Getting security notifications for 2.0.5. Perhaps bump rack.

I have a short online course, "Generalized Additive Models in R," that I would like to determine eligibility for submission. It is an interactive online course that uses external but free (Binder) resources to run student exercises on the back-end.

The code implementing the interface and interactivity comes from another open-source project, so my contribution is content, all of which is CC-BY. I believe I would submit it as a learning module.

Course (front end): https://noamross.github.io/gams-in-r-course/
Repository: https://github.com/noamross/gams-in-r-course

The website currently seems to suggest that you are open for submissions, but I don't see any submissions at https://github.com/openjournals/jose-reviews, so thought best to ask before I go ahead and submit my paper.

When clicking on the JOSS bibtex badges from our README of this repo:
https://github.com/barbagroup/pygbe

We get an error. (At least on Safari and Chrome.)

This is the URL the first badge points to:
https://www.doi2bib.org/bib/10.21105%2Fjoss.00043

I can't find any data in this repo that contains these blurbs:

I'm interested in updating my blurb.

Project repository URL: https://github.com/wrightaprilm/treesiftr

Hello,

I was thinking of submitting an educational resource here. It straddles the two submission types, in that it is an R package to generate and visualize phylogenetic trees (shiny app here), and I have some worksheets that go with it. A sample slide deck to discuss some of the common phylogenetic tree terms will be in the supplemental material.

I'm wondering if:

• This package is appropriate for JOSE, and if so, which track.
• If I should get the package on CRAN first, or submit here and then put on CRAN.

Obviously, there's still some formatting that would need to be done for JOSE, but I didn't want to do it before I knew if it was appropriate.

Thanks!
April

It would be nice to have documentation for JOSE like there is for JOSS. In openjournals/joss#491 (comment) it was suggested we create our own docs, using the JOSS ones as a starting place.

I'll be working on this issue. Let me know if anyone has any questions or comments on this though.

Project repository URL: https://github.com/curiousDTU/cc-gag

I am teaching a course "Introduction to open source and open standards" to first semester students. I am trying to make students learn git and github. The above repository is the assignment I gave to my students. They are enjoying learning it.
I want to know can I write a research article on it. As it is very basic and at the same time very useful. Any suggestions or advice would be highly appreciated.

Thanks & Regards,
Shobha Tyagi
Assistant Professor,
Department of Computer Science & Engineering,
Faculty of Engineering & Technology,
MRIIRS, Faridabad, New Delhi
GNOME Foundation Member since 2013

The GitHub corner logo on a paper page, for example:
https://doi.org/10.21105/jose.00016

... points to the JOSS repo, not the JOSE repo.

Respected Admin,

Our paper, "1build: Frictionless way of managing project-specific commands" was submitted before a month by the first author @gopinath-langote, but the review hasn't started yet.

This publication matters a lot to me to be done in time.

Therefore I request you to kindly look into this issue.

Thanks

This is interesting and relevant to the efforts here.

https://www.authorea.com/inst/18768

Instead of rolling our own journal software, etc, we could ask if they will brand a journal. Much like PubPub is doing.

It seems JOSS got a makeover, but those changes did not propagate to JOSE. It'd be nice if JOSE somehow kept up with the technological and style upgrades that JOSS gets. Is this possible? I'm guessing that the backend software for the journals is not independent, otherwise we'd have seen these changes in JOSE.

Potential security vulnerability in prior releases.

Hello all,

I have written a tool for web-based data collection and analysis/reporting. This submission/project was kindly rejected from JOSS as it was not considered research software that would fit within their scope.

I am kindly asking if this project fits in JOSE's scope. I am a researcher working in a school board and so this platform is something I designed to help researchers in education primarily; however, web-based surveys and reporting tools are useful for researchers in general.

Repository

https://github.com/Alcampopiano/OpenQuestion

Paper

https://github.com/Alcampopiano/OpenQuestion/blob/master/paper/paper.pdf

Docs

https://alcampopiano.github.io/OpenQuestion/

Project description:

OpenQuestion is a survey building and reporting platform for web-based data collection. Surveys can be developed using a GUI or programatically by writing Python code. To report on survey results, OpenQuestion provides a Jupyter-like environment for data visualization and document creation.

