Meeting notes

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
   • Set of workflows for different datasets
     • Focus more on practical workflows
     • Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses
   • Review of different metagenomic + metabolomic integration methods
     • The workflows can later be extended so that they include different statistical method (review and benchmarking)
     • The "upstream" workflows would be nice bonus and "must-to-have", but the focus would be more on comparing different statistical methods
     • Multitable Methods for Microbiome Data Integration
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: