Skip to content

Update fbc version 3 information, add sbml2cellml converter - #73

Merged
luciansmith merged 1 commit into
mainfrom
update-fbc-v3-sbml2cellml
Sep 28, 2026
Merged

luciansmith merged 1 commit into
mainfrom
update-fbc-v3-sbml2cellml

Conversation

@matthiaskoenig

Copy link
Copy Markdown
Collaborator

Changes

  • fbc package page: notes on the Version 3 release (2026-01-06) with links to the Version 3 Release 1 specification PDF and the JIB publication, plus third-party support for Version 3 (sbmlutils, sbml4humans).
  • Publications: added "SBML Level 3 Package: Flux Balance Constraints version 3" (https://doi.org/10.1515/jib-2026-0006).
  • sbml-package layout: the release number was read from the version column, so the status table showed e.g. "Version 2 Release 2". It now reads the release column.
  • Converters: added sbml2cellml to the "From CellML" and "To CellML" sections; sbmlutils now links to its documentation.
  • FAQ: the 2020 Molecular Systems Biology paper is now the primary recommended citation; updated sbmlutils link.
  • News: replaced a dead sbmlutils Read the Docs link.

Follow-up outside this repository

The status table at the top of the fbc page is generated from the SBML Level 3 Package Status spreadsheet. The fbc row still describes Version 2 and needs to be updated (specification link, date, version 3, release 1, citation, DOI 10.1515/jib-2026-0006). Note that the identifiers.org/combine.specifications/sbml.level-3.version-1.fbc.version-3.release-1 URL does not resolve yet, because the entry is missing in combine-org/combine-specifications.

Testing

Built with the CI image klakegg/hugo:0.68.0 and checked the fbc, publications and converters pages in the browser.

🤖 Generated with Claude Code

- fbc package page: add notes on the Version 3 release, specification PDF,
  publication and third-party support
- publications: add the fbc version 3 publication
- sbml-package layout: read the release number from the release column
  instead of the version column
- converters: add sbml2cellml to the "From CellML" and "To CellML" sections,
  link sbmlutils to its documentation
- FAQ: recommend the 2020 Molecular Systems Biology paper as primary
  citation, update sbmlutils link
- news: replace dead sbmlutils Read the Docs link
@matthiaskoenig

Copy link
Copy Markdown
Collaborator Author

Someone has to update the spreadsheet for fbc v3: https://docs.google.com/spreadsheets/d/1pa01Z72t1UKrjliAXBhxjjN1nnOf00gXcfm4_pWXOxA/edit?gid=0#gid=0
The pull request for the specification is here: combine-org/combine-specifications#45

@matthiaskoenig

Copy link
Copy Markdown
Collaborator Author

@luciansmith Could you merge this. Documentation fixes and adding the fbc-v3 info.

Comment thread site/content/documents/faq/_index.md
@luciansmith
luciansmith merged commit a10c300 into main Sep 28, 2026
@luciansmith
luciansmith deleted the update-fbc-v3-sbml2cellml branch September 28, 2026 18:22
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants