class Object
Constants
- APCP
- APC_activation
REMARK: Just like in CI, this section has to be band-aided.
- APC_change
- APC_inactivation
- A_end_s
- A_phase
Empirical places (in arbitrary units); output of the cell cycle.
- A_phase_end
- A_phase_f
Assignment transitions that control the state of the places
A_phase
,S_phase
andCdc20A
.- A_phase_start
- A_start_s
- ActCycA
- ActCycA_degradation
band-aided
- ActCycA_freeing_due_to_degradation_of_CKI
- ActCycA_freeing_due_to_dissociation_from_CKI
- ActCycA_synthesis
- ActCycB
- ActCycB_asociation_with_CKI
- ActCycB_creation_by_dephosphorylation_of_CycB
- ActCycB_degradation
- ActCycB_freeing_due_dissoociation_from_CKI
- ActCycB_freeing_due_to_degradation_of_CKI
- ActCycB_phosphorylation_by_Wee1
- ActCycB_synthesis
- ActCycE
- ActCycE_degradation
REMARK: band-aided in CI not to go under 0, fine-stepped here.
- ActCycE_freeing_due_to_degradation_of_CKI
- ActCycE_freeing_due_to_dissociation_from_CKI
- ActCycE_synthesis
- B
Golbeter-Koshland function used in Csikasznagy2006agm.
- CASE
Csikasznagy2006agm distinguishes 2 cases and has optional G2 module.
- CELL_CYCLE
Define the empty
CELL_CYCLE
net (its contents is to be added by the particular implemented cell cycle types).- CELL_GROWTH_NET
Net that defines cell growth, to be used eg. for testing or separate use.
- CELL_GROWTH_RATE
- CELL_MASS_DOUBLING_TIME
Constants as per Csikasznagy2006agm
- CKI
Module 8¶ ↑
- CKI_degradation
- CKI_synthesis
Module 8¶ ↑
- Cc_duration_s
Figure them out as numbers in seconds.
- Cdc14
Module 1¶ ↑
- Cdc20A
- Cdc20A_change
- Cdc20A_degradation
- Cdc20A_e
- Cdc20A_end
- Cdc20A_f
- Cdc20A_inactivation
- Cdc20A_s
- Cdc20A_start
- Cdc20T
Module 1¶ ↑
- Cdc20T_change
A timed stoichiometric transition representing the change of anaphase-promoting factor (
Cdc20T
). Its stoichiometry is thus { Cdc20T: 1 }. Its rate depends on the level of activated cyclinB
(ActCycB
) andCdc20T
). The function is modified to enable larger execution step with :pseudo_euler method.- Cdc20T_degradation
- Cdc20T_synthesis
Cdc20T
synthesis and degradation functions defined as lambda expressions according to the definitions in Csikasznagy2006agm.- Cdc20_activation
Cdc20 activation, inactivation and degradation functions defined as lambdas as per Csikasznagy2006agm.
- Cdc25
Module 5 (G2 module) – not included in mammalian cycle¶ ↑
- Cdh1
Module 2¶ ↑
- Cdh1_activation
REMARK:
Cdh1
activation and inactivation joined into 1 and band-aided in CI, and same has to be done here.- Cdh1_change
- Cdh1_inactivation
- Cdk1P_CycB
- Cdk1_CycB_CKI
- Cell_cycle_duration
Constants that control the cell cycle settings.
- Cell_growth
This creates a timed stoichiometric (TS) transition representing cell growth. Cell growth changes
Mass
(domain), and its stoichiometry is { Mass: 1 }, that is,Mass
simply increases at the rate indicated by the transition's function. The function (rate) is given by the formula m *CELL_GROWTH_RATE
, where m is the current mass of the cell, andCELL_GROWTH_RATE
a constant given by the model authors.- Ck_license
License that ensures that the cytokinesis occurs not more than once per cycle.
- Clock
The clock transition
- CycA
Module 13¶ ↑
- CycA_degradation
- CycA_synthesis
Module 13¶ ↑
- CycB
Module 4¶ ↑
- CycB_DIVISION_THRESHOLD
- CycB_degradation
- CycB_synthesis
Module 4¶ ↑
- CycD
PLACES WITH ASSIGNMENT TRANSITIONS =========================================¶ ↑
- CycE
Module 10¶ ↑
- CycE_degradation
- CycE_synthesis
Module 10¶ ↑
- Cytokinesis
This creates an assignment (A) transition representing cytokinesis. It changes 2 places (codomain):
Mass
, andCk_license
.Mass
is the cell mass,Ck_license
is a special place that was added to the Petri net to preventCytokinesis
transition from accidentally firing twice in a row in the same cycle. Firing depends on, in order,Mass
,Ck_license
, andActCycB
(domain). The function thus takes 3 arguments (mass, license, b). IfActCycB
is under the threshold specified by the model authors (CycB_DIVISION_THRESHOLD
), andCk_license
is cocked (equal to 1), then the mass is halved and the license is consumed (set to 0). Otherwise, the [ mass, license ] pair is returned unchanged. The :pseudo_euler simulation method fires the transition once after each simulation step.- DATA
Following are the data from Czikasznagy2006agm supplementary materials. Abbreviations meanings:
BY -- budding yeast MA -- mammalian, FY -- fission yeast, G2 -- G2 module, XE -- xenopus embryo
- FreeCKI
REMARK: Band-aided not to go under 0
- G2_MODULE
- GK
- License_cocking
An assignment transition that controls the
Ck_license
cocking (codomain), and whose firin depends onCk_license
and the level ofActCycB
(domain). The assignment function cocks the license (sets it to 1) if the level ofActCycB
is aboveCycB_DIVISION_THRESHOLD
plus 10% margin. Otherwise, the license is unchanged. Again, the :pseudo_euler simulation method fires the transition once after each simulation step.- MPF_phosphorylation
Module 5¶ ↑
- Mass
Cell mass
- PARAMETER_SET
Mammalian parameter set will be chosen.
- PreMPF
Module 5¶ ↑
- PreMPF_degradation
- PreMPF_dephosphorylation
- S_end_s
- S_phase
- S_phase_duration
- S_phase_end
- S_phase_f
- S_phase_start
- S_start_s
- TFB
Module 3¶ ↑
- TFE
- TFI
Module 7 – Not included in the mammalian cycle¶ ↑
- Timer
Timer
place- TriA
Module 12¶ ↑
- TriB
Module 6¶ ↑
- TriB_assembly
Module 6¶ ↑
- TriB_decrease_due_to_CKI_degradation
- TriB_decrease_due_to_CycB_degradation
- TriB_dissociation
- TriE
Module 9¶ ↑
REMARK: Band-aided not to go under 0.
- V25
- Vatf
Module 11¶ ↑
- Vda
Module 13¶ ↑
- Vdb
- Vde
Module 10¶ ↑
- Vdi
- Vsb
Module 4¶ ↑
- Vsi
Module 8¶ ↑
- Vwee
- Wee1
Public Instance Methods
# File lib/cell_cycle/virginia_tech.rb, line 23 def fod &nullary_block; FirstOrderDegradation.new &nullary_block end