Top Level Namespace

Defined Under Namespace

Modules: CellCycle Classes: FirstOrderDegradation, Float, Numeric

Constant Summary

CELL_CYCLE =

Define the empty CELL_CYCLE net (its contents is to be added by the particular implemented cell cycle types).

Net()

S_phase_duration =

Constants that control the cell cycle settings.

12.h

S_phase_start =

5.h

S_phase_end =

S_phase_start + S_phase_duration

A_phase_start =

3.h

A_phase_end =

S_phase_end

Cdc20A_start =

22.h

Cdc20A_end =

1.h

S_s =

Figure them out as numbers in seconds.

S_phase_start.in :s

S_e =

S_phase_end.in :s

A_s =

A_phase_start.in :s

A_e =

A_phase_end.in :s

Cdc20A_s =

Cdc20A_start.in :s

Cdc20A_e =

Cdc20A_end.in :s

Timer =

Timer place

Place m!: 0

Clock =

The clock transition

Transition stoichiometry: { Timer: 1 }, rate: 1

A_phase =

Empirical places (in arbitrary units); they are the output of the cell cycle.

Place m!: 0

S_phase =

in situ

Place m!: 0

Cdc20A =

Place m!: { 1 => 0.708, 2 => 0.76 }[ CASE ]

A_phase_f =

Assignment transitions that control the state of the places A_phase, S_phase and Cdc20A.

Transition assignment: -> t { t > A_s && t < A_e ? 1 : 0 },
domain: Timer,
codomain: A_phase

S_phase_f =

Transition assignment: -> t { t > S_s && t < S_e ? 1 : 0 },
domain: Timer,
codomain: S_phase

Cdc20A_f =

Transition assignment: -> t { t < Cdc20A_e || t > Cdc20A_s ? 1 : 0 },
domain: Timer,
codomain: Cdc20A

CASE =

Csikasznagy2006agm distinguishes 2 cases and has optional G2 module.

1

G2_MODULE =

true

Mass =

Cell mass

Place m!: { 1 => 1.098, 2 => 1.568 }[ CASE ]

Ck_license =

License that ensures that the cytokinesis occurs not more than once per cycle.

Place m!: 0

Cdc20T =

Module 1

Place m!: { 1 => 2.66, 2 => 2.7 }[ CASE ]

APCP =

Place m!: { 1 => 0.717, 2 => 0.78 }[ CASE ]

Cdh1 =

Module 2

Place m!: { 1 => 0.999, 2 => 0.999 }[ CASE ]

CycB =

Module 4

Place m!: { 1 => 0.289, 2 => 0.5 }[ CASE ]

ActCycB =

Place m!: { 1 => 0.289, 2 => 0.22 }[ CASE ]

PreMPF =

Module 5

Place m!: { 1 => 0, 2 => 0.29 }[ CASE ]

TriB =

Module 6

Place m!: { 1 => 0, 2 => 0 }[ CASE ]

CKI =

Module 8

Place m!: { 1 => 0.343, 2 => 0.26 }[ CASE ]

CycE =

Module 10

Place m!: { 1 => 0.414, 2 => 0.73 }[ CASE ]

ActCycE =

Place m!: { 1 => 0.181, 2 => 0.53 }[ CASE ]

CycA =

Module 13

Place m!: { 1 => 0.0280, 2 => 0.062 }[ CASE ]

ActCycA =

Place m!: { 1 => 0.0124, 2 => 0.045 }[ CASE ]

