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Published March 25, 2026 | Version v2.11.0
Software Open

SysBioChalmers/RAVEN: v2.11.0

Authors/Creators

  • 1. Chalmers University of Technology
  • 2. TMY Life
  • 3. AIxBIO
  • 4. BioInnovation Institute
  • 5. ELIXIR Europe
  • 6. Novonesis
  • 7. @SysBioChalmers
  • 8. Aalto University
  • 9. Gitter
  • 10. KTH Royal Institute of Technology / Science For Life Laboratory
  • 11. @merckgroup

Description

  • fix:
    • predictLocalization and parseScores to correctly handle output from CELLO
    • setParam report reactions not found in model
    • mergeModels will only make new metFrom, rxnForm and geneFrom fields if none of the initial models have these fields
    • handling of subSystems in various functions, RAVEN supports both cell arrays and nested cell arrays
    • YAML file I/O for models without genes
    • runINIT retains params as flag for optimizeProb input
    • copyToComps does not add or modify metFrom, rxnForm or geneFrom fields
    • addRxns makes sure that subSystems are nested cell arrays
    • fitTasks parses correct arguments to fillGaps
  • refactor:
    • exportModel speed-up subSystems handling
  • chore:
    • updated BLAST+, DIAMOND, MAFFT and HMMER binaries
    • update KEGG to release 116.0, retrained HMMs
  • feat:
    • runRAVENtests runs RAVEN unit tests
    • findRAVENroot stores RAVEN root as MATLAB preference during checkInstallation, to avoid problems when running on HPC clusters
  • doc:
    • parseTaskList clarifies that it can handle both *.txt and *.xlsx as input

Files

SysBioChalmers/RAVEN-v2.11.0.zip

Files (190.2 MB)

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md5:26fe8ee87d5e1e67e15d7010f17dbc33
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Additional details

Related works

Is supplement to
Software: https://github.com/SysBioChalmers/RAVEN/tree/v2.11.0 (URL)

Software

Repository URL
https://github.com/SysBioChalmers/RAVEN