catohaste / neighbourhood-streak

Implementation of two models which study how positional information is encoded and interpreted in the developing embryo.

Implementation of two models which study how positional information is encoded and interpreted in the developing embryo.

The models were developed alongside experiments performed in chick embryos, before the formation of the primitive streak. The site of the initiation of streak formation breaks radial symmetry, defining the posterior of the embryo. The experiments involved grafting beads soaked in compounds which either induce or inhibit streak formation.

We model a ring of cells around the circumference of the embryo, in a region called the marginal zone which has been shown to be key for the formation of the primitive streak. Each cell has a defined concentration of streak-inducer and -inhibitor. Cells use these concentrations to make the binary decision to initiate the formation of a streak, or not.

Both models involve cells balancing their concentrations of inducer and inhibitor. The key differences for models A and B are that

1. cells assess their values of inducer/inhibitor autonomously without reference to their neighbours,
2. cells compare their own values of inducer/inhibitor with those of their neighbours.

Quickstart

Code has been tested with Python 3.7.9.

Download code

git clone https://github.com/catohaste/neighbourhood-streak.git
cd neighoubourhood-streak

Create and activate virtual environments with all required packages

python3 -m venv env
source env/bin/activate
python -m pip install -r requirements.txt

Run files

python main_signal_slope.py

Jupyter demo

python -m ipykernel install --user --name=env
jupyter notebook

Open 'demo.ipynb' and change kernel to the virtualenv created, if not already done so.

Clean up

jupyter kernelspec uninstall env
deactivate
rm -r env