8000 Systems Biology Research Group · GitHub
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@SBRG

Systems Biology Research Group

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  1. cobradb cobradb Public

    COBRAdb loads genome-scale metabolic models and genome annotations into a relational database. It already powers BiGG Models, and it is available under the MIT license.

    Python 20 12

  2. ssbio ssbio Public

    A Python framework for structural systems biology

    Python 109 30

  3. cobrame cobrame Public

    A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

    Python 40 16

  4. ecolime ecolime Public

    Data and tools necessary to construct iJL1678b-ME, a genome-scale model of E. coli K-12 MG1655 metabolism and expression

    Python 5 12

  5. bigg_models bigg_models Public

    The BiGG Models website server

    Python 93 20

  6. precise-db precise-db Public

    A high-fidelity E. coli RNA-seq compendium

    Jupyter Notebook 33 20

Repositories

Showing 10 of 86 repositories
  • PMkbase Public

    All code files for PMkbase.com

    SBRG/PMkbase's past year of commit activity
    HTML 0 2 0 0 Updated Oct 25, 2026
  • NutrICA_Nitrogen_Metabolic_Modeling Public

    Python notebooks to analyze proteome allocation and fluxes on various nitrogen sources in E coli K12

    SBRG/NutrICA_Nitrogen_Metabolic_Modeling's past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Oct 8, 2026
  • ME-script Public

    Notebooks for solving COBRAme models

    SBRG/ME-script's past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Sep 26, 2026
  • pyphylon Public

    Python package for analyzing and visualizing co-occuring gene / allele sets (phylons) within a pangenome

    SBRG/pyphylon's past year of commit activity
    Python 3 MIT 3 6 1 Updated Sep 10, 2026
  • iModulonMiner_2.0 Public

    The Repository for iModulonMiner 2.0 Manuscript

    SBRG/iModulonMiner_2.0's past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Aug 14, 2026
  • Bacterial_TRN_Dominance_and_Independence Public

    Repository for manuscript 'Disentangling factors affecting bacterial transcriptional regulatory network inference'

    SBRG/Bacterial_TRN_Dominance_and_Independence's past year of commit activity
    Jupyter Notebook 1 MIT 0 0 0 Updated Feb 20, 2026
  • StressME-DynamicME Public Forked from arjunpatel96/StressME-DynamicME

    run simulations from terminal + input files, w/visualization tools

    SBRG/StressME-DynamicME's past year of commit activity
    Jupyter Notebook 0 1 0 0 Updated Feb 2, 2026
  • Pseudomonas_putida_GEMs Public

    Analysis of P. putida pan GEMs

    SBRG/Pseudomonas_putida_GEMs's past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Oct 17, 2025
  • cobrame-webapp-feedback Public

    Issue tracking and planning for the COBRA Metabolism and Expression Modeling Web Application

    SBRG/cobrame-webapp-feedback's past year of commit activity
    0 MIT 0 0 0 Updated Oct 10, 2025
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