Repositories list

• MSCommunity

  Public
  A repository of FBA community modeling functions within the ModelSEED ecosystem

  Python

  •0•0•0•0•Updated Jan 5, 2026Jan 5, 2026

• anme-thermodynamic-modeling

  Public
  ANME-SRB thermodynamic metabolic flux analysis notebooks

  Jupyter Notebook

  •0•0•0•0•Updated Jan 2, 2026Jan 2, 2026

• ADP1Notebooks

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Dec 29, 2025Dec 29, 2025

• MicrobiomeNotebooks

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Dec 23, 2025Dec 23, 2025

• ModelSEEDDatabase

  Public
  This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach

  modelseed

  HTML

  •

  Other

  •41•64•22•2•Updated Dec 12, 2025Dec 12, 2025

• ModelSEEDTemplates

  Public
  Python

  •

  MIT License

  •1•1•0•0•Updated Dec 12, 2025Dec 12, 2025

• 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

• 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 Dec 6, 2025Dec 6, 2025

• ModelSEED-UI

  Public
  ModelSEED UI (beta)

  HTML

  •

  MIT License

  •7•9•27•5•Updated Dec 5, 2025Dec 5, 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

• ModelSEEDpy

  Public
  Python package for building and analyzing models using ModelSEED

  cobracobrapymodelseed

  Python

  •

  MIT License

  •20•24•6•3•Updated Apr 18, 2025Apr 18, 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

• ProjectNotebooks

  Public archive
  Repository for Jupyter notebooks and associated data for various research projects of the ModelSEED team

  Jupyter Notebook

  •3•1•0•1•Updated Jan 12, 2024Jan 12, 2024