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License: Other
Simulation of continuous labeling assays
License: Other
We decided to split the code between simulator and the parameter estimation. This repository should only contain the simulator, so we need to remove the parameter estimation part from here.
There are still 3 occurences of brdu in the code. Probably just in comments, but we should clean this up.
I updated the documentation of run
. I realised that the return value of run
was not documented, yet. I wrote that it is a list of labelled cells. Did I document it correctly?
Further, I please make sure that run
also returns the time for each measurement. This could be done like this:
tt = [t for t in times for i in range(samples)]
animal
is a leftover from the beginning. We call it sample
now.
I tried to install pybrdu on my MPI PKS machine which runs OpenSuse. Installation worked fine, but I get an error when importing clapy
:
In [1]: import clapy
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-1-4637408733ed> in <module>()
----> 1 import clapy
~/Nextcloud/projects/continuous_labelling_assays/source/clapy/clapy/__init__.py in <module>()
----> 1 from .cla import run
~/Nextcloud/projects/continuous_labelling_assays/source/clapy/clapy/cla.py in <module>()
----> 1 from . import ccla as _cla
2
3
4 def run(mode=2,samples = 1000,nCells=100,mCells=100,times=[0.0,0.2],GF=1,G1=0.2,S=0.3,G2M=0.5,sSamples=0.01,sPopulation=0.01,seed = 42,**args):
5 '''
~/Nextcloud/projects/continuous_labelling_assays/source/clapy/clapy/ccla.py in <module>()
7 #__loader__ = None; del __bootstrap__, __loader__
8 #imp.load_dynamic(__name__,__file__)
----> 9 __bootstrap__()
~/Nextcloud/projects/continuous_labelling_assays/source/clapy/clapy/ccla.py in __bootstrap__()
2 #global __bootstrap__, __loader__, __file__
3 import sys, pkg_resources, imp, os
----> 4 __soname__ = [f in os.listdir('.')]
5 print(__soname__)
6 #__file__ = pkg_resources.resource_filename(__name__,'ccla.so')
NameError: name 'f' is not defined
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