Survey development

Report development

Automatic chart creation and templating process

Thank you for JOSE and JOSS. I sincerely appreciate the work that goes into these journals.

Any feedback would be much appreciated!

Sincerely,
Allan

The authors will need to self-identify which type of article they are submitting (lesson material, or software). We'll need to add that to the submission form so that the bot can pull up the proper review checklist.

Project repository URL: To be uploaded

Dear Editors,

JOSE is a great idea, and I support its mission. Congratulations!

We have developed a comprehensive step-by-step guide to encourage academics to share and open source their Matlab code by making it easier to port it to Octave. As the open science and open source movement is picking up steam, the desire to convert existing Matlab codebases (which still occupies a large fraction of biomedical research) into more open Octave is significant. We believe our manual based on covering a large and complex neuroscience pipeline, along with setup and validation scripts , would make future conversions much easier and tolerable than would be otherwise. Does this sound suitable for publication in JOSE?

The guide would be in Markdown and published as a website cross-referring to a code repository.

Thanks,
Pradeep

Dear editor

The team behind R4DS-ES has written an article detailing how we created software carpentry to translate the datasets used in the original book R for Data Science. We would like to publish a short form article with Open Journals.

Please find our package here:
Datos: datasets translations to promote diversity, equity, and inclusion

There's a typo in the "JOSE paper" section of the reviewer checklist: "Does it describe how it has been used in the classroom or other settings, and how someone might adotp it?"

Received a vulnerability warning. It would be good to update the Gemfile.

Respected Admin,

Our paper was rejected despite of being abiding by the scope of JOSE.

Review link: openjournals/jose-reviews#84 (comment)

According to the definition of the "educational software tools" as defined on JOSE official website:

What do you mean by "educational software tools"?
Open-source software that serves as educational technology; examples include (but are not limited to) alternatives to learning management systems, autograders, cloud systems for lesson delivery, student collaboration tools. For these tools, peer review will follow a similar process as JOSS.

The 1Build tool is a project management tool.

1build is an automation tool used for research and development projects that arms you with the convenience to configure project-local command line aliases – and then run the commands quickly and easily. It is particularly helpful when you deal with multiple projects and switch between them all the time. It is often the fact that different projects use different build tools and have different environment requirements – and then switching from one project to another is becoming increasingly cumbersome. That is where 1build comes into play.

What do users of 1Build learn?

Need of how to manage multiple projects.
Indirectly learn the need for CI/CD.
Learns to write commands and hence to code.

Which I believe completely lies in scope of JOSE.

Therefore, I request you to give it a second opportunity and reconsider the submission.

Thanks,
Deepak Ahire

I tried to create a new submission on the JOSE site but something with the ORCID credentials did not work.

Various things need to be included in a guidance document in the about page.

• Size of a publishable unit (module)
• Meaning of computational curriculum
• Links to guides and research on design of content (e.g. report from MIT on future of education).

The footer on anything but the landing page have the JOSS footer.

This is a submission pager:

This is a published-paper page:

albi3ro/M4
I've written multiple Julia Jupyter notebooks, most of which fall under computational condensed matter physics. Some just fall in adjacent areas, like numerics, programming, or physics in general.

I also enumerate out different skill levels and prerequisites, so some posts are readable for high school students (Projectile Motion), while some would are written for graduate students (Quantum Anomalous Hall Effect and the Chern Number).

Most are standalone, but some can be read in sequence. For example, Monte Carlo Calculation of Pi to Markov Chain to Monte Carlo Ferromagnet to Phase Transitions.

How could I handle a submission given this variety of subjects and levels?

I see that citations go in the paper.md. But shouldn't the citations go in the work itself? I don't really understand how to cite a statement of need or a summary. Or maybe that just doesn't apply to me.

Also, how would it work when I end up writing more? When I write more, could I end up submitting them?

Hope this would be a good submission.

We can apply here: http://loc.gov/issn/form/

I've begun filling out the form, but will keep this open as a todo...

The link to the submission archive on the paper pages is broken for all our published papers so far. It has a pre-pended string with the JOSE-papers website on the DOI URL.

Like this:
http://jose.theoj.org/papers/%22https://doi.org/10.5281/zenodo.1312617%22