Boolean transcription factor network for hierarchical differentiation of myeloid progenitor cells

Abstract

• Language: python3 >= 3.8
• Library dependencies: ipywidgets, matplotlib, numpy, pandas, tellurium.
• License: GPL >= v3
• Date: autumn 2023
• Author: Elmar Bucher
• Contact: https://github.com/elmbeech/grn_myeloid_progenitor/issues
• 
• User manual: this README.md file
• Description: python3 tellurium implementation and analysis from krumsiek et al.'s 2011 published myeloid progenitor cells differentiation gene regulatory network.
• This notebook is my semester work for class ENGR E542 Introduction to Computational Bioengineering by Prof. James Glazier.

Run on google colab

1. In a web browser open: https://github.com/elmbeech/grn_myeloid_progenitor/blob/main/engr_e542_fall2023_sysbio_network_project_sim.ipynb
2. Click the: Open in Colab link.
3. Run the first code cell to install libncurses5 C and tellurium python3 library.
4. Once the first cell is run, it will crash with the message: Your session crashed for an unknowenreason.
5. No worries! All fine. Now you can continue to run the other cells as usual.

Run locally

1. It is assumed python3 and all library dependencies are installed and running.
2. Clone the notebook locally: git clone https://github.com/elmbeech/grn_myeloid_progenitor.git
3. Open the notebook: jupyter lab engr_e542_fall2023_sysbio_network_project_sim.ipynb
4. Skip the first cell! libncurses5 and tellurium should already be installed.
5. From the second code cells onwars, run the notebook as usual.

Cite

@Misc{bucher2023,
  author    = {Bucher, Elmar},
  title     = {elmbeech/grn_myeloid_progenitor: python3 tellurium myeloid progenitor cells differentiation gene regulatory network implementation and analysis.},
  year      = {2023},
  copyright = {Open Access},
  doi       = {10.5281/ZENODO.10343911},
  publisher = {Zenodo},
}