test/examples/demonstrator_4.rb in y_petri-2.2.4 vs test/examples/demonstrator_4.rb in y_petri-2.3.2
- old
+ new
@@ -1,7 +1,9 @@
#encoding: utf-8
+# Unfinished demonstration of TTP pathway simulation, search for FIXME.
+
require 'y_petri'
include YPetri
require 'sy'
require 'mathn'
@@ -44,14 +46,15 @@
DeoxyUridine = Place m!: 0.6 # Traut1994pcp
DeoxyUMP = Place m!: 2.70 # Traut1994pcp
DeoxyUDP = Place m!: 0.5 # Traut1994pcp
DeoxyUTP = Place m!: 0.7 # Traut1994pcp
-DeoxyThymidine = Place m!: 0.5 # Traut1994pcp
+Thymidine = Place m!: 0.5 # Traut1994pcp
DeoxyTMP = Place m!: 0.0 # in situ
DeoxyTDP = Place m!: 2.4 # Traut1994pcp
DeoxyTTP = Place m!: 17.0 # Traut1994pcp
+DeoxyT23P = Place m!: 2.4 + 17.0
# === Empirical places (in arbitrary units)
A_phase = Place m!: 1 # in situ
S_phase = Place m!: 1 # in situ
@@ -73,22 +76,20 @@
TK1di_P = Place m!: 0 # in situ; TK1 in the dimer form, phosphorylated
TK1tetra = Place m!: 0 # TK1 in the tetramer form (phosphorylation prevents 4merization)
# Assignment transition keeping TK1_di level based on total TK1 monomer
Transition name: :TK1_di_ϝ,
- assignment: true,
domain: TK1,
codomain: TK1di,
- action: lambda { |monomer| # solution of a quadratic equation for dimer / tetramer balance
+ assignment: lambda { |monomer| # solution of a quadratic equation for dimer / tetramer balance
TK1_4mer_Kd / 4 * ( ( 1 + 4 / TK1_4mer_Kd * monomer ) ** 0.5 - 1 )
}
# Assignment transition keeping TK1_tetra level based on total TK1 tetramer
Transition name: :TK1_tetra_ϝ,
- assignment: true,
domain: [ TK1, TK1di ],
codomain: TK1tetra,
- action: lambda { |monomer, dimer| # based on equation monomer = dimer * 2 + tetramer * 4
+ assignment: lambda { |monomer, dimer| # based on equation monomer = dimer * 2 + tetramer * 4
monomer / 4 - dimer / 2
}
# Dissociation constants [µM]