Blog for the Journal of Open Source Software • https://joss.theoj.org

Five years ago, we introduced a second criterion,

 “substantial scholarly effort”

, to ensure that we publish meaningful contributions to research software. Our benchmark at the time – at least roughly three months of developer time – offered a practical, human-centered proxy for effort. For that era, it served us well. Today, the landscape is fundamentally different.

Preparing JOSS for a generative AI future: From code to human creativity and design

University of Illinois Urbana-Champaign

The Journal of Open Source Software (JOSS) is committed to the Principles of Open Scholarly Infrastructure, and here we summarize our status in doing so, followed by a more detailed discussion of how we do so, as well as explaining some when we do not, and some work in progress.

JOSS’s Commitment to the Principles of Open Scholarly Infrastructure

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Apple, Spotify, YouTube, RSS Mats van Es joins Arfon and Abby to discuss reproducible science and the functionality he added to FieldTrip, a MATLAB software toolbox for analyzing brain imaging data. Mats is a cognitive neuroscientist at the University of Oxford. You can follow Mats on Twitter/X @mats_van_es.

JOSSCast #9: Reproducibility in Neuroscience – Mats van Es on FieldTrip reproducescript

The Journal of Open Source Software (JOSS) is a free, open-access online journal, with no article processing charge (APC). We are committed to operating as a free service to our community, and we do so thanks to the volunteer labor of editors and reviewers, and by taking advantage of existing infrastructure.

Cost models for running an online open journal

On March 12th of this year, we suspended new submissions to JOSS in order to reduce the load on our volunteer team of editors and reviewers. We revisited this suspension in early April and decided to continue the pause on new submissions for at least another month. Over the past two weeks, we’ve been reviewing our current status and discussing what it might look like to reopen JOSS.

Reopening JOSS

Once again we’re looking to grow our editorial team at JOSS. We’re especially interested in recruiting editors with expertise in bioinformatics, material science, physics, R/statistics, and the social sciences. Since our launch in May 2016, our existing editorial team has handled over 800 submissions (830 published at the time of writing, 119 under review) and the demand from the community continues to grow.

Call for editors

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Apple, Spotify, YouTube, RSS In this episode of Open Source for Researchers hosts Abby and Arfon explore the world of open source software in astronomy with Dr. Taylor James Bell, a BAER Institute postdoc at NASA Ames. Eureka! is an end-to-end pipeline designed for JWST (James Webb Space Telescope) time series observations.

JOSSCast #2: Astronomy in the Open – Dr. Taylor James Bell on Eureka!

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Apple, Spotify, YouTube, RSS Irea Mosquera-Lois and Seán Kavanagh join Arfon and Abby to discuss releasing software based on important research observations, earning a PhD, and building ShakeNBreak, a defect structure searching method that better identifies low-energy structures. Irea is a PhD Student at Imperial College London. Seán is an Environmental Fellow at Harvard University.

JOSSCast #10: Defect Structure Searching – Irea Mosquera-Lois and Seán Kavanagh on ShakeNBreak

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Apple, Spotify, YouTube, RSS Giulia Crocioni joins Arfon and Abby to discuss DeepRank2, a deep learning framework for 3D protein structure predictions. Giulia is a Research Software Engineer at the Netherlands eScience Center where she uses different machine learning techniques to develop and contribute to methodologies and applications to answer life sciences research questions.

JOSSCast #8: Deep Learning for 3D Protein Structure Predictions – Giulia Crocioni on DeepRank2

Once again, we’re looking to grow our editorial team at JOSS! Since our launch in May 2016, our existing editorial team has handled over 2000 submissions (1838 published at the time of writing, 215 under review) and the demand from the community continues to be strong. JOSS now consistently publishes a little over one paper per day, and we see no sign of this demand dropping.

JOSS is continuing to grow, and we are looking to add more editors again. We’re especially interested in recruiting editors with expertise in bioinformatics, neuroinformatics/neuroimaging, material science, ecology, machine learning &amp; data science, and the social sciences.

