Included Files

In [1]:

    

################################   NOTES   ##############################ex
# Lines of code that are to be excluded from the documentation are      #ex
# marked with `#ex` at the end of the line.                             #ex
#                                                                       #ex
# To ensure that figures are displayed correctly together with widgets  #ex
# in the sphinx documentation we will include screenshots of some of    #ex
# the produced figures.                                                 #ex
# Do not run cells with the `display(Image('path_to_image'))` code to   #ex
# avoid duplication of results in the notebook.                         #ex
#                                                                       #ex
# Some reStructuredText 2 (ReST) syntax is included to aid in           #ex
# conversion to ReST for the sphinx documentation.                      #ex
#########################################################################ex
notebook_dir = %pwd                                                     #ex
%matplotlib inline                               
import pysces                                                           #ex
import psctb                                                            #ex
import numpy                                                            #ex
from os import path                                                     #ex
from IPython.display import display, Image                              #ex


    

    




Matplotlib "Tkagg" backend not set, defaulting to: "TkAgg"
Matplotlib interface loaded (pysces.plt.m)
Pitcon routines available
NLEQ2 routines available
You are using NumPy (1.8.2) with SciPy (0.13.3)
PySundials available
RateChar is available
Parallel scanner is available

PySCeS environment
******************
pysces.model_dir = /home/carl/Pysces/psc
pysces.output_dir = /home/carl/Pysces


***********************************************************************
* Welcome to PySCeS (0.9.0) - Python Simulator for Cellular Systems   *
*                http://pysces.sourceforge.net                        *
* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2013  *
* Triple-J Group for Molecular Cell Physiology                        *
* Stellenbosch University, ZA and VU University Amsterdam, NL         *
* PySCeS is distributed under the PySCeS (BSD style) licence, see     *
* LICENCE.txt (supplied with this release) for details                *
***********************************************************************






    




:0: FutureWarning: IPython widgets are experimental and may change in the future.

In [28]:

    

mod = pysces.model('lin5_hill')


    

    




Assuming extension is .psc
Using model directory: /home/carl/Pysces/psc
/home/carl/Pysces/psc/lin5_hill.psc loading ..... 
Parsing file: /home/carl/Pysces/psc/lin5_hill.psc
Info: "P" has been initialised but does not occur in a rate equation
 
Calculating L matrix . . . . . . .  done.
Calculating K matrix . . . . . . .  done.
 

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mg = psctb.ModelGraph(mod)


    

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mg.width = 800


    

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mg.height = 300


    

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mg.show()


    

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mg.save('/home/carl/Documents/Code/Projects/PyscesToolbox/documentation/source/included_files_files/lin5_hill.svg')


    

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