 465 to 595 nm, and it is the increase
                  in absorption at 595 nm which is monitored. This assay is very
                  reproducible and rapid with the dye binding process virtually
                  complete in approximately 2 min with good color stability for
                  1 hr. There is little or no interference from cations such as
                  sodium or potassium nor from carbohydrates such as sucrose. A
                  small amount of color is developed in the presence of strongly
                  alkaline buffering agents, but the assay may be run accurately
                  by the use of proper buffer controls. The only components
                  found to give excessive interfering color in the assay are
                  relatively large amounts of detergents such as sodium dodecyl
                  sulfate, Triton X-100, and commercial glassware detergents.
                  Interference by small amounts of detergent may be eliminated
                  by the use of proper controls.}
}

@online{chatops,
  title = {Chatops-{{Driven Publishing}} | {{Arfon Smith}}},
  author = {Smith, Arfon},
  url = {https://www.arfon.org/chatops-driven-publishing},
  urldate = {2022-04-22},
  keywords = {joss,whedon},
}
@article{upper1974,
  title = {The Unsuccessful Self-Treatment of a Case of "Writer's Block"},
  author = {Upper, D.},
  date = {1974},
  journaltitle = {Journal of Applied Behavior Analysis},
  shortjournal = {J Appl Behav Anal},
  volume = {7},
  number = {3},
  eprint = {16795475},
  eprinttype = {pmid},
  pages = {497},
  issn = {0021-8855},
  doi = {10.1901/jaba.1974.7-497a},
  langid = {english},
  pmcid = {PMC1311997},
}

@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}
}

@online{yaml_website,
  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}
}

@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}
}