Notebook
This iPython notebook illustrates how you can use gene duplication within StochPy's cell division module.
We use an extended immigration-death model which consists of two different mRNAs that are both transcribed from a different part of the genome. Gene duplication doubles the transcription rate of the corresponding mRNA.
Written by TR Maarleveld, Amsterdam, The Netherlands
E-mail: tmd200@users.sourceforge.net
Last Change: August 10, 2015
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# #
# Welcome to the interactive StochPy environment #
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# StochPy: Stochastic modeling in Python #
# http://stochpy.sourceforge.net #
# Copyright(C) T.R Maarleveld, B.G. Olivier, F.J Bruggeman 2010-2015 #
# DOI: 10.1371/journal.pone.0079345 #
# Email: tmd200@users.sourceforge.net #
# VU University, Amsterdam, Netherlands #
# Centrum Wiskunde Informatica, Amsterdam, Netherlands #
# StochPy is distributed under the BSD licence. #
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Version 2.3.0
Output Directory: /home/timo/Stochpy
Model Directory: /home/timo/Stochpy/pscmodels
We start using this model without adding gene duplication. We set both genes as non-dividing species to ensure that the gene is passed from mother to daughter for each generation.
G1 1.020
mRNA1 34.486
G2 1.020
mRNA2 34.558
We do not observe any significant changes between the mRNA copy number levels. This is expected because we use the same set immigration and death rate for mRNA1 and mRNA2.
Now we add gene duplication for mRNA1 and mRNA2 which occur as 25% and 75% of the interdivision time, respectively. We expect that in steady state mRNA1 > mRNA2.
G1 1.750
mRNA1 44.521
G2 1.284
mRNA2 31.396