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    53 repositories

    • MicrobiomeNotebooks

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Apr 15, 2026Apr 15, 2026

    • modelseed-api

      Public
      Modern REST API backend for the ModelSEED metabolic modeling platform
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 14, 2026Apr 14, 2026

    • ModelSEEDTemplates

      Public
      Python
      •
      MIT License
      •1•1•0•0•Updated Apr 10, 2026Apr 10, 2026

    • ModelSEED-UI

      Public
      ModelSEED UI (beta)
      HTML
      •
      MIT License
      •8•9•28•6•Updated Apr 10, 2026Apr 10, 2026

    • MSCommunity

      Public
      A repository of FBA community modeling functions within the ModelSEED ecosystem
      Python
      •0•0•0•0•Updated Apr 1, 2026Apr 1, 2026

    • ADP1Notebooks

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 16, 2026Mar 16, 2026

    • ModelSEEDpy

      Public
      Python package for building and analyzing models using ModelSEED
      cobracobrapymodelseed
      cobracobrapymodelseed
      Python
      •
      MIT License
      •20•26•7•3•Updated Feb 11, 2026Feb 11, 2026

    • PlantSEED

      Public
      Repository for containing code and files that pertain to the use of PlantSEED in the ModelSEED environment
      Perl
      •9•6•13•0•Updated Feb 2, 2026Feb 2, 2026

    • ModelSEEDDatabase

      Public
      This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach
      modelseed
      modelseed
      HTML
      •
      Other
      •43•68•22•2•Updated Jan 6, 2026Jan 6, 2026

    • anme-thermodynamic-modeling

      Public
      ANME-SRB thermodynamic metabolic flux analysis notebooks
      Jupyter Notebook
      •0•0•0•0•Updated Jan 2, 2026Jan 2, 2026

    • AISynbioPipeline

      Public
      Autonomous lab system for adaptive lab evolution of ADP1 with LIMS Google Sheets synchronization
      Python
      •1•0•0•0•Updated Dec 12, 2025Dec 12, 2025

    • KB-ModelSEEDReconstruction

      Public
      Python
      •
      MIT License
      •1•3•0•0•Updated Dec 11, 2025Dec 11, 2025

    • GenomeImporter

      Public
      Module for importing a genome into KBase from SEED, PATRIC, or RAST
      Perl
      •
      MIT License
      •0•0•0•0•Updated Dec 4, 2025Dec 4, 2025

    • SynbioWeb

      Public
      SynbioWeb
      HTML
      •0•0•0•0•Updated Nov 10, 2025Nov 10, 2025

    • ProbModelSEED

      Public
      Perl
      •
      Other
      •3•2•31•0•Updated Nov 4, 2025Nov 4, 2025

    • SynbioDataService

      Public
      Synbio LIMS Data Service
      Python
      •2•0•0•1•Updated Jun 27, 2025Jun 27, 2025

    • KBaseNotebooks

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

    • editEscher

      Public
      A library for editing Escher Metabolic Network maps
      0•0•0•0•Updated Oct 25, 2024Oct 25, 2024

    • ModelSEED2Notebooks

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Oct 8, 2024Oct 8, 2024

    • AGORA2_genomes

      Public
      The genomes associated with the AGORA2 gut microbiome models
      0•0•0•0•Updated Sep 11, 2024Sep 11, 2024

    • MSGoogleColab

      Public
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Sep 4, 2024Sep 4, 2024

    • MSDatabaseNotebooks

      Public
      Notebooks that manipulate the ModelSEED Database
      Jupyter Notebook
      •1•0•0•0•Updated Aug 1, 2024Aug 1, 2024

    • KB-ModelSEEDCommunity

      Public
      KBase SDK module for community modeling apps created and managed by the ModelSEED team
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 3, 2024Apr 3, 2024

    • OntologyNotebooks

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Mar 14, 2024Mar 14, 2024

    • PhenotypeNotebooks

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Feb 1, 2024Feb 1, 2024

    • KB-CommunityModeling

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 16, 2024Jan 16, 2024

    • KB-ProbabilisticModeling

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 16, 2024Jan 16, 2024

    • MAGNotebooks

      Public
      0•0•0•0•Updated Jan 15, 2024Jan 15, 2024

    • BRAVENotebooks

      Public
      0•0•0•0•Updated Jan 15, 2024Jan 15, 2024

    • SynBioNotebooks

      Public
      0•0•0•0•Updated Jan 15, 2024Jan 15, 2024
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