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@Gibbons-Lab

Gibbons Lab

The Gibbons Lab -- Microbes + Ecology + Medicine @ the Institute for Systems Biology.

Gibbons Lab

Our lab is located at the Institute for Systems Biology in Seattle, Washigton. We are interested in the ecology, evolution, and emergent function of host-microbial systems. The team is led by Dr. Sean Gibbons. Our toolset includes ecological and evolutionary theory, applied math and biostatistics, and computational systems biology. Most of our work is within the computational domain, but we occaisionally run our own experiments. Our fundamental aim is to discover and formalize the biological rule sets governing host-microbe systems, and apply these rules to engineer microbial ecoystems to improve human and environmental health.

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  1. wiki wiki Public

    General good-to-know stuff.

    1

  2. manuals-and-policies manuals-and-policies Public

    2 2

  3. pipelines pipelines Public

    Pipelines used in the lab.

    Nextflow 15 3

  4. mbtools mbtools Public

    R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.

    R 24 9

  5. isb_course_2022 isb_course_2022 Public

    Materials and presentation for the 2022 ISB Microbiome course.

    Jupyter Notebook 27 13

  6. american-gut-app american-gut-app Public

    Source repository for the American Gut App.

    Python 1 1

Repositories

Showing 10 of 46 repositories
  • Gibbons-Lab/isb_course_2024’s past year of commit activity
    Jupyter Notebook 5 Apache-2.0 8 1 11 Updated Dec 31, 2025
  • Gibbons-Lab/2024_probiotic_engraftment’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Dec 23, 2025
  • Gibbons-Lab/manuals-and-policies’s past year of commit activity
    2 2 0 0 Updated Nov 24, 2025
  • 2025_schoch_methane Public

    Jasmine's work using MICOM to model methane production in the rumen microbiome (rumen metagenomes from Andersen paper)

    Gibbons-Lab/2025_schoch_methane’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Aug 17, 2025
  • Gibbons-Lab/cdiff_invasion’s past year of commit activity
    Jupyter Notebook 2 0 0 0 Updated Jun 18, 2025
  • Metagenomic_Biomass_Quantification_2024 Public

    Scripts for gut bacterial biomass analysis

    Gibbons-Lab/Metagenomic_Biomass_Quantification_2024’s past year of commit activity
    Python 0 0 0 0 Updated Jun 18, 2025
  • Gibbons_Genome541_2025 Public

    Materials, data and notebooks for GENOME 541, Spring 2025

    Gibbons-Lab/Gibbons_Genome541_2025’s past year of commit activity
    0 0 0 0 Updated May 11, 2025
  • medi Public

    Metagenomic Estimation of Dietary Intake and Content.

    Gibbons-Lab/medi’s past year of commit activity
    Nextflow 38 Apache-2.0 6 14 1 Updated Apr 17, 2025
  • pipelines Public

    Pipelines used in the lab.

    Gibbons-Lab/pipelines’s past year of commit activity
    Nextflow 15 Apache-2.0 3 0 0 Updated Mar 26, 2025
  • 2025_aobrian_rotation Public

    Statin Efficacy for Varying Diets and Gut Microbes

    Gibbons-Lab/2025_aobrian_rotation’s past year of commit activity
    Jupyter Notebook 1 MIT 0 0 0 Updated Mar 21, 2025