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Simulation code for stochastic models of transcriptional autorepression
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troubleshooting.md

README.md

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):

Please see the file troubleshooting.md for known installation errors.

File structure

  • /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_figures from scratch by re-running all simulations.
    • The file test_infrastructure contains 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/data contains 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 test_ with 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

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