CycD =

PLACES WITH ASSIGNMENT TRANSITIONS =========================================

ϝ Mass do |m| m * CycD⁰ end

Cdc14 =

Module 1

ϝ :Cdc20A do |a| a end

TFB =

Module 3

ϝ :ActCycB do |b| GK.( Kafb * b, Kifb, Jafb, Jifb ) end

Vsb =

Module 4

ϝ :TFB do |tfb| Ksbp + Ksbpp * tfb end

Vdb =

ϝ :Cdh1, :Cdc20A do |cdh1, a| Kdbp + Kdbpp * cdh1 + Kdbppp * a end

Cdk1P_CycB =

ϝ :CycB, :ActCycB, :TriB do |b, ab, triB| b - ab - triB end

Cdk1_CycB_CKI =

ϝ :CycB, :ActCycB, :PreMPF do |b, ab, f| b - ab - f end

Cdc25 =

Module 5 (G2 module) – not included in mammalian cycle

ϝ :ActCycB, :Cdc14 do |b, cdc14|
  # Rescue 0 makes the closure return 0 rather than raising error over Ki25p etc.
  # constants being equal to nil (not present in the mammalian cycle).
  GK.( Ka25 * b, Ki25p + Ki25pp * cdc14, Ja25, Ji25 ).to_f_nan_0 rescue 0
end

V25 =

ϝ :Cdc25 do |cdc25| ( K25p + K25pp * cdc25 ).to_f_nan_0 rescue 0 end

Vwee =

ϝ :Wee1 do |wee1| ( Kweep + Kweepp * wee1 ).to_f_nan_0 rescue 0 end

Wee1 =

ϝ :Cdc14, :ActCycB do |cdc14, b|
  GK.( Kaweep + Kaweepp * cdc14, Kiwee * b, Jawee, Jiwee ).to_f_nan_0 rescue 0
end

TFI =

Module 7 – Not included in the mammalian cycle

ϝ :Cdc14, :ActCycB do |cdc14, actCycB|
  GK.( Kafi * cdc14, Kifip + Kifipp * actCycB, Jafi, Jifi ).to_f_nan_0 rescue 0
end

TriA =

Module 12

ϝ :CycA, :ActCycA do |a, actCycA| [ a - actCycA, 0 ].max rescue 0 end

Vsi =

Module 8

ϝ :TFI do |tfi| ( Ksip + ( Ksipp * tfi ) ).to_f_nan_0 rescue 0 end

Vdi =

The function used depends on the parameter set.

case PARAMETER_SET # The function used depends on the parameter set.
when :BY then
  ϝ :ActCycA, :ActCycB, :ActCycE, :CycD, :Cdc14 do |a, b, e, d, cdc14|
    ( Kdip + Kdipp * a + Kdippp * b + Kdipppp * e + Kdippppp * d ) /
    ( 1 + cdc14 / J14di ) # <---- problem, J14di is 0
  end
else
  ϝ :ActCycA, :ActCycB, :ActCycE, :CycD, :Cdc14 do |a, b, e, d, _|
    Kdip + Kdipp * a + Kdippp * b + Kdipppp * e + Kdippppp * d
  end
end

FreeCKI =

REMARK: Band-aided not to go under 0

ϝ :CKI, :TriA, :TriB, :TriE do |cki, a, b, e|
  [ cki - a - b - e, 0.0 ].max
end

TriE =

Module 9

REMARK: Band-aided not to go under 0.

ϝ :CycE, :ActCycE do |e, actCycE|
  [ e - actCycE, 0 ].max
end

Vde =

Module 10

ϝ :ActCycA, :ActCycB, :ActCycE do |a, b, e|
  Kdep + Kdepp * e + Kdeppp * a + Kdepppp * b
end

Vatf =

Module 11

ϝ :ActCycA, :ActCycE, :CycD do |actCycA, actCycE, d|
  Katfp + Katfpp * actCycA + Katfppp * actCycE + Katfpppp * d
end

TFE =

ϝ :Vatf, :ActCycA, :ActCycB do |v, a, b|
  GK.( v, Kitfp + Kitfpp * b + Kitfppp * a, Jatf, Jitf )
end

Vda =

Module 13

ϝ :Cdc20A, :Cdc20T do |a, t| Kdap + Kdapp * a + Kdappp * t end

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.

Transition domain: Mass,
stoichiometry: { Mass: 1 },
rate: -> m { m * CELL_GROWTH_RATE }

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.

Transition codomain: [ Mass, Ck_license ],
domain: [ Mass, Ck_license, ActCycB ],
assignment: -> mass, license, b do
  if license == 1 and b < CycB_DIVISION_THRESHOLD then
    [ mass / 2, 0 ] # mass is halved, license is set to 0
  else
    [ mass, license ] # nothing happens
  end
end

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.

