Additional information for the publication:

Aurine Verkest, Carmem Lara de O. Manes, Steven Vercruysse, Sara Maes, Els Van Der Schueren, Tom Beeckman, Pascal Genschik, Martin Kuiper, Dirk Inzé, and Lieven De Veylder,
The cyclin dependent kinase inhibitor KRP2 controls the onset of the endoreduplication cycle during Arabidopsis leaf development through inhibition of mitotic CDKA;1 kinase complexes.

Below we present the three discussed simulation scenarios.
You need the simulator SIM-plex (download SIM-plex here) if you want to try out and change the network definitions yourself.

Col-0   (wild-type)     - download network definition or condensed definition.

fixedcomp CDKB11  0 0, add 11   0, add 2  10, add 2  -10, add 5 0,
                       add 11.1 0, add 1.9 9, add 1.9 -9, add 5.1 0,
                       add 11.3 0, add 1.7 7, add 1.7 -7, add 5.3 0  blue2
comp KRP2   6  0.02  red
comp CDKA1 14        green3
comp KRP2ph

timepoints 0 to 80

if true then KRP2 0.5
if CDKB11 > 4 then transform KRP2 to KRP2ph 3

if true then CDKA1 1
if KRP2 > 8 then CDKA1 -0.9

CDKB1;1.N161   (less CDKB1;1 activity)     - download network definition or condensed definition.

fixedcomp CDKB11  0 0, add 11.2 0, add 1.8 8, add 1.8 -8, add 5.2 0,
                       add 11.3 0, add 1.7 7, add 1.7 -7, add 5.3 0,
                       add 11.5 0, add 1.5 5, add 1.5 -5, add 5.5 0  blue2
comp KRP2   6  0.02  red
comp CDKA1 12        green3
comp KRP2ph

timepoints 0 to 80

if true then KRP2 0.5
if CDKB11 > 4 then transform KRP2 to KRP2ph 3

if true then CDKA1 1
if KRP2 > 8 then CDKA1 -0.9

KRP2^OE   (more KRP2 activity)     - download network definition or condensed definition.

fixedcomp CDKB11  0 0, add 11   0, add 2  10, add 2  -10, add 5   0,
                       add 11.1 0, add 1.9 9, add 1.9 -9, add 5.1 0,
                       add 11.3 0, add 1.7 7, add 1.7 -7, add 5.3 0  blue2
comp KRP2   7  0.02  red
comp CDKA1 12        green3
comp KRP2ph

timepoints 0 to 80

if true then KRP2 0.55
if CDKB11 > 4 then transform KRP2 to KRP2ph 3

if true then CDKA1 1
if KRP2 > 8 then CDKA1 -0.9

Presented together, as in the publication:

Overview of the network definition textfiles:

KRP2_simulation_01_-_wild_type.txt

fixedcomp CDKB11  0 0, add 11   0, add 2   10, add 2   -10, add 5   0,
                       add 11.1 0, add 1.9  9, add 1.9  -9, add 5.1 0,
                       add 11.3 0, add 1.7  7, add 1.7  -7, add 5.3 0  blue2
comp KRP2  6  0.02 red
comp CDKA1 14      green3
comp KRP2ph

timepoints 0 to 80

if true then KRP2 0.5
if CDKB11 > 4 then transform KRP2 to KRP2ph 3

if true then CDKA1 1
if KRP2 > 8 then CDKA1 -0.9

KRP2_simulation_02_-_less_CDKB11.txt

fixedcomp CDKB11  0 0, add 11.2 0, add 1.8  8, add 1.8 -8, add 5.2 0,
                       add 11.3 0, add 1.7  7, add 1.7 -7, add 5.3 0,
                       add 11.5 0, add 1.5  5, add 1.5 -5, add 5.5 0  blue2
comp KRP2  6  0.02 red
comp CDKA1 12      green3
comp KRP2ph

timepoints 0 to 80

if true then KRP2 0.5
if CDKB11 > 4 then transform KRP2 to KRP2ph 3

if true then CDKA1 1
if KRP2 > 8 then CDKA1 -0.9

KRP2_simulation_03_-_more_KRP2.txt

fixedcomp CDKB11  0 0, add 11   0, add 2   10, add 2   -10, add 5   0,
                       add 11.1 0, add 1.9  9, add 1.9  -9, add 5.1 0,
                       add 11.3 0, add 1.7  7, add 1.7  -7, add 5.3 0  blue2
comp KRP2  7  0.02 red
comp CDKA1 12      green3
comp KRP2ph

timepoints 0 to 80

if true then KRP2 0.55
if CDKB11 > 4 then transform KRP2 to KRP2ph 3

if true then CDKA1 1
if KRP2 > 8 then CDKA1 -0.9

The condensed network definitions:

KRP2_simulation_short_01_-_wild_type.txt

fixedcomp CDKB11 0 0, 11 0, 13 10, 15 0, 31.1 0, 33 9, 34.9 0, 51.3 0, 53 7, 54.7 0
comp KRP2   6  0.02
comp CDKA1 14
comp KRP2ph

timepoints 0 to 80

if true then KRP2 0.5
if CDKB11 > 4 then transform KRP2 to KRP2ph 3

if true then CDKA1 1
if KRP2 > 8 then CDKA1 -0.9

KRP2_simulation_short_02_-_less_CDKB11.txt

fixedcomp CDKB11 0 0, 11.2 0, 13 8, 14.8 0, 31.3 0, 33 7, 34.7 0, 51.5 0, 53 5, 54.5 0
comp KRP2   6  0.02
comp CDKA1 12
comp KRP2ph

timepoints 0 to 80

if true then KRP2 0.5
if CDKB11 > 4 then transform KRP2 to KRP2ph 3

if true then CDKA1 1
if KRP2 > 8 then CDKA1 -0.9

KRP2_simulation_short_03_-_more_KRP2.txt

fixedcomp CDKB11 0 0, 11 0, 13 10, 15 0, 31.1 0, 33 9, 34.9 0, 51.3 0, 53 7, 54.7 0
comp KRP2   7  0.02
comp CDKA1 12
comp KRP2ph

timepoints 0 to 80

if true then KRP2 0.55
if CDKB11 > 4 then transform KRP2 to KRP2ph 3

if true then CDKA1 1
if KRP2 > 8 then CDKA1 -0.9