Peer-reviewed Publication

[CaptainSifff]

No description provided.

[CaptainSifff]

We had the idea, of publishing with F1000 Research as an opinion article (similar to previous publications)
The major hurdle, I currently see is the publication costs, of 1390$ (maybe with tax): https://f1000research.com/for-authors/article-processing-charges

[CaptainSifff]

Stuttgart: https://riojournal.com/

[CaptainSifff]

The Book of the Dagstuhl seminar?

[BeastyBlacksmith]

What I gathered:
APC Free:

• ITEGAM-JETIA
• JOHEPAL

APC could by covered by university:

• PLoS ONE

[jngrad]

Stuttgart uses DFG grant 512689491 to cover the costs of open access journals up to 2400 Euros after tax, but one of the conditions is for at least one Stuttgart co-author to be a corresponding author. It's also unclear, whether the grant covers policy papers (all papers funded by this grant seem to have conducted research, in one case it was simply a RSE survey). A full list of conditions can be found here: https://www.oa.uni-stuttgart.de/oa-finanzierung/fonds/

[mhagdorn]

The Charité covers up to 2000 Euro but only if the corresponding author is member of the Charité. There are various other strings attached but I think we would fulfill those.

[CaptainSifff]

So from what I gather, I still would have to pay for most of the things:
https://www.bibliothek.uni-wuerzburg.de/forschen-publizieren/open-access/sonderkonditionen/

Since F1000 is in taylor and francis group, I get a 15% rebate. and from the remaining ~1000€ 800€ would have to be paid by me.

[sdruskat]

The Book of the Dagstuhl seminar?

This will now be a special issue "Research Software Engineering: Discovering and Bridging Knowledge Gaps" in IEEE Computing in Science & Engineering. Those of you who attended the Seminar will have received an initial email about this.

[knarrff]

I opened a local request to see whether I could get the fees for either F1000Research or JORS covered.

(for own reference and likely not useful for anyone else: https://servicedesk.uni-jena.de/plugins/servlet/desk/portal/140/FSU040THUL-3920)

[knarrff]

I opened a local request to see whether I could get the fees for either F1000Research or JORS covered.

The answer: both could be covered by the University Jena, up to a cost of 2k€ (incl. VAT).

[mhagdorn]

JORS

JORS did spring to my mind as well. I think that might be quite a good match, not sure what the impact is, if that is something we are worried about.

[hvwaldow]

Journal	APC	OA?	Covered by DEAL?	notable RSE publications
F1000	$ 1595	yes	no	An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action
IEEE Computing in Science & Engineering	0 ?	no	no	Research Software Science: Expanding the Impact of Research Software Engineering
IEEE Software	0 ?	no	no	The Four Pillars of Research Software Engineering
Journal of Open Research Software (JORS)	£495.00	yes	no	What Do We (Not) Know About Research Software Engineering?
Software and Systems Modeling	?	hybrid	yes	Research software engineering and the importance of scientific models

[sdruskat]

CiSE is hybrid. And has had many RSE-relevant special issues, e.g.

• Computational Modeling of Ice Sheets and Glaciers
• Future of RSEs in the US
• Scientific Software Teams
• Computational Science and Engineering Education in Different Countries
• Software & Data Citation
• ...

APCs are pretty high I think.

[knarrff]

Is this issue the same as #83?

[CaptainSifff]

I wrote to the editors of PLOS CompBio, let's see what kind of reply we get.

[CaptainSifff]

hmpf:
Thank you for your email. We no longer accept presubmission inquiries. All submissions are handled in our submission system, Editorial Manager.

In order to make an assessment of the manuscript, we would ask that you submit the full paper to our system for consideration by the journal’s senior editors. Please log into Editorial Manager using your username or ORCiD and choose the appropriate article type when following the steps to submit a new manuscript.

Please note that the editors have not assessed your manuscript. Their assessment will take place after you have submitted your full manuscript via Editorial Manager here
https://www.editorialmanager.com/pcompbiol/default.aspx

[jcohen02]

Hmmm, well I guess we should do a bit of a scan of the sort of related content the journal has published previously. If we are sufficiently convinced that this is in the right space for this journal and we meet any other requirements they set out, then we could go ahead and submit and see what happens.