Transition codomain: Ck_license,
domain: [ Ck_license, ActCycB ],
assignment: -> license, b do
  if b > CycB_DIVISION_THRESHOLD * 1.1 then
    1
  else
    license
  end
end

Cdc20T_synthesis =

Cdc20T synthesis and degradation functions defined as lambda expressions according to the definitions in Csikasznagy2006agm.

-> b { x = b ** N; ( Ks20p + Ks20pp * x ) / ( J20 ** N + x ) }

Cdc20T_degradation =

-> cdc20T { cdc20T * Kd20 }

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.

Transition domain: [ ActCycB, Cdc20T ],
stoichiometry: { Cdc20T: 1 },
rate: -> b, t {
  step = world.simulation.step.to_f
  fine_step = step / 50.0
  orig = t
  # Fine-step the function.
  50.times do
    t += ( Cdc20T_synthesis.( b ) - Cdc20T_degradation.( t ) ) * fine_step
  end
  ( t - orig ) / step # get the positive change rate
}

Cdc20_activation =

Cdc20 activation, inactivation and degradation functions defined as lambdas as per Csikasznagy2006agm.

-> t, a, apcp { x = t - a; Ka20 * apcp * x / ( Ja20 + x ) }

Cdc20A_inactivation =

-> a { a * Ki20 / ( Ji20 + a ) }

Cdc20A_degradation =

-> a { a * Kd20 }

Cdc20A_change =

TS Cdc20T, Cdc20A, APCP, Cdc20A: 1 do |t, a, apcp|
  step = world.simulation.step.to_f
  fine_step = step / 50.0
  orig = a
  50.times do
    a = a +
      ( Cdc20_activation.( t, a, apcp ) -
        Cdc20A_inactivation.( a ) -
        Cdc20A_degradation.( a )
        ) * fine_step
  end
  ( a - orig ) / step # return the positive change rate
end

APC_activation =

REMARK: Just like in CI, this section has to be band-aided.

-> b, apcp { x = 1 - apcp; KaAPC * b * x / ( JaAPC + x ) }

APC_inactivation =

-> apcp { KiAPC * apcp / ( JiAPC + apcp ) }

APC_change =

TS ActCycB, APCP, APCP: 1 do |b, apcp|
  step = world.simulation.step.to_f
  fine_step = step / 50.0
  orig = apcp
  50.times do
    apcp += ( APC_activation.( b, apcp ) - APC_inactivation.( apcp ) ) * fine_step
  end
  ( apcp - orig ) / step
end

Cdh1_activation =

REMARK: Cdh1 activation and inactivation joined into 1 and band-aided in CI, and same has to be done here.

-> cdc14, cdh1 {
  x = 1 - cdh1; ( Kah1p + Kah1pp * cdc14 ) * x / ( Jah1 + x ) # orig. formula
}

Cdh1_inactivation =

-> a, b, d, e, cdh1 {
  ( Kih1p + Kih1pp * a + Kih1ppp * b + Kih1pppp * e + Kih1ppppp * d ) *
    cdh1 / ( Jih1 + cdh1 )
}

Cdh1_change =

TS ActCycA, ActCycB, CycD, ActCycE, Cdc14, Cdh1, Cdh1: 1 do
  |a, b, d, e, cdc14, cdh1|
  step = world.simulation.step.to_f
  fine_step = step / 500
  orig = cdh1
  500.times do # fine-stepped formula
    cdh1 += ( Cdh1_activation.( cdc14, cdh1 ) -
              Cdh1_inactivation.( a, b, d, e, cdh1 ) ) * fine_step
  end
  ( cdh1 - orig ) / step
end

CycB_synthesis =

Module 4

TS Vsb, Mass, CycB: 1 do |v, m| v * m end

CycB_degradation =

TS Vdb, CycB, CycB: -1 do |v, b|
  fod { v }.fine_step( world.simulation.step, 50 ).( b )
  # v * b
end

