doc, docx, or .rtf output for F1000 research

[CaptainSifff]

F1000 Research only accepts, doc, docx, or rtf... I managed to get this through for now by wrapping the pdf in a zip(which they accept)

But I can't imagine that this holds forever... Can someone, @jngrad , @MakisH look into the toolchain on how to get a quick .doc out of it? F1000 research typesets the titlepage by itself, so the most difficult thing I suppose is the layout of the tables...

[jcohen02]

😮 That's very surprising - I can understand that they don't take LaTeX source but really surprised that they don't accept PDFs!

[CaptainSifff]

[CaptainSifff]

This paper makes it a bit difficult to find reviewers who have not published with any of the main authors during the past years: https://experts.illinois.edu/en/publications/what-do-we-not-know-about-research-software-engineering together with the FAIR4RS paper....

[CaptainSifff]

OK, I've received the notification, that .pdf is not ok...

[CaptainSifff]

This is the command that I use for converting the .md file: pandoc --standalone --bibliography=bibliography.bib --biblatex --filter pandoc-xnos --toc --number-sections -o comp.docx competencies.md It gets the refs wrong and the organization table wrong. For converting the tex file that is generated as an intermediate file in our pipeline, I use: pandoc --standalone -o comp.docx --bibliography=bibliography.bib --filter pandoc-xnos --toc --number-sections --biblatex competencies.tex and I get the seniority table rendered wrong, and also no bibliography list.

[CaptainSifff]

files. compmd.docx comptex.docx

[jngrad]

I don't really know a good toolchain for such a transformation. Since this manuscript is already published on ArXiv, there's no harm in uploading it to a free conversion server, such as the Adobe PDF to Word tool. It produces a rather decent file. @CaptainSifff I would recommend you go with that option. The bibliography is a numbered list, instead of being dynamically generated from a MS Word bibliography database, and the glossaries aren't stored in a data structure. It probably isn't too much of an issue, given the journal accepts RTF files, which also don't have a bibliography database and glossary feature, as far as I know.

For completeness, I also tried opening the PDF in MS Word. While most of the styling is preserved, the more complex tables are broken, and the competency icons are really damaged, sometimes multiple icons are fused into the same vector graphic element and can no longer flow with the text. Lastly, I tried opening it in Google Docs and exporting it to MS Word format, but the entire structure is broken.

competencies-adobe.docx competencies-ms-word.docx competencies-google-docs.docx

Also, unrelated to the problem at hand, while manually repairing the competencies-ms-word.docx file, I found out the manuscript contains a seemingly broken sentence: "the RSE’s obligation to In addition to the values".

[MakisH]

Also, unrelated to the problem at hand, while manually repairing the competencies-ms-word.docx file, I found out the manuscript contains a seemingly broken sentence: "the RSE’s obligation to In addition to the values".

This is now fixed in #367

Based on the discussion on Matrix, let's wait and see if LaTeX is ok before investing more effort on the conversion.

[CaptainSifff]

Thank you for your work!

[CaptainSifff]

Got a reply: No latex ....

[CaptainSifff]

that adobe converter is sick. Almost indistinguishable from the pdf. All the icons are there, AND all the tables! competencies-adobe.docx

One wonders, why it has issues with some page breaks... I'll attach it here fore [reference.

[CaptainSifff]

Now it's with F1000 again.

[jcohen02]

that adobe converter is sick. Almost indistinguishable from the pdf. All the icons are there, AND all the tables! competencies-adobe.docx

The conversion is very impressive, it seems to have come out very nicely.

[jpthiele]

Here's what Adobe Acrobat (2015 classic) made out of the PDF. competencies-acrobat.docx

[CaptainSifff]

F1000 doesn't do appendices. Any suggestions how to integrate our appendices?

[jngrad]

F1000 doesn't do appendices. Any suggestions how to integrate our appendices?

That's really unfortunate. We moved this content to the appendix to give us more flexibility in splitting the main text into self-contained sections.

Here is one way to integrate the material back into the main body:

5 How much do different people need to know? 5.1 Career level 5.2 Helpful RSE skills for researchers in an academic career 5.3 Project team structures :heavy_exclamation_mark: 5.4 Designing a generalist RSE framework :heavy_exclamation_mark: 5.4.1 An example master’s programme for research software engineering (formerly A.1) :heavy_exclamation_mark: 5.4.2 An example of a possible career path (formerly A.2) 6 RSE specialisations 6.1 Specialisations within the core RSE competencies 6.2 Specialisations outside the core RSE competencies :heavy_exclamation_mark: 6.3 Existing frameworks for specialised RSE roles :heavy_exclamation_mark: 6.3.1 Bioinformatics skills and certification (formerly A.3.2) :heavy_exclamation_mark: 6.3.2 HPC skills and certification (formerly A.3.1)

The main downside here is that 5.4 and 6.3 are now disconnected, while in the original appendix, the generalist RSE framework actually appeared after the specialised RSE frameworks.

[MakisH]

One solution could be:

• A.3 (Existing frameworks) -> compress and make part of the introduction
• A.1 (An example master’s programme for research software engineering) and A.2 (An example of a possible career path) -> Combine with chapter 6 (RSE specialisations) into a "Next steps" or "Application" or similar chapter.

[CaptainSifff]

I went with the solution of @jngrad since it keeps more parts of the paper. And we still want the position paper to kind of cite the F1000 version. 157778-Compared1-HV-revision.docx

[CaptainSifff]

and back to F1000

[CaptainSifff]

it's accepted! Let's see which editing requests come next...