Pre-flight check

[markziemann]

Hi @pierrepo @sminot @anusuiyaxbora , The article is nearing completion so we need to go through some pre-flight checks. Here is the live version: https://ziemann-lab.net/public/5pillars/5pillars.html

My plan is to submit to briefings in bioinformatics, which hasn't published a best practices article like this for many years. I'll also be depositing the preprint at the same time - probably to https://osf.io/

Before I do that, there are some recent changes that I need you to check:

• Your names, affiliations and ORCID information
• The overall content
• Conclusion
• Key points (this is a requirement for BiB)
• Author biographies (this is a requirement for BiB)
• Funding: if you would like to acknowledge specific funding sources. Otherwise I will write "The authors received no specific funding for this work."

• If you have noticed something that needs addressing, please raise a new issue and I will manage the changes.

We will provide a supplementary file listing some recommended learning resources. Here is the link (https://ziemann-lab.net/public/5pillars/practical_guides.html). If you have any suggestions, please add them to issue #15

I'm hoping to have this round of changes completed on the ~16th June. If you approve of the manuscript please reply "approve" below. After this, I will send out the pdf version for proof reading and approval.

Thanks for your contribution!

[pierrepo]

@markziemann I've re-read the whole paper and proposed a couple of references and small additions in PR #20. I also double-checked the conclusion, key points and author bio. I do not have specific funding for this work.

[pierrepo]

Also I add a quick look at Briefings in Bioinformatics author guidelines:

• I did not find any limit regarding the number of references (we should have about a hundred after PR #20)
• Reviews should be in the 2000 - 7000 words limit. We are currently at 6500 (also with PR #20).

[markziemann]

Awesome work @pierrepo these have been incorporated. 5785 words and 105 citations.

[markziemann]

There was a slight change in some of the wording and fig4 was altered to avoid possible copyright problems.

@pierrepo and @anusuiyaxbora please let me know if you approve for submission.

5pillars.pdf 5pillars.docx

[anusuiyaxbora]

I have read the manuscript and everything looks great to me! I am fine with the affiliation, author biography and funding as well!

[pierrepo]

Hello :wave: Everything is almost fine for me. I have one correction:

• In the paragraph mentionning Software Heritage, I messed up with references Software Heritage [[46]; abramatic2018] is the universal software archive. I probably forgot a @ in front of abramatic2018.

And two suggestions.

• In the abstract, I'll suggest for the very first sentence (looks more fluid to me):

  Computational reproducibility is a simple premise in theory, but is difficult to achieve in practice.

• In the last paragraph before the Conclusion, I would mention the software Carpentries endeavour:

  Specific workshop-based training in these areas could help. The Software Carpentry initiative [cite https://f1000research.com/articles/3-62/v2] is remarkable to this aim. But the most scalable solution would be to provide comprehensive beginner-friendly step-by-step guides for frequently used routines...

Let me know what you think. I can make a PR.

[markziemann]

Good suggestions. I will fix these now.

[markziemann]

5797 words and 108 references.

@pierrepo please check those relevant sections.

5pillars_20230613.docx

5pillars_20230613.pdf

[pierrepo]

@markziemann :pray:

This is all good for me :tada:

[markziemann]

It has been submitted - let's see what the reviewers say