ActCycB_synthesis =

v * b

TS Vsb, Mass, ActCycB: 1 do |v, m| v * m end

ActCycB_freeing_due_to_degradation_of_CKI =

TS Vdi, CycB, PreMPF, ActCycB, ActCycB: 1 do |v, b, preMPF, actCycB|
  v * ( b - preMPF - actCycB )
end

ActCycB_freeing_due_dissoociation_from_CKI =

TS CycB, PreMPF, ActCycB, ActCycB: 1 do |b, preMPF, actCycB|
  Kdib * ( b - preMPF + actCycB )
end

ActCycB_creation_by_dephosphorylation_of_CycB =

TS V25, CycB, TriB, ActCycB, ActCycB: 1 do |v, b, triB, actCycB|
  v * ( b - triB - actCycB )
end

ActCycB_phosphorylation_by_Wee1 =

TS Vwee, ActCycB, ActCycB: -1 do |v, b| v * b end

ActCycB_asociation_with_CKI =

TS FreeCKI, ActCycB, ActCycB: -1 do |freeCKI, b| freeCKI * b * Kasb end

ActCycB_degradation =

TS Vdb, ActCycB, ActCycB: -1 do |v, b|
  fod { v }.fine_step( world.simulation.step, 50 ).( b )
  # v * b
end

MPF_phosphorylation =

Module 5

TS Vwee, CycB, PreMPF, PreMPF: 1 do |v, b, preMPF|
  v * ( b - preMPF )
end

PreMPF_dephosphorylation =

TS V25, PreMPF, PreMPF: -1 do |v, preMPF| v * preMPF end

PreMPF_degradation =

TS Vdb, PreMPF, PreMPF: -1 do |v, preMPF| v * preMPF end

TriB_assembly =

Module 6

TS CycB, TriB, FreeCKI, TriB: 1 do |b, triB, freeCKI|
  Kasb * ( b - triB ) * freeCKI
end

TriB_dissociation =

TS TriB: -1, rate: Kdib

TriB_decrease_due_to_CycB_degradation =

TS Vdb, TriB, TriB: -1 do |vdb, triB| vdb * triB end

TriB_decrease_due_to_CKI_degradation =

TS Vdi, TriB, TriB: -1 do |vdi, triB| vdi * triB end

CKI_synthesis =

Module 8

TS Vsi, CKI: 1 do |v| v end

CKI_degradation =

TS Vdi, CKI, CKI: -1 do |v, cki|
  fod { v }.fine_step( world.simulation.step, 50 ).( cki )
 # v * cki
end

CycE_synthesis =

Module 10

TS TFE, Mass, CycE: 1 do |f, m| ( Ksep + Ksepp * f ) * m end

CycE_degradation =

TS Vde, CycE, CycE: -1 do |v, e|
  # v * e
  fod { v }.fine_step( world.simulation.step, 50 ).( e )
end

ActCycE_synthesis =

TS TFE, Mass, ActCycE: 1 do |f, m| ( Ksep + Ksepp * f ) * m end

ActCycE_freeing_due_to_degradation_of_CKI =

TS Vdi, TriE, ActCycE: 1 do |v, triE| v * triE end

ActCycE_freeing_due_to_dissociation_from_CKI =

TS TriE, ActCycE: 1 do |triE| Kdie * triE end

ActCycE_degradation =

REMARK: band-aided in CI not to go under 0, fine-stepped here.

TS Vde, FreeCKI, ActCycE, ActCycE: -1 do |v, freeCKI, e|
  # ( v + Kase * freeCKI ) * e
  fod { v + Kase * freeCKI }.fine_step( world.simulation.step, 50 ).( e )
end

CycA_synthesis =

Module 13

TS TFE, Mass, CycA: 1 do |f, m| ( Ksap + Ksapp * f ) * m end

CycA_degradation =

TS Vda, CycA, CycA: -1 do |v, a|
  # v * a
  fod { v }.fine_step( world.simulation.step, 50 ).( a )
end

