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A guide to the COMBINE: Navigating through specifications, mailing lists and tools

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A guide to the COMBINE: Navigating through specifications, mailing lists and tools

  1. 1. A guide to the Computational Modeling in Biology Network (COMBINE): Navigating through specifications, mailing lists and tools e:med Systems Medicine, Nov 28-30 2022, Heidelberg, Germany Dagmar Waltemath1 on behalf of The COMBINE coordination board2 1. Medical Informatics Laboratory, University Medicine Greifswald, Germany https://www.medizin.uni-greifswald.de/medizininformatik/ 2. COmputational Modeling in BIology NEtwork (COMBINE), global https://co.mbine.org/
  2. 2. © Copyright Universitätsmedizin Greifswald Publication of model-based results
  3. 3. © Copyright Universitätsmedizin Greifswald Publication of model-based results Model deposition
  4. 4. © Copyright Universitätsmedizin Greifswald Publication of model-based results Model deposition Model reuse
  5. 5. © Copyright Universitätsmedizin Greifswald FAIRsharing: ComputationalModelingCOMBINE; Computational Modeling (COMBINE), FAIRsharing ID: https://fairsharing.org/3495, Last Accessed: Monday, November 28th 2022, 22:47 Publication of model-based results Making model-based results reproducible (FAIR+) COMBINE Archive: Bergmann et al. (2014). DOI: https://doi.org/10.1186/s12859-014-0369-z Findable Accessible Interoperable Reusable Biomodels: Malik-Sheriff et al (2020). DOI: https://doi.org/10.1093/nar/gkz1055
  6. 6. © Copyright Universitätsmedizin Greifswald Publication of model-based results Making model-based results reproducible (FAIR+) Reproducible?! Left: Tiwari et al (2020). DOI: https://doi.org/10.15252/msb.20209982
  7. 7. © Copyright Universitätsmedizin Greifswald Publication of model-based results Making model-based results reproducible (FAIR+) Reproducible Left: Tiwari et al (2020). DOI: https://doi.org/10.15252/msb.20209982
  8. 8. © Copyright Universitätsmedizin Greifswald COMBINE 12 years coordinated standardisation of data and models 10 yrs COMBINE, Heidelberg 2019 | https://doi.org/10.1515/jib-2020-0005 COMBINE: Waltemath et al. (2019). DOI: https://doi.org/10.1515/jib-2020-0005
  9. 9. © Copyright Universitätsmedizin Greifswald COMBINE 9 Left: Schreiber et al (2020). DOI: https://doi.org/10.1515/jib-2020-0022 Right: Keating et al (2020). DOI: https://doi.org/10.15252/msb.20199110 Coordination of standards development Model encoding (SBML)
  10. 10. © Copyright Universitätsmedizin Greifswald COMBINE 10 Left: Schreiber et al (2020). DOI: https://doi.org/10.1515/jib-2020-0022 Right: Rougny et al (2021). DOI: https://doi.org/10.1093/bib/bbab049 Coordination of standards development Model visualisation (SBGN)
  11. 11. © Copyright Universitätsmedizin Greifswald COMBINE 11 Left: Schreiber et al (2020). DOI: https://doi.org/10.1515/jib-2020-0022 Right: Bergmann et al (2017). DOI: https://doi.org/10.1093/bioinformatics/btw812 Coordination of standards development Simulation (SED-ML)
  12. 12. © Copyright Universitätsmedizin Greifswald COMBINE 12 Follow us in social media (tba) JIB: https://www.degruyter.com/journal Coordination of standards development Further information on latest standards - read the specs: annual Special Issue @ JIB - read the docs: https://combine-org.github.io/
  13. 13. © Copyright Universitätsmedizin Greifswald COMBINE 13 Libraries, tool support, interoperability SED-ML: Waltemath et al (2011). DOI: https://doi.org/10.1186/1752-0509-5-198 • Each standard must be implemented in > 2 software tools, who can show to exchange the data without information loss. • Libraries and tools are partially developed by the community. • Annual hackathons for coding, testing, breaking, fixing help improving the software ecosystem.
  14. 14. © Copyright Universitätsmedizin Greifswald COMBINE 14 SBML tool support and libraries: https://sbml.org/software/ Libraries, tool support, interoperability SBML discussion forums: https://sbml.org/community/ Further information on tool support and libraries - Check websites, e.g. SBML: - Join the mailing lists - Come to the hackathons: https://co.mbine.org/events Feedback, Feedback, Feedback
  15. 15. © Copyright Universitätsmedizin Greifswald COMBINE 15 Left: Tiwari et al (2020). DOI: https://doi.org/10.15252/msb.20209982 Meta-data, harmonization, guidelines
  16. 16. © Copyright Universitätsmedizin Greifswald COMBINE 16 Left: Tiwari et al (2020). DOI: https://doi.org/10.15252/msb.20209982 Meta-data, harmonization, guidelines COMBINE Metadata recommendation: Gennari et al (2021). DOI: https://doi.org/10.1515/jib-2021-0020
  17. 17. © Copyright Universitätsmedizin Greifswald COMBINE 17 Left: Tiwari et al (2020). DOI: https://doi.org/10.15252/msb.20209982 Meta-data, harmonization, guidelines COMBINE Roadmap for semantic annotations: Neal et al (2019). DOI: https://doi.org/10.1093/bib/bby087 Roadmap towards harmonized semantic annotations 1. Use RDF, identifiers.org-URIs and BioModels.netqualifiers to encode semantic annotations 2. Store annotations in a separate file 3. Establish a dedicated group for developing a software library that supports semantic annotation standards 4. Document which knowledge resources should be used for annotation and why 5. Establish a repository of reusable annotations 6. Ensure high-quality semantic annotations through training and quality control processes 7. Establish and maintain collaborations with knowledge resource developers
  18. 18. © Copyright Universitätsmedizin Greifswald COMBINE 18 Left: Tiwari et al (2020). DOI: https://doi.org/10.15252/msb.20209982 Meta-data, harmonization, guidelines COMBINE fully featured COMBINE archive: Scharm & Waltemath (2016). DOI: https://f1000research.com/articles/5-2421/v1 How to… build a COMBINE Archive
  19. 19. © Copyright Universitätsmedizin Greifswald COMBINE 19 Left: Tiwari et al (2020). DOI: https://doi.org/10.15252/msb.20209982 Meta-data, harmonization, guidelines Quick tips for SBGN diagrams: Toure et al (2018). DOI: https://doi.org/10.1371/journal.pcbi.1005740 How to… make a comprehensive network visualisation
  20. 20. © Copyright Universitätsmedizin Greifswald COMBINE 20 Left: Tiwari et al (2020). DOI: https://doi.org/10.15252/msb.20209982 Training Reproducible modeling: https://reproduciblebiomodels.org/tutorials-2022/ How to… learn everything about reproducible modeling
  21. 21. © Copyright Universitätsmedizin Greifswald Get in touch HARMONY | Spring 23 | Seattle Picture: Olga Krebs (HITS)
  22. 22. © Copyright Universitätsmedizin Greifswald Thank you for your attention! https://combine-org.github.io/ Editorial boards Tool developers Repositories … and you?

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