Valorisation check-list

This is the check-list that I follow to valorise the computational work associated with a published study.

New version of the analysis

Status: In Preparation

It happens when:

• submitting the manuscript
• sharing on BioRXiv
• revising the manuscript

1. On the GitHub repository:
   Make sure that the index.html is up-to-date with new files
   Draft the README as the other repositories
   Add a new tag
   Associate a new release to the tag

2. On the Zenodo record:
   Put the GitHub archive
   Draft the description as the other records
   Release a new version

3. On the GitHub repository, add the DOI from Zenodo:
   In the release message
   In the badge in the README

At this stage, everything can be private.

In the last revision step or proof,

Status: In Revision or In Press

1. On the GitHub repository:
   Edit the repository name: Author_keywords_year
   Make the repository public
   Activate the GitHub Pages
   Make sure the latest version is the accepted one

2. In the manuscript, in the “Code & Data Availability” section
   Update the GitHub repository name and link
   Check the associated DOI from Zenodo (good version)

As this stage, everything must be public.

Once the DOI of the article is available

Status: Published

1. On the GitHub repository, in the README:
   Add the badge with the DOI
   Add the journal name
   Check the citation: authors, title, year
   Update the citation with the DOI

2. On the Zenodo record:
   Edit the metadata, Section “Additional details”, fill in “Is published in” with the DOI
   Check the title and authors of the record: same as the article
   If the analysis uses the Apptainer container on Zenodo, edit the description of its Zenodo record

3. On my GitHub Pages (here!):
   Edit the “Analyses” page

4. On ORCID, if not automatically done by CrossRef:
   Add a new contribution using the DOI to the “Work” section