ActCycA_synthesis =

TS TFE, Mass, ActCycA: 1 do |f, m| ( Ksap + Ksapp * f ) * m end

ActCycA_freeing_due_to_degradation_of_CKI =

TS Vdi, TriA, ActCycE: 1 do |v, triA| v * triA end

ActCycA_freeing_due_to_dissociation_from_CKI =

TS TriA, ActCycA: 1 do |triA| Kdia * triA end

ActCycA_degradation =

band-aided

TS Vda, FreeCKI, ActCycA, ActCycA: -1 do |v, freeCKI, a|
  # ( v + Kasa * freeCKI ) * a
  fod { v + Kasa * freeCKI }.fine_step( world.simulation.step, 50 ).( a )
end

CELL_GROWTH_NET =

Net that defines cell growth, to be used eg. for testing or separate use.

Net()

B =

Golbeter-Koshland function used in Csikasznagy2006agm.

-> a1, a2, a3, a4 do a2 - a1 + a3 * a2 + a4 * a1 end

GK =

-> a1, a2, a3, a4 do
  b = B.( a1, a2, a3, a4 )
  2 * a4 * a1 / ( b + ( b**2 - 4 * ( a2 - a1 ) * a4 * a1 )**0.5 )
end

CELL_MASS_DOUBLING_TIME =

Constants as per Csikasznagy2006agm

{ 1 => 24.h, 2 => 14.h }[ CASE ].in :s

CELL_GROWTH_RATE =

Math.log( 2 ) / CELL_MASS_DOUBLING_TIME

CycB_DIVISION_THRESHOLD =

0.3

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

{
  J20:       { BY: 100,    MA: 100,      FY: 0.05,  G2: nil,  XE: nil   },
  Ja20:      { BY: 10,     MA: 0.005,    FY: 0.001, G2: nil,  XE: 0.1   },
  Ja25:      { BY: nil,    MA: nil,      FY: 0.01,  G2: 0.1,  XE: 0.1   },
  JaAPC:     { BY: 0.1,    MA: 0.01,     FY: 0.001, G2: nil,  XE: 0.01  },
  Jafb:      { BY: 0.1,    MA: 0.1,      FY: nil,   G2: nil,  XE: nil   },
  Jafi:      { BY: 10,     MA: nil,      FY: nil,   G2: nil,  XE: nil   },
  Jah1:      { BY: 0.03,   MA: 0.01,     FY: 0.01,  G2: nil,  XE: nil   },
  Jatf:      { BY: 0.01,   MA: 0.01,     FY: 0.01,  G2: nil,  XE: nil   },
  Jawee:     { BY: nil,    MA: nil,      FY: 0.01,  G2: 0.05, XE: 0.3   },
  Ji20:      { BY: 10,     MA: 0.005,    FY: 0.001, G2: nil,  XE: 0.1   },
  Ji25:      { BY: nil,    MA: nil,      FY: 0.01,  G2: 0.1,  XE: 0.1   },
  JiAPC:     { BY: 0.1,    MA: 0.01,     FY: 0.001, G2: nil,  XE: 0.01  },
  Jifb:      { BY: 0.1,    MA: 0.1,      FY: nil,   G2: nil,  XE: nil   },
  Jifi:      { BY: 10,     MA: nil,      FY: nil,   G2: nil,  XE: nil   },
  Jih1:      { BY: 0.03,   MA: 0.01,     FY: 0.01,  G2: nil,  XE: nil   },
  Jitf:      { BY: 0.01,   MA: 0.01,     FY: 0.01,  G2: nil,  XE: nil   },
  Jiwee:     { BY: nil,    MA: nil,      FY: 0.01,  G2: 0.05, XE: 0.3   },
  J14di:     { BY: 0.0833, MA: nil,      FY: nil,   G2: nil,  XE: nil   },
  K25p:      { BY: nil,    MA: nil,      FY: 0.001, G2: 0.05, XE: 0.1   },
  K25pp:     { BY: nil,    MA: nil,      FY: 1,     G2: 05,   XE: 1.9   },

