; In this file are concatenated all the configuration files of StochSim simulation.
; This is made necessary by PLoS ONE constraints on supplementary materials.
; Copy the text of each section in a different INI file
; section ARRAY.INI
[General]
Arrays = Hexamer1,Hexamer2,Hexamer3,Hexamer4,Hexamer5,Hexamer6,Hexamer7,Hexamer8,Hexamer9,Hexamer10,Hexamer11,Hexamer12,Hexamer13,Hexamer14,Hexamer15,Hexamer16,Hexamer17,Hexamer18,Hexamer19,Hexamer20,Hexamer21,Hexamer22,Hexamer23,Hexamer24,Hexamer25,Hexamer26,Hexamer27,Hexamer28,Hexamer29,Hexamer30,Hexamer31,Hexamer32,Hexamer33,Hexamer34,Hexamer35,Hexamer36,Hexamer37,Hexamer38,Hexamer39,Hexamer40,Hexamer41,Hexamer42,Hexamer43,Hexamer44,Hexamer45,Hexamer46,Hexamer47,Hexamer48,Hexamer49,Hexamer50,Hexamer51,Hexamer52,Hexamer53,Hexamer54,Hexamer55,Hexamer56,Hexamer57,Hexamer58,Hexamer59,Hexamer60
DumpInterval = 0.001
NumSnapshotVariables = 1
[Hexamer1]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer2]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer3]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer4]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer5]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer6]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer7]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer8]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer9]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer10]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer11]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer12]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer13]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer14]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer15]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer16]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer17]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer18]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer19]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer20]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer21]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer22]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer23]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer24]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer25]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer26]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer27]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer28]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer29]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer30]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer31]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer32]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer33]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer34]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer35]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer36]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer37]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer38]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer39]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer40]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer41]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer42]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer43]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer44]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer45]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer46]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer47]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer48]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer49]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer50]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer51]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer52]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer53]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer54]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer55]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer56]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer57]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer58]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer59]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Hexamer60]
Description =
Complex = CaMKII
NeighbourSensitive = 1
Geometry = Line
XDimension = 6
YDimension = 1
CreateDumpFile = 1
XBoundaryCondition = 1
YBoundaryCondition = 1
EquilibrationInterval = 1e-3
[Snapshot Variable 1]
Name = openone
Array = Hexamer1
StoreInterval = 0.0001
AveragedOutput = 0
AverageInterval = 0.1
SampleInterval = 1e-5
States = 1????,
; section COMPLEX.INI
[General]
Symbols = CaMKII,calm,PP1
NumDisplayVariables = 1
; *********************************************
; Component information
; *********************************************
[Component CaMKII]
Name = CaMKII
[Component calm]
Name = calm
[Component PP1]
Name = PP1
; *********************************************
; Complex Type information
; *********************************************
[Complex Types]
NumRapidEqm = 0
NumberOfSets = 3
Set1 = CaMKII
Comp1 = CaMKII
Set2 = calm
Comp2 = calm
Set3 = PP1
Comp3 = PP1
; *********************************************
; Initial Levels information
; *********************************************
[Initial Levels]
CaMKII = 360
calm = 450
PP1 = 0
; *********************************************
; Special Complex Types information
; *********************************************
[Special Complex Types]
SpecialTypes = Multistate_Complex
Multistate_Complex = CaMKII
CaMKIIINIFile = MS_1.INI
; *********************************************
; Neighbour Sensitive Complex Types information
; *********************************************
[Neighbour Sensitive Complex Types]
NeighbourSensitiveComplexes = CaMKII
CaMKII_NS_INIFile = NS_1.INI
; *********************************************
; Information on the variables to display
; *********************************************
[Display Variable 1]
Name = calm
Types = calm
; section DYNAMIC.INI
[General]
NumberOfSets = 2
Set1 = 0
Set2 = 30
[Time 0]
actcalm = 4.2e6
[Time 30]
actcalm = 0
; section MESSAGE.INI
[Messages]
1 = "Insufficient memory has been allocated to store the Variable Values."
2 = "An error has occurred while opening the [?] output file."
3 = "An attempt has been made to create a new Complex. There are no free Complexes available."
4 = "The probability for a reaction is too small. The probability of a reaction has to be larger than the resolution of the random number generator. Use larger time increments to increase the probabilities. [?]"
5 = "The probability for a reaction is too large to maintain accuracy within the model. Use smaller time increments to decrease the probabilities. [?]"
6 = "An error has occurred while reading from [?] file."
7 = "An error has occurred while writing to [?] file."
8 = "Out of memory. There is insufficient free memory available for [?]."
9 = "An error has occurred while testing the random number generator. A negative number was generated: [?]."
