In this notebook, we show how the computational of the fixpoints of qualitative regulatory networks can be done with different methods, which should give equivalent results, using GINsim and Pint.

Model loading

We load a simple model available on http://ginsim.org/node/41

In [1]:
from colomoto_jupyter import tabulate # for displaying list of fixpoints
import ginsim
In [2]:
th17 = ginsim.load("http://ginsim.org/sites/default/files/Th_17.zginml")

Computation of fixpoints with bioLQM

In [3]:
import biolqm
In [4]:
th17_lqm = ginsim.to_biolqm(th17)
In [5]:
fps_lqm = biolqm.fixpoints(th17_lqm)
tabulate(fps_lqm)
Out[5]:
IFNg IFNgR STAT1 Tbet SOCS1 IFNb IFNbR IL18 IL18R IRAK IL12 IL12R STAT4 IL4 IL4R STAT6 GATA3
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1
2 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0
3 2 1 1 2 1 0 0 0 0 0 0 0 0 0 0 0 0

Computation of fixpoints with Pint

In [6]:
import pypint
In [7]:
th17_an = biolqm.to_pint(th17_lqm)
In [8]:
fps_an = pypint.fixpoints(th17_an)
tabulate(fps_an)
Out[8]:
IFNg IFNgR STAT1 Tbet SOCS1 IFNb IFNbR IL18 IL18R IRAK IL12 IL12R STAT4 IL4 IL4R STAT6 GATA3
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1
2 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0
3 2 1 1 2 1 0 0 0 0 0 0 0 0 0 0 0 0

Display fixpoint using GINsim

In [9]:
ginsim.show(th17, fps_lqm[1]) # or fps_an[1]
Out[9]:
In [ ]: