Academic publishing

Some notes to the connection between reproducibility, scholarly discovery, intellectual property peer-review, academic business models and such.

Realpolitik of journals

Journal rank and journal impact factor etc. Who cares? Your funders care, against your advice but whatever, they have the money, so you need to care too in order that they will keep funding you.

Latrobe explains it. Scimago Journal rank is the Google Pagerank-inspired slightly hipper journal ranking. Their search tool is probably what you want. Impact factors come from the 60s and are still around, h-Index is also a thing.

According to Latrobe, we have the following indices and (partial list of) weaknesses.


Hirsch index: The number of articles in a journal [h] that have received at least [h] citations over a citation period.


  • Editors can manipulate by requiring contributors to add citations from their journals

  • Increases with age so bias towards researchers with long publication records


Journal Impact Factor: Citations to a journal in the JCR year to items published in the previous two years, divided by the total number of citable items (articles and reviews) published in the journal in the previous two years.


  • Limited to journals within Web of Science

  • Cannot be used to compare journals across different subject categories


SCImago Journal Rank: Average number of weighted citations received in a year, by articles published in a journal in the previous 3 years.

Weaknesses are that it is “complicated” and that the numbers are small.

So I guess if you must do a journal ranking this is the least bad method?


Tom Gauld, Suggested methods of presenting your findings

See also academic reading workflow for reader-oriented tips.


    A platform for scholarly publishing and peer review that empowers researchers with the

    • Autonomy to pursue their passions,
    • Authority to develop and disseminate their work, and
    • Access to engage with the international community of scholars.
  • unpaywall:

    Millions of research papers are available for free on government and university web servers, legally uploaded by the authors themselves, with the express permission of publishers. Unpaywall automatically harvests these freely shared papers from thousands of legal institutional repositories, preprint servers, and publishers, making them all available to you as you read.

  • Zenodo “is an open dependable home for the long-tail of science, enabling researchers to share and preserve any research outputs in any size, any format and from any science.”

    • Research. Shared. — all research outputs from across all fields of science are welcome!
    • Citeable. Discoverable. — uploads gets a Digital Object Identifier (DOI) to make them easily and uniquely citeable…
    • Flexible licensing — because not everything is under Creative Commons.
    • Safe — your research output is stored safely for the future in same cloud infrastructure as research data from CERN’s Large Hadron Collider.

    A major win is the easy DOI-linking of data and code for reproducible research. (for free)

  • Open Conference Systems (OCS)

    is a free Web publishing tool that will create a complete Web presence for your scholarly conference. OCS will allow you to:

    • create a conference Web site
    • compose and send a call for papers
    • electronically accept paper and abstract submissions
    • allow paper submitters to edit their work
    • post conference proceedings and papers in a searchable format
    • post, if you wish, the original data sets
    • register participants
    • integrate post-conference online discussions
  • Peeriodicals

    A peeriodical is a lightweight virtual journal with you as the Editor-in-chief, giving you complete freedom in setting editorial policy to select the most interesting and useful manuscripts for your readers.

    I did not find that explanation so useful as the interview the creators gave.

  • The Winnower

    is an open access online scholarly publishing platform that employs open post-publication peer review. You guessed it! We think transparency from start to finish is critical in scientific communication. […]

  • Retraction Watch for sufficiently-high-profile-research is a watchdog blog that has somehow ended up doing a lot of well-regarded gatekeeping/exposure.


Iterations of how this system of review and dissemination system could work better? See Peer review.

The new universal libraries

open access

Various open access (and occasionally also open source) journals attempt to disrupt the incumbent publishers with new business models based around the low cost of internet stuff. As with legacy journals, they have variying degrees of success

One cure boutique example:

Open Journals

Open Journals is a collection of open source, open access journals. We currently have four main publications:

All of our journals run on open source software which is available under our GitHub organization profile:

Creative Commons Licence All of our journals are open access publications with content licensed under a Creative Commons Attribution 4.0 International License. Copyright remains with the submitting authors.

Afonso, Alexandre. 2013. “How Academia Resembles a Drug Gang.” Impact of Social Sciences. December 11, 2013.

Björk, Bo-Christer, and David Solomon. 2013. “The Publishing Delay in Scholarly Peer-Reviewed Journals.” Journal of Informetrics 7 (4): 914–23.

Bogich, Tiffany L, Sebastien Balleseteros, Robin Berjon, Chris Callahan, and Leon Chen. n.d. “On the Marginal Cost of Scholarly Communication.”

Himmelstein, Daniel S., Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, and Anthony Gitter. 2019. “Open Collaborative Writing with Manubot.” Edited by Dina Schneidman-Duhovny. PLOS Computational Biology 15 (6): e1007128.

Krikorian, Gaëlle, and Amy Kapczynski. 2010. Access to Knowledge in the Age of Intellectual Property. New York; Cambridge, Mass.: Zone Books ; Distributed by the MIT Press.

Potts, Jason, John Hartley, Lucy Montgomery, Cameron Neylon, and Ellie Rennie. 2016. “A Journal Is a Club: A New Economic Model for Scholarly Publishing.” SSRN Scholarly Paper ID 2763975. Rochester, NY: Social Science Research Network.

Schimmer, Ralf, Geschuhn, Kai Karin, and Vogler, Andreas. 2015. “Disrupting the Subscription Journals’ Business Model for the Necessary Large-Scale Transformation to Open Access.”

Van Noorden, Richard. 2013. “Open Access: The True Cost of Science Publishing.” Nature 495 (7442): 426–29.