genericInteractionNetwork

Commandline app to create pathway object from a json file.

Must run from the outermost directory of the project.

Any file that follows with It is for the user to use and apply.

Should take over this notebook: https://colab.research.google.com/drive/1I-t0NpRuObLX94VFRltOoGqI-xL5sAZE

Each user module has flag options to customize experience.

1. Create and activate virtual environment (venv, conda)
2. Then install requirements: pip3 -r install requirements.txt
3. ...Explain modules and flags

• Ideas:
  • kinetics (cooperative, feedback loop)
  • genetic algorithm (customizable to what parameters, what data, constraints, and fitting hyperparameters) --> for prototype may implement the following packages initially (geneticalgorithm or pyGAD)
  • active/inactive enzyme states (manage rates appropriately in modify, dynamic, and fitting)
  • network diagram pointing to arrows and double arrows to signify reversibility
  • dynamic graphing module
  • complete statistics and modify modules
  • logging and documentation (including code comments)
• Goals:
  • Once fitted examine:
    • dynamics in steady state and stress
    • sensitivity of dynamics to each key signalling molecule
    • machine learning to predict outcomes (Ca2+ levels, phagocytosis, etc.) based on an input of key signalling state
      • perhaps the type of stimuli could be inputs?