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 and Cdc20A.

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 cyclin B (ActCycB) and Cdc20T). 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, and CELL_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, and Ck_license. Mass is the cell mass, Ck_license is a special place that was added to the Petri net to prevent Cytokinesis transition from accidentally firing twice in a row in the same cycle. Firing depends on, in order, Mass, Ck_license, and ActCycB (domain). The function thus takes 3 arguments (mass, license, b). If ActCycB is under the threshold specified by the model authors (CycB_DIVISION_THRESHOLD), and Ck_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 on Ck_license and the level of ActCycB (domain). The assignment function cocks the license (sets it to 1) if the level of ActCycB is above CycB_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

fod(&nullary_block;) click to toggle source
# File lib/cell_cycle/virginia_tech.rb, line 23
def fod &nullary_block; FirstOrderDegradation.new &nullary_block end