NLI_macrophage_iron_regulation

This NLI_macrophage_iron_regulation repository contains all resources pertaining to the mathematical model of iron control in macrophages during invasive pulmonary aspergillosis (IPA). This model will allow us to study iron regulation within a macrophage and its effect on iron level in the local environment in the context of IPA.

Files in this repository are arranged as such:

├── Macrophage_model_3state.py
├── Wiring_diagram_macModel.png
├── README.md
├── LICENSE.md
└── .gitignore

macrophage_model_3state.py

This script contains a discrete dynamical system model that converts a static network into a dynamical model and computes steady state for the model. The model consists of generalized Boolean functions of how nodes (molecules) in the static network interact with each other and evolve with time. The nodes in the model takes 0, 1 or 2 state representing low, medium or high expression level, respectively.

This static network is available here

The static network and the dynamic model is constructed by inferring relationships based on bioinformatics analysis, functional enrichment analysis and literature.

• Bioinformatics analysis is here

Prerequisites

Running the code depends on the following packages.

• Python 3.0 or newer

Run command

The code can be run on terminal using the following command. Before running the model, the states of external parameters (fungal, iron levels - FE2, FE3, EHEME) need to fixed to the desired state.

python Macrophage_model.py outputfile.txt number_of_iterations

Code output

A text file with

1. steady state - fixed and cyclic - of the systems
2. the number of basins that converge to a steady state
3. Intermediate steps to converge to a steady state

Authors

• Bandita Adhikari -PhD student, UConn Health, Farmington, CT -Current affiliation - Postodoctoral Fellow, The University of Pennsylvania, Philadelphia, PA
• Joseph Masison -MD/PhD student, UConn Health, Farmington, CT
• Luis Sordo Vieira -Postdoctoral Associate, The University of Florida, Geinesville, CT
• Reinhard Laubenbacher -Professor, The University of Florida, Geinesville, CT

License

This project is licensed under the MIT License - see LICENSE.md file for details.