tl;dr – JOSS is introducing new submission criteria whereby submissions under 1000 lines of code will automatically be flagged as potentially being out of scope, and those under 300 lines desk-rejected. This blog post describes some of the motivations behind this decision. Sometime in 2020, JOSS will publish its 1000th paper – an incredible achievement by a volunteer team of editors and reviewers. Since its inception a little over four years ago, the primary goal of JOSS has always been to provide credit for authors of research software. Quoting from the original blog post announcing JOSS: The primary purpose of a JOSS paper is to enable citation credit to be given to authors of research software. One challenge we’ve always struggled with as an editorial team is defining clear guidelines for submissions allowed (and not allowed) in JOSS. Our current submission criteria are available online and include language about software having to be a significant contribution, feature complete, and having an obvious research application. In these criteria we also explicitly exclude a category of software we generally call “minor utilities”. The challenge of defining a unit of publication credit We think of JOSS essentially granting “1 publication credit” for each software package that is reviewed and published in the journal. In empirical research, a publication is often the result of years of work. In engineering research, rarely does a paper represent less than one year of work. Other fields may vary, but let’s say that a scientific paper resulting from work measured in just months is rare or exceptional. Since the earliest days of the journal, there has been a range of views within the editorial team on what level of effort we should require from authors for a submission to be allowed in JOSS – some JOSS editors feeling that every useful piece of software should be considered, others believing that the “bar” for publishing in JOSS should be higher than it currently is. Building trust in JOSS As an editorial team we want JOSS papers to count the same as any other publication in the CV of researchers who write software. With career credit the stated primary reason for starting JOSS, if this isn’t true then the mission of the journal is at risk. In reality this means that our editorial policy requires us to balance two competing needs: Providing an excellent service to authors by offering peer-review of their software and the opportunity to receive career credit for their work. Building the trust of an existing academic culture to accept a JOSS paper as equal to any peer-reviewed journal paper. These two aspects are in tension with each other because while we would dearly love to publish any and all research software in JOSS regardless of size/scale and level of effort to implement, part of building and maintaining that trust with the community relies on us ensuring that our published authors can continue to expect JOSS papers to “count” in their future merit reviews and promotions. Updates to our submission requirements and scope-checking procedures Over the past couple of years, as the number of submissions to JOSS has grown, we’ve found that our existing submission criteria and protocol for rejecting papers as out of scope have been taking a significant fraction of our editorial team time. With a volunteer team of editors, it’s essential that we use their time carefully and an update to our procedures for handling scope assessments is long overdue. Going forward we’re going to adopt the following new process: Automatically flagging small submissions As part of the pre-review process, incoming submissions that are under 1000 lines of code1 (LOC) will be automatically flagged as potentially out of scope by the EiC on rotation. Submissions under 300 lines2 of code will be desk rejected with no further review. Mandatory “Statement of need” section in JOSS papers While this has always been preferred, a clear Statement of need section in the JOSS paper is usually extremely valuable in helping the editorial team understand the rationale for the development of the software. Gauging the scholarly content of the software as part of the review Reviewers will be asked if the software under review is a “substantial scholarly effort” and guidelines will be provided on how they can make that assessment. A streamlined editorial review process Rather than each paper that is potentially out-of-scope being discussed in a separate thread on our editorial mailing list, JOSS is going to move to a weekly review of such papers by our editorial team. Topic editors will be asked to review papers flagged as potentially out of scope in their area and help the EiC team make a decision. References Smith A. Announcing The Journal of Open Source Software - Arfon Smith. Published online May 5, 2016. Accessed July 7, 2020. https://www.arfon.org/announcing-the-journal-of-open-source-software In a high-level language such as Python or R. More verbose languages such as Java, C++, Fortran etc. will require more LOC. &#8617; We realize that introducing numerical thresholds may encourage some authors to unnecessarily “pad” their submissions with additional lines of code to meet our thresholds. As reviewers are already asked to judge the standard of the implementation as part of their review we expect that situations like these will usually be flagged during the review. &#8617;

Sometime in 2020, JOSS will publish its 1000

 th

paper – an incredible achievement by a volunteer team of editors and reviewers. Since its inception a little over four years ago, the primary goal of JOSS has always been to provide credit for authors of research software.

Minimum publishable unit

The Journal of Open Source Software (JOSS) started with one editor-in-chief (EiC) and 10 topic editors, and in our first year, we published about 100 papers. Three years later, the rate of publication has increased to 300 papers per year. How did we scale up to this point, and how can we continue scaling the journal? Scaling to-date   Today, we have one editor-in-chief (EiC), three associate editors-in-chief (AEiCs), and 23 topic editors.

Scaling the Journal of Open Source Software (JOSS)

JOSS is expanding its editorial board and we’re opening this opportunity to the open source research software community at large. If you think you might be interested, take a look at our editorial guide which describes the editorial workflow at JOSS and also some of the reviews for recently accepted papers. Between these two, you should be able to get a good overview of what editing for JOSS looks like.

Today we’re starting something new at JOSS: we’re collaborating with American Astronomical Society (AAS) Journals to offer software reviews for some of the papers submitted to their journals. As part of this process, AAS Publishing will make a small contribution to our parent organization NumFOCUS to support the running costs of JOSS.

A new collaboration with AAS publishing

Once again, we’re looking to grow our editorial team at JOSS! Since our launch in May 2016, our existing editorial team has handled nearly 4100 submissions (~2700 published at the time of writing, 340 under review) and the demand from the community continues to be strong. JOSS now consistently publishes 40-45 papers per month, and this is gradually increasing.

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Apple, Spotify, YouTube, RSS Juliette Hayer joins Arfon and Abby to discuss Baargin, an open source tool she created to analyze bacterial genomes, especially those resistant to antibiotics.

JOSSCast #3: Studying Superbugs – Juliette Hayer on Baargin

JOSS is continuing to grow, and we are looking to add more editors with expertise in the area of astronomy &amp; astrophysics. Since our launch in May 2016, our existing editorial team has handled nearly 1900 submissions (1684 published at the time of writing, 205 under review) and the demand from the community continues to grow. In particular, we have seen an increase in the number of astronomy &amp;

Call for editors: Astronomy &amp; Astrophysics

This week JOSS reached a big milestone – publishing our 2000th paper! It also happens to be our 7th birthday, and we thought we’d take this opportunity to review our submission stats from the last few years, discuss some of the changes to JOSS we’ve made of late, and reflect on some of the challenges we have faced as a journal.

