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
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.
- PyPACMESL.
datacontains the smFISH measurements of IL-1b and TNF-a transcriptions in response to LPS over 4 experimental conditions (No treatment, MG132, U0126, MG132+U0126).modulescontains 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_analysiscontains scripts for the core data fitting tasks as well as Jupyter notebooks that plot the results and output them into figures and tables.