This is one example that I don't see as Comp Bio specific (maybe we already spoke about this?): Ten simple rules for writing Dockerfiles for reproducible data science

(Our appendices are quite lengthy. I wonder if one option is to self-publish them as a separate report on arXiv or similar and link to them from the paper?)

[CaptainSifff]

So for the submission, we have the following options:

Research Article
Review
Education
Perspective

Perspectives reflect an author's viewpoint on a particular development in science and how this development evidences or can lead to change in how science is conducted or interpreted. Perspectives are intended to be more prospective than retrospective.

Methods
Software

I feel perspective is the right thing here.

[CaptainSifff]

If PLOS accepts, we need to get rid of our footnotes.... or make refs from them(Which we might consider anyway).

[jcohen02]

So for the submission, we have the following options:
...
I feel perspective is the right thing here.

I've not had a chance to look at the options and see what description they provide for the other options but I agree that "perspective" seems reasonable from the description you've provided above - maybe "education" could also be a relevant option?

[CaptainSifff]

The description for education sounds more like it's for tutorials

[mhagdorn]

I think the word count of perspectives is limited to 2500 words: https://journals.plos.org/ploscompbiol/s/other-article-types

[CaptainSifff]

duh...
I will go for it anyway, now that I managed to upload all the contact details of the author.
And it says should not exceed 2500 words.... Maybe they accept it as a longer "perspective"
education would have the same restriction.

[CaptainSifff]

submitted!

[jngrad]

For completeness and future reference, let's also mention the Open Research Europe journal (scope), which is constructed around the F1000 model. I just checked their online submission portal, and it looks like I'm eligible through my EuroHPC JU project. According to their help pages, processing charges are waived (link), the editorial team seeks external reviewers (link), and publications are CC-BY.

The paper could be submitted in the Science and Technology category as an Open Letter. They have several venues:

• project-specific gateways (full list)
  • not applicable, meant for EU project outcomes
• community gateways (full list)
  • the Software issue would be the right place
  • although the wording in the scope is very specific and seems limited to scientific codes, libraries and compiler, in practice there seems to be a bit of leeway
  • notable RSE publication: Catala et al. 2023 Establishing a national research software award
• collections (full list)
  • available areas don't really overlap with RSE
  • the closest area is The Future of Work, bullet point "Skills and skill validation"

They use post-publication peer-review. Articles are indexed after the first positive peer-review. They are indexed on Scopus, PubMed, and Web of Science (but not in the core collection).

[CaptainSifff]

Great find!

[knarrff]

Where do we go from here? Plos declined due to the length. Do we now target F1000?

[sdruskat]

Where do we go from here? Plos declined due to the length. Do we now target F1000?

Discussion is in progress (see above).

[jngrad]

We are currently going with F1000 and possibly a shorter version in Dagstuhl Seminar (2024-09-30 meeting minutes).

[sdruskat]

possibly a shorter version in Dagstuhl Seminar (2024-09-30 meeting minutes).

🎉

Re the comment in the minutes:

IEEE: maybe too specific to CS/engineering fields

It's not really. In fact, it sits snugly between the CS/engineering fields and RSEng and is viewed by software engineering researchers in CS as a magazine catering towards the RSEng community (not the other way around)...

[CaptainSifff]

And back to F1000
f1000res157778_florian.goth_CorrectionsPDF.pdf

[CaptainSifff]

We have a DOI:
https://doi.org/10.12688/f1000research.157778.1

now let's wait how they do review....

[CaptainSifff]

Dagstuhl thing submitted.

[CaptainSifff]

first review in:
https://f1000research.com/articles/13-1429/v1#referee-response-345505

[CaptainSifff]

And the second review: https://f1000research.com/articles/13-1429/v1#referee-response-345501

[sdruskat]

This is good news. We should now work to prepare a revision that addresses reviewers comments, no?

[CaptainSifff]

It still might be that we get additional reviews:
As your article has now received the required approval from the reviewers to be indexed, it should appear on PubMed, PMC, Scopus, Embase and other indexing sites within a few weeks.

Although your article has now passed peer review, you can still revise or update it at any point now or in the future. For information on how to submit a new version, please visit Article Guidelines (new versions). Please bear in mind that new submissions need to be created and submitted using the submitting author’s account.

We are expecting to receive other peer review reports within the next few weeks; we will let you know if and when they are published.

[mhagdorn]

I guess we could start distributing some of the bigger tasks and those from #385 on Monday.