Supplementary code for the paper "Quantitative and real-time analysis of neurogenesis with single cell resolution in mouse tissue reveals stochastic and periodic expression dynamics of HES5"
Dependencies (tested on Ubuntu 16.04):
- PyDDE (https://github.com/hensing/PyDDE)
- the ubuntu package python-tk (sudo apt install python-tk)
Please see the file
troubleshooting.md for known installation errors.
/src/contains the main Python module for this repository,
hes5.py. It includes functions to simulate stochastic and deterministic model traces, to calculate summary statistics of expression and power spectra etc.
/test/contains the code to generate simulated data in the paper, and to make the paper figures. The main modules in this folder are
test_make_final_figures.py, which can be used to regenerate all figures in the paper from data saved in this repository and
test_make_analysis_for_paper.py, which can be used to generate all data needed in
test_make_final_figuresfrom scratch by re-running all simulations.
- The file
test_infrastructurecontains functional tests for the most important functions the
/src/hes5.py, and can be used to test whether the installation is working.
- All remaining files in this folder contain additional analysis that was conducted when writing the paper.
/test/datacontains simulated data for this paper in the form of Python numpy arrays.
Running the code
We use the nosetests testing infrastructure to run all code in this project. Code can be run using the nostests command like this:
cd ./test nosetests -s test_infrastructure.py
This will run all functions in
test/test_infrastructure.py whose name starts with
test_, and it is possible to toggle whether individual functions are run by renaming them, for example by replacing
xest_. The same concept applies to all python modules in the
/test folder. The file
test_infrastructure contains a few functional tests for main functions in
src/hes5.py, and the nosetests command above can be used to see whether the project is correctly set up.
For any questions concerning this repository, please email Jochen Kursawe at
jochen dot kursawe at manchester dot ac dot uk