Code

Code for many lab papers and projects is accessible on the Elowitz Lab GitHub page

We archive all data and code for each publication in the publicly accessible Caltech Research Data Repository.

EasyFlowQ

EasyFlowQ is an open source, user-friendly, native GUI app on Windows and macOS for flow cytometry analysis. It’s UI interface is designed based on the original MATLAB version of EasyFlow (by @ayaron). It provides an "all-in-one” package for analyzing flow cytometry data, without requiring installation (or prior knowledge) of dependencies like MATLAB or Python. Please refer to the source code in GitHub, if you’re interested in contributing.

Cellerie

Cellerie is a streamlined web-based visual tool engineered to enable biologists to dynamically track, filter, and compare gene expression patterns across multiple cell lineage tree data sets simultaneously. Cellerie was developed originally as part of Caltech/JPL/ArtCenter Summer Data Visualization Program [ http://datavis.caltech.edu/ ] with the Elowitz Lab.

Schnitzcells

Schnitzcells is MATLAB software that allows for quantitative analysis of fluorescent time-lapse movies of living cells. The package is developed for bacteria and has been instrumental in analyzing E.coli and B. subtilis movies.

Software Website

Kin Correlation Analysis

Kin Correlation Analysis allows inference of cell state transition rates from lineage information and end-point cell state measurements.

See: S. Hormoz, Z. Singer et al, Cell Systems (2016).

Code and example data for performing KCA can be found here.  

Data

Plasmids on Addgene

The Michael Elowitz Lab has deposited plasmids at Addgene for distribution to the research community. Addgene is a nonprofit plasmid repository dedicated to improving life science research.

Elowitz Lab Addgene Repository

Cell Lines and Organisms

Drosophila memoiphila is a resource for in situ lineage analysis in flies. It contains the intMEMOIR genetic memory array, which can be stochastically edited to generate up to 59,049 possible outcomes for lineage or clonal reconstruction. All edit outcomes can be read out through imaging, in conjunction with endogenous genes of interest, by fluorescence in situ hybridization (FISH), thereby enabling simultaneous analysis of single cell spatial organization, gene expression, and lineage in the same tissue. The image on the right shows FISH in a cross-section of D. memoiphila's brain.

Additional information and link to Bloomington Drosophila stock center.