Publishing software papers

--- tags: unconference title: Publishing software papers --- # Publishing software papers Publications are the currency for researchers and number and distribution of publications can often be a tie-breaker for getting fundings, so let’s talk about where to publish research software papers. ## Where do you publish your software? - [Journal of Open Source Software (JOSS)](https://joss.theoj.org/) - peer reviewed - open access - no fee - [Journal of Open Research Software (JORS)](https://openresearchsoftware.metajnl.com/) - peer reviewed - open access - publication fee, but can be waived? [see here](https://openresearchsoftware.metajnl.com/about/submissions/) - [software-X](https://www.journals.elsevier.com/softwarex/) - [Geoscientific Model Development (GMD)](https://www.geoscientific-model-development.net/index.html) - open peer reviewed - open access - publication fee - [Applied Physics Reviews](https://aip.scitation.org/journal/are) - Field-specific journals can let you publish a software paper or software update paper, as long as the manuscript also shows practical applications of the software/method on a scientific topic within the scope of the journal. This is more work, but it has the advantage that the paper provides a use case of the software in your field. For chemistry and biology: [JCIM](https://pubs.acs.org/page/jcisd8/about.html), [JCTC](https://pubs.acs.org/page/jctcce/about.html), [JCAMD](https://www.springer.com/journal/10822), [Plos Comp Biol](https://journals.plos.org/ploscompbiol/s/journal-information), [Bioinformatics](https://academic.oup.com/bioinformatics/pages/About), [Proteins](https://onlinelibrary.wiley.com/page/journal/10970134/homepage/productinformation.html). ## Some questions to start discussion - What are the forums that accept research software papers? There are e.g. JOSS, JORS, softwareX, do you know others? - What to publish there? When is a research software "good enough" to be published in a journaArtl? - It depends on the level or size of the software (package/module -> earth system model). - How do these journals compare to traditional journals? When should you choose a "traditional" forum and when a software forum, what are the advantages and disadvantages of each? - How are these journals ranked compared to other ones? Some countries (e.g. Finland and Norway) have a ranking system of publication forums. How are these forums ranked? How should they be ranked? - For example according to the Finnish publication forums ranking system (JUFO) has 3 degrees for "good" forums: 1, 2, 3. And JUFO 0 for both "suspicious" forums and small/new ones. JUFO 0 publications cannot e.g. be included into PhD dissertations and are not well seen in funding applications. JOSS and JORS are JUFO 0. Software-X is JUFO 1. - Is there enough awareness of these forums? Are all RSEs and researchers aware of these forums and related issues? What can we do to increase awareness (if needed)? ## Notes comments about the discussion - articles are no longer found by looking at table of contents - using google scholar it almost does not matter anymore where one publishes other than what eg universities require (?) for the article being found by other researchers - referee process should be more of a dialogue than getting a review and answering it once (it used to be more like that) - 'the internet' will probably also hit the publishing industry at some point - in arxiv one can submit paper+code+data - JOSS interactive discussion on review and public - acceptance rate can be super high - which may paradoxically be a reason for it being JUFO 0 (in Finland) - paper is submitted as part of the repository (in markdown) - When is your code good enough for a software paper? - software papers "freeze" the software in time - how to cope for software getting updated but paper not - encourange to check repository intead of the paper - Zenodo DOI -> bibtex? - (in eg Zotero one can input the DOI and it gives the information which can be exported into bibtex (not tried if it works with Zenodo publications)) - https://zenodo.org/record/4891793#.YNxt3m6xWqQ - it's at the bottom ~~left~~ (or bottom right ;-)) of the page, you can export the BiBTeX. - We need to start citing from Zenodo/github releases etc - Zenodo ## Is there enough awareness of software publishing practices and how to improve - For phd students, most software papers, if accepted in the fist place, would probably be considerd "secondary paper" - If more people coded, more people would value software papers/zenodo - how to measure skill level for eg PhD students to decide who should work on code/research - if current ranking systems gives monetary award for highest ranked publications (e.g. JUFO 2 and 3 in forums) how can software papers be ranked higher if e.g. JOSS has a more constructive review process so acceptance ratae is high