Covert Lab

wcEcoli Public

Whole Cell Model of E. coli

Python 41 12 150 2 Updated Aug 13, 2026

vEcoli Public

Whole cell model of E. coli implemented with Vivarium

Jupyter Notebook 31MIT 16 7 12 Updated Aug 13, 2026

arrow Public

Stochastic simulations in python

Python 3MIT 1 18 1 Updated Feb 23, 2026

orjson Public Forked from ijl/orjson

Fast, correct Python JSON library supporting dataclasses, datetimes, and numpy

Python 0Apache-2.0 330 0 0 Updated Apr 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, 2025

WholeCellEcoliRelease Public

Release of the whole cell E. coli model.

Python 77 19 1 6 Updated Dec 10, 2024

short-gene-alignment Public

Python 0 0 0 0 Updated Feb 28, 2024

Rend-seq-plots Public

Jupyter Notebook 0 1 0 0 Updated Feb 28, 2024

borealis Public

Run FireWorks workflows in Google Cloud.

Python 4MIT 1 1 3 Updated Jun 6, 2023

wcecoli-colony-analysis Public

Code and analysis for the "Whole-Colony Modeling of Escherichia coli" that is currently in preparation.

Python 0GPL-3.0 0 0 0 Updated Aug 23, 2022

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