Skip to content
@MicrocosmFoods

Microcosm Foods

Microcosm Foods
README.md

Welcome to @MicrocosmFoods!

We are on a mission to make the benefits of fermentation accessible to all while producing public goods. You can learn about what we are doing by:

  • Explore and build upon our repositories of open-source tools
  • Subscribe to our newsletter to follow along with research updates and other fun fermented foods blogs
  • Browse and reuse our open datasets on fermented foods such as curated microbial genomes from fermented foods, predicted molecules from thousands of genomes, and bioactivity predictions of fermented foods peptides
  • Questions? Have ideas for collaborations? Contact us through our website!

Popular repositories Loading

  1. fermented-food-peptidomics-mining-results fermented-food-peptidomics-mining-results Public

    Repository for analyzing results from publicly available fermented foods 'omics datasets

    HTML 2

  2. fermentedfood_mags_curation fermentedfood_mags_curation Public

    Curated publicly available genomic data of fermented foods + microbes

    Python 1

  3. bac-mining bac-mining Public

    A Nextflow workflow for bacterial genome annotation with an emphasis on bioactive molecules

    Python

  4. peptide-bioactivity-prediction peptide-bioactivity-prediction Public

    A Nextflow workflow to predict bioactivity and physiochemical characteristics of input peptide sequences

    Python

  5. metagenome-containment-profiler metagenome-containment-profiler Public

    Workflow for profiling containment of reference genomes in metagenomic samples using sylph

    R

  6. fermentedfood_metadata_curation fermentedfood_metadata_curation Public

    Curated metadata for microbial genomes from fermented foods

    Jupyter Notebook

Repositories

Showing 10 of 11 repositories
  • bac-mining Public

    A Nextflow workflow for bacterial genome annotation with an emphasis on bioactive molecules

    MicrocosmFoods/bac-mining’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Mar 11, 2026
  • fermented-food-peptidomics-mining-results Public

    Repository for analyzing results from publicly available fermented foods 'omics datasets

    MicrocosmFoods/fermented-food-peptidomics-mining-results’s past year of commit activity
    HTML 2 MIT 0 0 0 Updated Feb 23, 2026
  • peptide-model-curation Public

    Repository for documenting metadata and model curation associated with peptide bioactivity classification models

    MicrocosmFoods/peptide-model-curation’s past year of commit activity
    Python 0 0 0 0 Updated Feb 23, 2026
  • peptide-bioactivity-prediction Public

    A Nextflow workflow to predict bioactivity and physiochemical characteristics of input peptide sequences

    MicrocosmFoods/peptide-bioactivity-prediction’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Feb 20, 2026
  • metagenome-containment-profiler Public

    Workflow for profiling containment of reference genomes in metagenomic samples using sylph

    MicrocosmFoods/metagenome-containment-profiler’s past year of commit activity
    R 0 MIT 0 0 0 Updated Jan 20, 2026
  • spontaneous-oats Public

    Analysis repository for exploring microbial communities in spontaneously fermenting oats

    MicrocosmFoods/spontaneous-oats’s past year of commit activity
    R 0 0 0 0 Updated Dec 9, 2025
  • microcosmfoods.github.io Public

    Landing page for Microcosm Foods

    MicrocosmFoods/microcosmfoods.github.io’s past year of commit activity
    Astro 0 GPL-3.0 0 0 0 Updated Sep 9, 2025
  • fermentedfood_mags_curation Public

    Curated publicly available genomic data of fermented foods + microbes

    MicrocosmFoods/fermentedfood_mags_curation’s past year of commit activity
    Python 1 MIT 0 0 0 Updated Aug 20, 2025
  • .github Public
    MicrocosmFoods/.github’s past year of commit activity
    0 0 0 0 Updated Jul 10, 2025
  • global-food-omics-untargeted-gnps-scan Public

    GNPS scan of untargeted metabolomics data for fermented foods from the Global Food 'Omics Project

    MicrocosmFoods/global-food-omics-untargeted-gnps-scan’s past year of commit activity
    HTML 0 MIT 0 1 0 Updated Jun 27, 2025
View all repositories

Most used topics

Loading…