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    31 repositories

    • vEcoli

      Public
      Whole cell model of E. coli implemented with Vivarium
      Jupyter Notebook
      •
      MIT License
      •15•30•7•7•Updated Feb 25, 2026Feb 25, 2026

    • wcEcoli

      Public
      Whole Cell Model of E. coli
      Python
      •
      Other
      •9•38•150•4•Updated Feb 24, 2026Feb 24, 2026

    • arrow

      Public
      Stochastic simulations in python
      Python
      •
      MIT License
      •1•3•18•1•Updated Feb 23, 2026Feb 23, 2026

    • orjson

      Public
      Fast, correct Python JSON library supporting dataclasses, datetimes, and numpy
      Python
      •
      Apache License 2.0
      •294•0•0•0•Updated Apr 4, 2025Apr 4, 2025

    • BIOE101-Online-Companion

      Public
      This repository is an online companion to BIOE101/210: Systems Biology, providing code and resources to support the textbook.
      Jupyter Notebook
      •0•0•0•0•Updated Feb 10, 2025Feb 10, 2025

    • WholeCellEcoliRelease

      Public
      Release of the whole cell E. coli model.
      Python
      •
      Other
      •17•76•1•6•Updated Dec 10, 2024Dec 10, 2024

    • short-gene-alignment

      Public
      Python
      •0•0•0•0•Updated Feb 28, 2024Feb 28, 2024

    • Rend-seq-plots

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Feb 28, 2024Feb 28, 2024

    • borealis

      Public
      Run FireWorks workflows in Google Cloud.
      workflowgoogle-cloudfireworksgoogle-compute-engine
      Python
      •
      MIT License
      •1•4•1•3•Updated Jun 6, 2023Jun 6, 2023

    • wcecoli-colony-analysis

      Public
      Code and analysis for the "Whole-Colony Modeling of Escherichia coli" that is currently in preparation.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 23, 2022Aug 23, 2022

    • covert-scope-jobs

      Public
      Python
      •0•0•0•0•Updated Jul 1, 2021Jul 1, 2021

    • wcEcoliColoniesTEMPORARY

      Public
      Python
      •0•0•0•0•Updated Apr 12, 2021Apr 12, 2021

    • sisyphus

      Public
      Eternally execute tasks
      Clojure
      •1•0•11•0•Updated Dec 10, 2019Dec 10, 2019

    • cellunet

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 20, 2019Aug 20, 2019

    • CellTK

      Public
      Live-cell image analysis toolkit
      Python
      •
      MIT License
      •12•0•0•0•Updated Jul 12, 2019Jul 12, 2019

    • EvolveTransport

      Public
      scalable construction and optimization of kinetic transport systems for E. coli
      Python
      •0•0•0•0•Updated Jul 12, 2019Jul 12, 2019

    • 2018_Bacterial_Pipeline_riboseq

      Public
      Ribosome profiling pipeline for bacterial samples created by Fuad Mohammad.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •5•0•0•0•Updated Jun 24, 2019Jun 24, 2019

    • mboc_synergy_analysis

      Public
      Python
      •1•0•1•0•Updated Nov 2, 2018Nov 2, 2018

    • parest

      Public
      Workflow for E. coli glycolysis ODE model parameter estimation.
      Python
      •2•3•1•0•Updated Oct 30, 2018Oct 30, 2018

    • DeepCell

      Public
      Python
      •24•51•9•0•Updated Jun 26, 2018Jun 26, 2018

    • covertrace

      Public
      Python
      •
      MIT License
      •3•1•0•0•Updated Mar 28, 2018Mar 28, 2018

    • vatic

      Public
      Efficiently Scaling Up Video Annotation with Crowdsourced Marketplaces. IJCV 2012
      HTML
      •
      MIT License
      •254•0•0•0•Updated Sep 7, 2017Sep 7, 2017

    • covertrack

      Public
      Jupyter Notebook
      •
      MIT License
      •1•2•0•0•Updated Nov 11, 2016Nov 11, 2016

    • SingleCellSequencing

      Public
      Python
      •1•0•0•0•Updated Sep 27, 2016Sep 27, 2016

    • WholeCell

      Public
      Mycoplasma genitalium whole-cell model
      MATLAB
      •
      MIT License
      •38•125•0•0•Updated Oct 6, 2015Oct 6, 2015

    • NetworkPainter

      Public
      Web-based software program creating and animating signaling network diagrams
      ActionScript
      •
      Other
      •2•1•0•0•Updated May 25, 2015May 25, 2015

    • WholeCellSimDB

      Public
      WholeCellDB is a hybrid SQL/HDF database for storing and retrieving whole-cell model predictions.
      Python
      •
      Other
      •7•8•0•0•Updated Jul 24, 2014Jul 24, 2014

    • ktr_model

      Public
      Matlab code for the mathematical model of the kinase translocation reporter
      M
      •0•0•0•0•Updated Jul 24, 2014Jul 24, 2014

    • WholeCellKB

      Public
      WholeCellKB is a collection of free, open-source model organism databases designed specifically to enable comprehensive, dynamic simulations of entire cells and…
      Python
      •5•8•1•0•Updated Jun 25, 2014Jun 25, 2014

    • WholeCellViz

      Public
      Data visualization for whole-cell models
      JavaScript
      •
      MIT License
      •6•12•0•0•Updated Mar 3, 2014Mar 3, 2014