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.
We load a simple model available on http://ginsim.org/node/41
from colomoto_jupyter import tabulate # for displaying list of fixpoints
import ginsim
th17 = ginsim.load("http://ginsim.org/sites/default/files/Th_17.zginml")
import biolqm
th17_lqm = ginsim.to_biolqm(th17)
fps_lqm = biolqm.fixpoints(th17_lqm)
tabulate(fps_lqm)
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 |
import pypint
th17_an = biolqm.to_pint(th17_lqm)
fps_an = pypint.fixpoints(th17_an)
tabulate(fps_an)
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 |
ginsim.show(th17, fps_lqm[1]) # or fps_an[1]