Kalb_Vo_2021

This repository contains the code used for the data modeling and analysis presented in the publication

Daniel Kalb*, Huy D Vo*, Samantha Adikari, Elizabeth Hong-Geller, Brian Munsky, James Werner. Visualization and Modeling of Inhibition of IL-1β and TNFα mRNA Transcription at the Single-Cell Level. Scientific Reports 11, 2021. DOI: https://doi.org/10.1038/s41598-021-92846-0

Dependencies

For all tasks:

• Python 3.8+.

For plotting the analysis results:

• NumPy.
• Matplotlib.

For conducting the parameter fitting tasks:

• SciPy.
• PyGMO 2.
• MPI for Python 2+.
• PACMENSL v 0.0.
• PyPACMESL v 0.0.

Directory structure

• data contains the smFISH measurements of IL-1b and TNF-a transcriptions in response to LPS over 4 experimental conditions (No treatment, MG132, U0126, MG132+U0126).
• modules contains useful functions for loading and binning the data (data_io), calculating moments from the model (moments), generating parallel random numbers (mpi4rng), and routines to make PyGMO work with MPI (mpi4pygmo).
• single_gene_analysis contains scripts for the core data fitting tasks as well as Jupyter notebooks that plot the results and output them into figures and tables.