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Tuomas Borman edited this page Oct 15, 2026 · 20 revisions

Meeting 15.10.2026, 13.00-14.00 (CET)

Present: Tuomas, Johannes, Vilhelm, Leo

  1. Data

  2. Publication

    • Metabonaut was published in metabolomics journal (tutorial, educational resources): https://link.springer.com/journal/11306
    • Nature Reviews Protocols (1st priority)
    • JOSE is not anymore supported by Bioconductor so that is not suitable anymore

  3. This project is part of microbiome working group in Bioconductor

    • Invite relevant people

  4. How much upstream processing we should have?

    • Data integration already is a big contribution
    • If we cover a lot upstream tasks that is lots of work
    • We should show the preprocessing, that adds value.
    • Cite to external resources. In paper, less emphasize. The full workflow can be in the public source code.

  5. Next steps

    • Leo asks data from Kati
    • When we know the data, next meeting will be scheduled
    • Tuomas will update the issues and project

Meeting 12.2.2026, 14.00-15.00 (CET)

Present: Tuomas, Johannes, Philippine, Vilhelm, Eliana, Leo

Agenda

  1. Previously, we identified that workflow is not enough for scientific contribution

    • End-to-end workflow could be nice to have.
    • Pretty valuable for the community
    • Workflow could be submitted to JOSE: https://jose.theoj.org/

  2. Paper includes suggestions for methods in different situations: https://www.nature.com/articles/s42003-025-08515-9

    • Multi-omics package that includes all these recommended methods?
    • Package is not the first step.

  3. Should we continue or cancel this project?

    • Continue.

  4. Next steps:

    • Add code of conduct link (Bioconductor) and instruction on how to contribute

    a. What data?:

    b. Do the raw data preprocessing separately:

    • Metabolomics: Johannes, Phili
    • Metagenomics: Tuomas, Vilhelm, Eliana, Leo

    c. Combine them to MultiAssayExperiment

    d. Maybe MultiAssayExperiment package with supported multi-omics tools

    • Analysis plan

    e. Maybe article to JOSE?

Meeting 31.10.2025, 14.00-15.00 (CET)

Present: Tuomas, Philippine, Vilhelm, Eliana, Leo

Agenda

  1. Existing literature
  2. What is unique for our project?
    • Focusing on one disease/topic...?
    • Check limitations, focus on one aspect: https://www.nature.com/articles/s42003-025-08515-9
    • Workflow: limitation is the novel thing, can we publish it? What problem it solves?
    • Workflow: there is no accessible workflow showing how microbiome + metabolome dataset is analysed
  3. Available data
  4. Available human resources
  5. BioFAIR Pathfinder Projects: https://biofair.uk/pathfinder-projects/ -> forget, only for UK people
    • Hackathon (Biohackathon)??
  6. Next steps

We discussed mainly what our approach can be / what unique or novel we can do. We did not find clear answer for that.

Bioconductor workflow from raw files to result could be very useful, but it lacks the unique aspect that we need (it might not be publishable). On the other hand, there are some papers that have already done benchmarking on metabolomics+metagenomics integration.

For the next meeting, we should more carefully screen the related publications, and determine the unique angle that we could have. It could be: combining workflow and benchmark, focusing on specific disease or topic or solving limitations described in previous literature...

Meeting 30.9.2025, 12.00-13.00 (UTC)

Present: Tuomas, Johannes, Philippine, Vilhelm, Eliana

Agenda

  1. Does this project sound feasible and worth doing?
    • Probably we know better after the meeting?
  2. Dataset
    • We should have open dataset so that results are replicable
    • The dataset should include metagenomics (or 16S) and metabolomics data
  3. Workflow proposal
    • The idea is to show how to proceed when researcher "ends up" having microbiome data with both metagenomic and metabolomic samples
    • Practical workflow from raw data to results (avoid overlap with OMA online book)
    • Sequencing data: 16S or metagenomic?
    • Metabolomic data: targeted or untargeted, mass-spectrometry or NMR?
  4. Continuation
  5. Next steps
    • Sub-channel (to mia channel in Zulip?)
    • Find usable dataset
    • We should have clear publication plan!
      • Publications important for academic work
      • We might end up spending lots of time and effort for low impact GH repo
  6. Next meeting
    • Might be better to agree with date already so that we have good momentum.
    • Every ~ 2 weeks?

Notes:

  1. Data
    • Untargeted mass spectrometry ("standard")
    • HoloFood?
    • Identify dataset
    • ENA, MetaboLights databases
  2. Publication plan
    • Workflow of methods
    • Check if there are papers on metagenomics + metabolomics
    • Bioconductor "workflow paper" working group searching journal
    • Benchmarking paper on statistical methods?
    • Other projects overlapping, can benefit
  3. Next steps
    • mia, metagenomics integration sub-channel
    • In the future: Working group?
    • Check if there are workflow papers available?
      • Google docs sheet
    • What data is available? (Try to find human data)
      • Google docs sheet
    • Publication and implementation plan ideas?
    • Who have time to do that?
      • Invite people outside Bioconductor?

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