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.
- Create and activate virtual environment (venv, conda)
- Then install requirements: pip3 -r install requirements.txt
- ...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?