Added some instructions on how to run the code

geneRegulation/README.md

 ## Introduction
+This directory contains all the code and data needed to recreate the analysis of the Gene Regulatory Network (GRN) in Figure 1 using
+spatial genetic information in the Atlas.
 
 ## Scripts and Methods
 
-## Main Contacts
+Setup (manual) assuming you have Python 3 (and pip) installed:
+```
+pip install -r ../requirements.txt
+pip install notebook
+pip install ../common/
+```
+or use the Docker image (see main directory) and cd to this directory.
+
+To run the code that analyses the GRN and produces new hypotheses using spatial genetic information as well
+as creating and testing random networks used as a baseline do the following:
+```
+python mk_fs.py
+jupyter nbconvert --to notebook --execute random_net.ipynb
+jupyter nbconvert --to notebook --execute fig6.ipynb
+```
+
+If you just want the subsequent analysis code that generates the figures in the paper, 
+```
+jupyter nbconvert --to notebook --execute fig6.ipynb
 
+```
+in which case the precomputed results available in this directory (.pkl files) will be used instead.
+
+## Main Contacts
+Argyris Zardilis argyris.zardilis@slcu.cam.ac.uk

growthAnalysis/README.md

 ## Introduction
+This directory contains code and data needed to recreate all the 
+growth and growth anisotropy analysis figures in the article.
+
 
 ## Scripts and Methods
 
+Setup (manual) assuming you have Python 3 (and pip) installed:
+```
+pip install -r ../requirements.txt
+pip install notebook
+pip install ../common/
+apt-get install parallel
+
+```
+or use the Docker image (see main directory) and cd to this directory.
+
+To run things:
+```
+
+# run specific for flower 1
+python -c 'import growth_control; growth_control.go()'
+jupyter nbconvert --to notebook --execute grates.ipynb
+jupyter nbconvert --to notebook --execute anisos.ipynb
+
+# run for all flowers
+parallel ./run-grate-distrs.sh {} ::: 1 2 3 4 5
+parallel ./run-aniso-distrs.sh {} ::: 1 2 3 4 5
+
+```
+or use the `run.sh` script that contains all the above instructions.
+
 ## Main Contacts
+Argyris Zardilis argyris.zardilis@slcu.cam.ac.uk