JOSS publishes 2000th paper

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Apple, Spotify, YouTube, RSS Gui Castelão and Luiz Irber join Arfon and Abby to discuss their work implementing the Gibbs Sea Water Oceanographic Toolbox of TEOS-10 in Rust, and the role of instrument builders in science. Gui is an oceanographer at the Scripps Institution of Oceanography, previously part of the Instrument Developing Group. Luiz is a Computer Science PhD at UC Davis and an avid Rustacean.

JOSSCast #5: Rewrite in Rust – Gui Castelão and Luiz Irber on Gibbs SeaWater Oceanographic Toolbox in Rust

Following our call for editors late last year, once again we’re looking to grow our editorial team.  Over the past ~40 months, our existing editorial team has handled close to 800 submissions (665 accepted at the time of writing, 101 under review) and the demand from the community continues to grow. The last three months have been our busiest yet, with JOSS publishing a little over one paper every day, and we see no sign of this demand dropping.

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Apple, Spotify, YouTube, RSS Jimmy Shen sat down with Arfon and Abby to discuss the role of defect analysis in semiconductor research, the Materials Project, and the development of pymatgen-analysis-defects. Jimmy is a postdoc at the Lawrence Livermore National Laboratory where he tries his best to automate himself away. You can follow Jimmy on GitHub @jmmshn, Linkedin, or on Google Scholar.

JOSSCast #7: Adding defect analysis to the Materials Project – Jimmy Shen on pymatgen-analysis-defects

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Apple, Spotify, YouTube, RSS Marjan Albooyeh and Chris Jones chat with Arfon and Abby about their experience building FlowerMD, an open-source library of recipes for molecular dynamics workflows. Marjan and Chris are both grad students in Dr. Jankowski’s lab at Boise State University where they use molecular dynamics to study materials for aerospace applications and organic solar cells.

JOSSCast #6: Streamlining Molecular Dynamics – Marjan Albooyeh and Chris Jones on FlowerMD

Once again, we’re looking to grow our editorial team at JOSS! Since our launch in May 2016, our existing editorial team has handled nearly 3000 submissions (2182 published at the time of writing, 265 under review) and the demand from the community continues to be strong. JOSS now consistently publishes a little over one paper per day, and we see no sign of this demand dropping.

Lorena A. Barba

JOSS is an adventure in next generation publishing, made possible by the volunteer work of many people. Our editors, of course, guide the style and the content of the journal. And our reviewers make a uniquely valuable contribution, both to the software they’ve reviewed and to the broader community of open-source research software. Some reviewers have been extra generous in contributing.

A special thanks to our most dedicated reviewers

Today we reached a huge milestone at JOSS – we published our 1000

 th

paper! JOSS is a developer friendly, free-to-publish, open-access journal for research software packages. Publishing 1000 papers (and reviewing the corresponding 1000 software packages) over the past ~4 years has been no small feat.

1000 papers published in JOSS

We’re once more looking to grow our editorial team at JOSS! Since our launch in May 2016, our existing editorial team has handled over 5000 submissions (over 3000 published at the time of writing, almost 500 under review) and the demand from the community continues to be strong. JOSS now consistently publishes 40-45 papers per month, and this is gradually increasing.

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Apple, Spotify, YouTube, RSS Nicolas Renaud joins Arfon and Abby to discuss QMCTorch, a PyTorch implementation of real-space Quantum Monte-Carlo simulations of molecular systems, and work to promote research software as a research output. Nico is the head of the Natural Sciences and Engineering section of the Netherlands eScience Center and Senior Researcher at the Quantum Application Lab.

JOSSCast #4: Applying ML to Quantum Monte Carlo simulations – Nicolas Renaud on QMCTorch

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Apple, Spotify, YouTube, RSS In the first episode of Open Source for Researchers, hosts Arfon and Abby sit down with Eva Maxfield Brown to discuss Speakerbox, an open source speaker identification tool. Originally part of the Council Data Project, Speakerbox was used to train models to identify city council members speaking in transcripts, starting with cities like Seattle.

JOSSCast #1: Eva Maxfield Brown on Speakerbox – Open Source Speaker Identification for Political Science

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Apple, Spotify, YouTube, RSS We’re thrilled to announce the launch of “JOSSCast: Open Source for Researchers” - a podcast exploring new ways open source can accelerate your work. Hosted by Arfon Smith and Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. There are 3 episodes available for you to listen to today!

Introducing JOSSCast: Open Source for Researchers 🎉

2019 has been a big year for JOSS: This year, we’ve already published 300 papers and are on target to reach ~360 papers by the end of the calendar year. We’ve substantially improved our website and made a number of important changes to our editorial team to help us scale further.

Journal of Open Source Software Blog |

A new collaboration with AAS publishing