  Ka20:      { BY: 1,      MA: 0.0833,   FY: 0.2,   G2: nil,  XE: 0.1   },
  Ka25:      { BY: nil,    MA: nil,      FY: 1,     G2: 1,    XE: 1     },
  KaAPC:     { BY: 0.1,    MA: 0.0117,   FY: 0.2,   G2: nil,  XE: 2     },
  Kafb:      { BY: 1,      MA: 0.167,    FY: nil,   G2: nil,  XE: nil   },
  Kafi:      { BY: 6,      MA: nil,      FY: nil,   G2: nil,  XE: nil   },
  Kah1p:     { BY: 0.01,   MA: 0.175,    FY: 5,     G2: nil,  XE: nil   },
  Kah1pp:    { BY: 0.8,    MA: 2.33,     FY: 50,    G2: nil,  XE: nil   },
  Kasa:      { BY: 50,     MA: 16.7,     FY: 500,   G2: nil,  XE: nil   },
  Kasb:      { BY: 65,     MA: nil,      FY: 1000,  G2: nil,  XE: nil   },
  Kase:      { BY: nil,    MA: 16.7,     FY: nil,   G2: nil,  XE: nil   },
  Katfp:     { BY: nil,    MA: 0.0,      FY: 1.5,   G2: nil,  XE: nil   },
  Katfpp:    { BY: 0.76,   MA: 0.05,     FY: nil,   G2: nil,  XE: nil   },
  Katfppp:   { BY: 0.76,   MA: 0.0833,   FY: nil,   G2: nil,  XE: nil   },
  Katfpppp:  { BY: 3.8,    MA: 0.055,    FY: nil,   G2: nil,  XE: nil   },
  Kaweep:    { BY: nil,    MA: nil,      FY: 0.25,  G2: 0.3,  XE: 0.1   },
  Kaweepp:   { BY: nil,    MA: nil,      FY: 0.25,  G2: nil,  XE: nil   },
  Kd20:      { BY: 0.05,   MA: 0.025,    FY: 0.1,   G2: nil,  XE: nil   },
  Kdap:      { BY: 0.01,   MA: 0.000333, FY: 0.01,  G2: nil,  XE: nil   },
  Kdapp:     { BY: 0.16,   MA: 0.333,    FY: 2,     G2: nil,  XE: nil   },
  Kdappp:    { BY: nil,    MA: nil,      FY: 0.02,  G2: nil,  XE: nil   },

  Kdbp:      { BY: 0.003,  MA: 0.000833, FY: 0.02,  G2: nil,  XE: 0.015 },
  Kdbpp:     { BY: 0.4,    MA: 0.333,    FY: 0.75,  G2: nil,  XE: nil   },
  Kdbppp:    { BY: 0.15,   MA: 0.0167,   FY: 1.5,   G2: nil,  XE: nil   },
  Kdep:      { BY: 0.12,   MA: 0.00167,  FY: nil,   G2: nil,  XE: nil   },
  Kdepp:     { BY: nil,    MA: 0.0167,   FY: nil,   G2: nil,  XE: nil   },
  Kdeppp:    { BY: nil,    MA: 0.167,    FY: nil,   G2: nil,  XE: nil   },
  Kdepppp:   { BY: nil,    MA: 0.167,    FY: nil,   G2: nil,  XE: nil   },
  Kdia:      { BY: 0.06,   MA: 0.167,    FY: 1,     G2: nil,  XE: nil   },
  Kdib:      { BY: 0.05,   MA: nil,      FY: 1,     G2: nil,  XE: nil   },
  Kdie:      { BY: nil,    MA: 0.167,    FY: nil,   G2: nil,  XE: nil   },
  Kdip:      { BY: 0.02,   MA: 0.167,    FY: 0.1,   G2: nil,  XE: nil   },
  Kdipp:     { BY: 0.2,    MA: 0.833,    FY: 2,     G2: nil,  XE: nil   },
  Kdippp:    { BY: 0.9,    MA: 1.67,     FY: 100,   G2: nil,  XE: nil   },
  Kdipppp:   { BY: 0.12,   MA: 0.833,    FY: nil,   G2: nil,  XE: nil   },
  Kdippppp:  { BY: 0.66,   MA: nil,      FY: 1,     G2: nil,  XE: nil   },
  Ki20:      { BY: 0.05,   MA: 0.0417,   FY: 0.05,  G2: nil,  XE: 0.095 },
  Ki25p:     { BY: nil,    MA: nil,      FY: 0.25,  G2: 0.3,  XE: 0.125 },
  Ki25pp:    { BY: nil,    MA: nil,      FY: 0.25,  G2: nil,  XE: nil   },
  KiAPC:     { BY: 0.15,   MA: 0.03,     FY: 0.08,  G2: nil,  XE: 0.15  },
  Kifb:      { BY: 0.15,   MA: 0.0167,   FY: nil,   G2: nil,  XE: nil   },

