Repositories list

• pymodulon

  Public
  Python package for analyzing and visualizing iModulons

  Python

  •

  MIT License

  •1414 forks•1515 stars•1010 issues•33 pull requests•Updated Apr 27, 2026Apr 27, 2026

• PMkbase

  Public
  All code files for PMkbase.com

  HTML

  •22 forks•00 stars•00 issues•00 pull requests•Updated Apr 27, 2026Apr 27, 2026

• Bacterial_TRN_Dominance_and_Independence

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

  Jupyter Notebook

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Feb 20, 2026Feb 20, 2026

• iModulonMiner_2.0

  Public
  The Repository for iModulonMiner 2.0 Manuscript

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 19, 2026Feb 19, 2026

• StressME-DynamicME

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

  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated Feb 2, 2026Feb 2, 2026

• Pseudomonas_putida_GEMs

  Public
  Analysis of P. putida pan GEMs

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 17, 2025Oct 17, 2025

• cobrame-webapp-feedback

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

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 10, 2025Oct 10, 2025

• yarrowia_lipolytica_ICA

  Public
  iModulon analysis of Y. lipolytica transcriptomes from DTU Biosustain

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 19, 2025Aug 19, 2025

• pyphylon

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

  Python

  •

  MIT License

  •33 forks•22 stars•66 issues•55 pull requests•Updated Aug 7, 2025Aug 7, 2025

• modulome_pst

  Public
  iModulon structure of Pseudomonas syringae pv. tomato DC3000

  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 18, 2025Jun 18, 2025

• GDS-Public

  Public
  Jupyter Notebook

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jun 11, 2025Jun 11, 2025

• dbgwas-network

  Public
  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 26, 2025Apr 26, 2025

• ChIPdb

  Public
  A Chromatin ImmunoPrecipitation database for PROkaryotic organisms.

  HTML

  •

  MIT License

  •22 forks•44 stars•11 issue•11 pull request•Updated Apr 21, 2025Apr 21, 2025

• PromoterModeling

  Public
  Sequence-based ML models of gene regulation

  Jupyter Notebook

  •

  MIT License

  •00 forks•44 stars•00 issues•00 pull requests•Updated Feb 8, 2025Feb 8, 2025

• iModulonMiner

  Public
  Workflow to download, process, and explore microbial RNA-seq data from NCBI SRA

  HTML

  •

  MIT License

  •2929 forks•2929 stars•44 issues•33 pull requests•Updated Nov 7, 2024Nov 7, 2024

• PM_Activity_Calls

  Public
  Python notebook workflow to make metabolic activity calls on PM samples

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 18, 2024Sep 18, 2024

• ElectricColi

  Public
  Modeling and data analysis code for the E. coli extracellular electron transfer project

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 29, 2024Jun 29, 2024

• noncoding_alleleome

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Apr 16, 2024Apr 16, 2024

• lifelike

  Public archive
  Turning big data into contextualized knowledge. Lifelike is a modern application platform for data extraction, analysis and visualization.

  pythondockerangular+ 5

  pythondockerangularbioinformaticsbig-datahelmknowledge-graphscientific-computing

  Python

  •

  Other

  •44 forks•2222 stars•00 issues•2828 pull requests•Updated Apr 4, 2024Apr 4, 2024

• MetPath

  Public
  MetPath is a set of functions for performing metabolic pathway-based gene expression analysis using genome-scale metabolic models

  MATLAB

  •

  MIT License

  •11 fork•33 stars•00 issues•00 pull requests•Updated Oct 19, 2023Oct 19, 2023

• precise1k-analyze

  Public
  Jupyter Notebook

  •

  MIT License

  •11 fork•11 star•00 issues•00 pull requests•Updated Oct 10, 2023Oct 10, 2023

• modulytics

  Public
  Visualization website for the modulome, a cross-species modularization of bacterial transcriptomes

  MIT License

  •44 forks•22 stars•22 issues•11 pull request•Updated Sep 16, 2023Sep 16, 2023

• precise1k

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•66 stars•11 issue•00 pull requests•Updated Aug 29, 2023Aug 29, 2023

• IM-ML

  Public
  Jupyter Notebook

  •11 fork•22 stars•00 issues•00 pull requests•Updated Jul 11, 2023Jul 11, 2023

• lifelike-website

  Public
  Lifelike landing website

  TypeScript

  •00 forks•00 stars•00 issues•1010 pull requests•Updated May 26, 2023May 26, 2023

• lifelike-fix-modified-date

  Public
  Python

  •00 forks•00 stars•00 issues•44 pull requests•Updated Mar 6, 2023Mar 6, 2023

• Ecoli_chem_tol_ALE

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 6, 2023Jan 6, 2023

• ROS-ALE

  Public
  Generates all figures for the manuscript "Laboratory evolution and advanced data analytics reveal systems biology of ROS tolerance" by Kevin Rychel, et al.

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 16, 2022Dec 16, 2022

• MASSpy

  Public
  Python

  •

  MIT License

  •77 forks•2626 stars•1010 issues•00 pull requests•Updated Dec 9, 2022Dec 9, 2022

• soplex_cython

  Public
  Cython bindings to soplex 3.1.1

  Python

  •33 forks•11 star•11 issue•11 pull request•Updated Nov 15, 2022Nov 15, 2022