Covert Lab

Shriram Center, Stanford University, Stanford CA 94305

Pinned Repositories

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Stochastic simulations in python
Language:Python3 20 301
borealis
Run FireWorks workflows in Google Cloud.
Language:Python4 9 31
DeepCell
Language:Python49 37 1526
vivarium-ecoli
Whole cell model of E. coli implemented with Vivarium
Language:Jupyter Notebook11 16 213
wcEcoli
Whole Cell Model of E. coli
Language:Python16 18 3693
WholeCell
Mycoplasma genitalium whole-cell model
Language:Matlab117 36 241
WholeCellEcoliRelease
Release of the whole cell E. coli model.
Language:Python57 12 1115
WholeCellKB
WholeCellKB is a collection of free, open-source model organism databases designed specifically to enable comprehensive, dynamic simulations of entire cells and organisms.
Language:Python7 8 35
WholeCellSimDB
WholeCellDB is a hybrid SQL/HDF database for storing and retrieving whole-cell model predictions.
Language:Python7 11 158
WholeCellViz
Data visualization for whole-cell models
Language:JavaScript11 11 06

Covert Lab's Repositories

CovertLab/WholeCell
Mycoplasma genitalium whole-cell model
Language:Matlab117 36 241
CovertLab/WholeCellEcoliRelease
Release of the whole cell E. coli model.
Language:Python57 12 1115
CovertLab/DeepCell
Language:Python49 37 1526
CovertLab/wcEcoli
Whole Cell Model of E. coli
Language:Python16 18 3693
CovertLab/vivarium-ecoli
Whole cell model of E. coli implemented with Vivarium
Language:Jupyter Notebook11 16 213
CovertLab/WholeCellViz
Data visualization for whole-cell models
Language:JavaScript11 11 06
CovertLab/WholeCellKB
WholeCellKB is a collection of free, open-source model organism databases designed specifically to enable comprehensive, dynamic simulations of entire cells and organisms.
Language:Python7 8 35
CovertLab/WholeCellSimDB
WholeCellDB is a hybrid SQL/HDF database for storing and retrieving whole-cell model predictions.
Language:Python7 11 158
CovertLab/borealis
Run FireWorks workflows in Google Cloud.
Language:Python4 9 31
CovertLab/arrow
Stochastic simulations in python
Language:Python3 20 301
CovertLab/covertrack
Language:Jupyter Notebook2 10 01
CovertLab/parest
Workflow for E. coli glycolysis ODE model parameter estimation.
Language:Python2 23 02
CovertLab/covertrace
Language:Python1 8 0
CovertLab/NetworkPainter
Web-based software program creating and animating signaling network diagrams
Language:ActionScript1 9 02
CovertLab/Rend-seq-plots
Language:Jupyter Notebook0 15 01
CovertLab/short-gene-alignment
Language:Python0 7 00
CovertLab/wcEcoliColoniesTEMPORARY
Language:Python0 7 00
CovertLab/2018_Bacterial_Pipeline_riboseq
Ribosome profiling pipeline for bacterial samples created by Fuad Mohammad.
Language:Jupyter Notebook2 0
CovertLab/CellTK
Live-cell image analysis toolkit
Language:Python9 01
CovertLab/cellunet
Language:Python9 0
CovertLab/covert-scope-jobs
Language:Python23 0
CovertLab/EvolveTransport
scalable construction and optimization of kinetic transport systems for E. coli
Language:Python15 0
CovertLab/ktr_model
Matlab code for the mathematical model of the kinase translocation reporter
Language:M7 0
CovertLab/mboc_synergy_analysis
Language:Python7 11
CovertLab/orjson
Fast, correct Python JSON library supporting dataclasses, datetimes, and numpy
Language:Python0 0
CovertLab/parWholeCell
Parallelized whole-cell model
Language:Matlab9 0
CovertLab/SingleCellSequencing
Language:Python9 01
CovertLab/sisyphus
Eternally execute tasks
Language:Clojure8 19
CovertLab/vatic
Efficiently Scaling Up Video Annotation with Crowdsourced Marketplaces. IJCV 2012
Language:HTML10 0
CovertLab/wcecoli-colony-analysis
Code and analysis for the "Whole-Colony Modeling of Escherichia coli" that is currently in preparation.
Language:Python7 0