  Kifip:     { BY: 0.008,  MA: nil,      FY: nil,   G2: nil,  XE: nil   },
  Kifipp:    { BY: 0.05,   MA: nil,      FY: nil,   G2: nil,  XE: nil   },
  Kih1p:     { BY: 0.001,  MA: nil,      FY: 1,     G2: nil,  XE: nil   },
  Kih1pp:    { BY: 0.64,   MA: 0.2,      FY: 40,    G2: nil,  XE: nil   },
  Kih1ppp:   { BY: 0.1,    MA: 0.667,    FY: 40,    G2: nil,  XE: nil   },
  Kih1pppp:  { BY: 0.032,  MA: nil,      FY: nil,   G2: nil,  XE: nil   },
  Kih1ppppp: { BY: 0.01,   MA: nil,      FY: 40,    G2: nil,  XE: nil   },
  Kitfp:     { BY: 0.6,    MA: 0.0417,   FY: 1,     G2: nil,  XE: nil   },
  Kitfpp:    { BY: 8,      MA: 0.0167,   FY: nil,   G2: nil,  XE: nil   },
  Kitfppp:   { BY: nil,    MA: 0.0167,   FY: 10,    G2: nil,  XE: nil   },
  Kiwee:     { BY: nil,    MA: nil,      FY: 1,     G2: 1,    XE: 3     },
  Ks20p:     { BY: 0.001,  MA: nil,      FY: 0.005, G2: nil,  XE: 1     },
  Ks20pp:    { BY: 10,     MA: 2.5,      FY: 0.1,   G2: nil,  XE: nil   },
  Ksap:      { BY: 0.0008, MA: nil,      FY: nil,   G2: nil,  XE: nil   },
  Ksapp:     { BY: 0.005,  MA: 0.00417,  FY: 0.02,  G2: nil,  XE: nil   },
  Ksbp:      { BY: 0.004,  MA: 0.00167,  FY: 0.02,  G2: nil,  XE: 0.1   },
  Ksbpp:     { BY: 0.04,   MA: 0.005,    FY: nil,   G2: nil,  XE: nil   },
  Ksep:      { BY: nil,    MA: 0.00133,  FY: nil,   G2: nil,  XE: nil   },
  Ksepp:     { BY: 0.15,   MA: 0.05,     FY: nil,   G2: nil,  XE: nil   },
  Ksip:      { BY: 0.036,  MA: 0.333,    FY: 0.3,   G2: nil,  XE: nil   },

  Ksipp:     { BY: 0.24,   MA: nil,      FY: nil,   G2: nil,  XE: nil   },
  Kweep:     { BY: nil,    MA: nil,      FY: 0.05,  G2: 0.2,  XE: 0.1   },
  Kweepp:    { BY: nil,    MA: nil,      FY: 0.5,   G2: 2,    XE: 0.9   },
  N:         { BY: 1,      MA: 1,        FY: 4,     G2: nil,  XE: nil   },
  CycD⁰:     { BY: 0.108,  MA: 0.5,      FY: 0.05,  G2: nil,  XE: nil   }
}

PARAMETER_SET =

Mammalian parameter set will be chosen.

:MA

Instance Method Summary

• #fod(&nullary_block) ⇒ Object

Instance Method Details

#fod(&nullary_block) ⇒ Object

# File 'lib/cell_cycle/virginia_tech.rb', line 23

def fod &nullary_block; FirstOrderDegradation.new &nullary_block end