Covert Lab

WholeCell

Mycoplasma genitalium whole-cell model

WholeCellEcoliRelease

Release of the whole cell E. coli model.

DeepCell

wcEcoli

Whole Cell Model of E. coli

vivarium-ecoli

Whole cell model of E. coli implemented with Vivarium

WholeCellViz

Data visualization for whole-cell models

WholeCellKB

WholeCellKB is a collection of free, open-source model organism databases designed specifically to enable comprehensive, dynamic simulations of entire cells and organisms.

WholeCellSimDB

WholeCellDB is a hybrid SQL/HDF database for storing and retrieving whole-cell model predictions.

borealis

Run FireWorks workflows in Google Cloud.

arrow

Stochastic simulations in python

covertrack

parest

Workflow for E. coli glycolysis ODE model parameter estimation.

covertrace

NetworkPainter

Web-based software program creating and animating signaling network diagrams

Rend-seq-plots

short-gene-alignment

wcEcoliColoniesTEMPORARY

2018_Bacterial_Pipeline_riboseq

Ribosome profiling pipeline for bacterial samples created by Fuad Mohammad.

CellTK

Live-cell image analysis toolkit

cellunet

covert-scope-jobs

EvolveTransport

scalable construction and optimization of kinetic transport systems for E. coli

ktr_model

Matlab code for the mathematical model of the kinase translocation reporter

mboc_synergy_analysis

orjson

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

parWholeCell

Parallelized whole-cell model

SingleCellSequencing

sisyphus

Eternally execute tasks

vatic

Efficiently Scaling Up Video Annotation with Crowdsourced Marketplaces. IJCV 2012

wcecoli-colony-analysis

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