The COMET toolkit for composing customizable genetic programs in mammalian cells
DOI 10.5281/zenodo.3533966


Description of files: 

generate_TXF_distribution.m: File for generating a matrix representing a heterogeneous population of cells transfected with
one or more plasmids (based upon the cell harvest method used in this study).

Z_TXF.mat: An output from generate_TXF_distribution.m for 200 cells transfected with up to six plasmids.

model_ZFa.m: Simulation of ZFa-inducible gene expression.

model_ZFa_ZFi_competitive.m: Simulation of ZFa-inducible and ZFi-inhibitable gene expression. The ZFi effect is represented
as purely competitive without affecting cooperative RNAPII recruitment.

model_ZFa_ZFi_dual.m: Simulation of ZFa-inducible and ZFi-inhibitable gene expression. The ZFi effect is represented as both
competitive and affecting cooperative RNAPII recruitment.

model_ZFa_ZFiDsRed_dual.m: Simulation of ZFa-inducible and ZFi-DsRed-inhibitable gene expression. The ZFi-DsRed effect is
represented as both competitive and affecting cooperative RNAPII recruitment.


1. System requirements

The code can be run using Matlab (https://www.mathworks.com/products/matlab.html) and run on an operating system that
supports Matlab. Code was developed and tested on macOS Sierra.

2. Installation guide

No other specific installations are required.

3. Demo

Files can be run in the Matlab command line with the input arguments described and examples provided at the start of each
file, and they will produce the output arguments as described.

The expected run time for each function, other than for generate_TXF_distribution.m, is << 1 second on a standard desktop
computer.

4. Instructions for use

Parameter values for new TFs and promoters can be estimated as described in the Supplementary Information.