datasets package and cnodata function

The cnodata is a function that retrieve the pathname of PKN and MIDAS files provided within CNO
The datasets is a package that contains sub-packages. Each of them being made of a prior knowledge network and a MIDAS data set.



In [14]:

    
%matplotlib inline
import matplotlib
matplotlib.rcParams['figure.dpi'] = 200
matplotlib.rcParams['figure.figsize'] = (12,8)
from cno import datasets, cnodata



In [20]:

    
print(dir(datasets))









    



['EGFR-ErbB_PCB2009', 'ExtLiverBMC2012', 'ExtLiverPCB', 'ExtLiverPriHuMCP2010', 'LiverDREAM', 'LiverMSB2009', 'Register', 'TCellPCB2007', 'ToyMMB', 'ToyMMB_Feedback', 'ToyMMB_FeedbackAnd', 'ToyMMB_T2', 'ToyMMB_added_link', 'ToyMSB2009', 'ToyPB', 'ToyPB_SBML', 'ToyPB_True', 'ToyPCB', '__all__', '__builtins__', '__doc__', '__file__', '__name__', '__package__', '__path__', 'cnodata', 'glob', 'names', 'os', 'register']



In [6]:

    
# the plot method uses cellnopt.core behind the scene to fetch the pknmodel
# and data set and CNOGraph data structure
datasets.ToyMMB.plot()

pathname to data and pknmodel are available given a tag name (e.g., ToyPB)



In [8]:

    
datasets.ToyMMB.model









    Out[8]:





'/home/cokelaer/Work/github/cellnopt/cno/datasets/ToyMMB/PKN-ToyMMB.sif'

another way to get the data set filename is to use the cnodata function



In [9]:

    
pknmodel = datasets.cnodata('PKN-ToyMMB.sif')

available datasets using cnodata



In [22]:

    
cnodata('MD*')









    



MD-ToyMMB_added_link.csv
MD-ExtLiverPriHuMCP2010.csv
MD-ToyMMB.csv
MD-ToyMSB2009.csv
MD-ExtLiverPCB.csv
MD-ToyPB.csv
MD-LiverDREAM.csv
MD-ToyPB_SBML.csv
MD-EGFR-ErbB_PCB2009.csv
MD-TCellPCB2007.csv
MD-ToyMMB_FeedbackAnd.csv
MD-ToyPCB.csv
MD-ToyMMB_T2.csv
MD-LiverMSB2009.csv
MD-ToyPB_True.csv
MD-ToyMMB_Feedback.csv
MD-ExtLiverBMC2012.csv



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