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Rename problems whose ID does not match the publication: * `Giordano_Nature2020` -> `Giordano_NatMed2020` (published in Nature Medicine) * `Schwen_PONE2014` -> `Schwen_PLoSOne2015` (published in 2015) * `Weber_BMC2015` -> `Weber_BMCSystBiol2015` (BMC is the publisher, not the journal) The new IDs use the ISO 4 journal abbreviation (as listed in PubMed). Other existing IDs use different abbreviations (e.g. `PNAS`, `MSB`, `JBC`); they are not wrong and are not changed here. The SBML model IDs and names are updated accordingly. The former IDs are still accepted by the accessor functions with a `FutureWarning` (`RENAMED_MODELS`), but are not part of `MODELS`. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
dweindl
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October 22, 2026 12:47
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Renames problems whose ID does not match the publication:
Giordano_Nature2020→Giordano_NatMed2020(published in Nature Medicine)Schwen_PONE2014→Schwen_PLoSOne2015(published in 2015)Weber_BMC2015→Weber_BMCSystBiol2015(BMC is the publisher, not the journal)The new IDs use the ISO 4 journal abbreviation (as listed in PubMed). Other existing IDs use different abbreviations (e.g.
PNAS,MSB,JBC,CellSystems); they are not wrong and are not changed here.The SBML model IDs and names are updated accordingly. The former IDs are still accepted by
get_problem,get_problem_yaml_path,get_simulation_df(v1 and v2), andget_metadata, with aFutureWarning; they are listed inRENAMED_MODELS, but are not part ofMODELS. Links to the old directories break.Closes #170.
Overlaps with #339: whichever is merged second needs the
referencesin the renamedmetadata.yamlfiles updated (BibTeX key = problem ID).🤖 Generated with Claude Code