10 = "An error has occurred while testing the random number generator. A number exceeded the maximum range: [?]."
11 = "An error has occurred while testing the random number generator. There have been more than [?] occurrences of the number [?]."
12 = "An error has occurred while testing the random number generator. There have been more than [?] occurrences of numbers between [?] and [?]."
13 = "An error has occurred while testing the random number generator. The running total has exceeded the maximum allowed: [?]."
14 = "There are too many substrates in a reaction. There can only be two substrates in each reaction."
15 = "There are too many products in a reaction."
16 = "An error has occurred while creating the following reaction: [?]"
17 = "Insufficient memory has been allocated to store reactions in each reaction set."
18 = "Insufficient memory has been allocated to store free Complexes."
19 = "Insufficient memory has been allocated to store Components."
20 = "An unrecognised Component has been found within the Complex Type [?]."
21 = "Insufficient memory has been allocated to store Components within the Complex Type [?]."
22 = "Insufficient memory has been allocated to store Complex Types."
23 = "The number of complexes exceeds the maximum number of complexes allowed."
24 = "An error has occurred while creating the reaction matrix."
25 = "An invalid reaction rate constant was specified for reaction number [?]."
26 = "An error has occurred while creating reaction number [?]."
27 = "An error has occurred while trying to identify Complex [?]."
28 = "The parameter [?] in section [?] could not be found in the INI file [?]."
29 = "An error has occurred while opening the input file [?]."
30 = "An error has occurred while initialising the system."
31 = "An error has occurred while running the system."
32 = "Press return to continue..."
33 = "An invalid number of display variables has been specified in the INI file."
34 = "An error has occurred while initialising the Display Variables for Complex Type: [?]."
35 = "Insufficient memory has been allocated to store Complex Types in the Display Variable [?]."
36 = "An error has occurred while opening the Random Number Generator Seeds input file."
37 = "An error has occurred while opening the Random Number Generator Seeds output file."
38 = "An invalid reaction volume has been specified in the INI file."
39 = "An invalid time increment has been specified in the INI file."
40 = "The interval between variable display times specified in the INI file is too large."
41 = "The interval between variable store times specified in the INI file is too large."
42 = "[?] time points will be saved to disk. Due to memory requirements, these will not be stored in memory during the simulation."
43 = "An invalid maximum number of complexes has been specified in the INI file."
44 = "Insufficient memory has been allocated to store Complexes."
45 = "An error has occurred while initialising the Components."
46 = "An error has occurred while initialising the Complex Types."
47 = "An error has occurred while initialising the Complex Levels."
48 = "An error has occurred while initialising the Reactions."
49 = "The Random Number Generator specified has not been recognised."
50 = "The component symbol [?] is contained within or contains the component symbol [?]. This could cause ambiguity when defining complex types."
51 = "An error has occurred while initialising the Fuzzy Complex Types."
52 = "Insufficient memory has been allocated to store Complex Types within Rapid Equilibrium number [?]."
53 = "Insufficient precision to handle the probabilities for a Fuzzy Complex Type."
54 = "The Complex Type [?] is being used in multiple rapid equilibria."
55 = "Variable values at time [?] ([?]% complete)"
56 = "[?]"
57 = "Insufficient memory has been allocated to store Storage Variables."
58 = "Sample Size : [?]"
59 = "Range : [?]"
60 = "Minimum Number : [?]"
61 = "Maximum Number : [?]"
62 = "Chi-Squared : [?]"
63 = "Average Number : [?]"
64 = "FP Gen Mean : [?]"
65 = "FP Gen Var : [?]"
66 = "Random number distribution:"
67 = " Number Frequency"
68 = " ------ ---------"
69 = " From To Frequency"
70 = " ---- -- ---------"
71 = "The time increment has been optimised. Every iteration represents [?] seconds."
72 = "Using [?] for random numbers."
73 = "1 pseudo-complex is being used for unimolecular reactions."
74 = "[?] pseudo-complexes are being used for unimolecular reactions."
75 = "Time to generate random numbers: [?] sec"
76 = "Time taken to complete calculations: [?] sec"
77 = "[?] iterations ([?] simulation seconds) will be performed."
78 = "The simulation will take approximately [?] seconds to complete."
79 = "An error has occurred while initialising the Special Complex Types."
80 = "The Special Complex Type [?] has not been recognised."
81 = "Insufficient memory has been allocated to store Multistate Complexes."
82 = "The Multistate Complex state flag [?] exceeds the maximum length allowed."
83 = "The Component symbol [?] exceeds the maximum length allowed."
84 = "An error has occurred while initialising Complex Type: [?]."
85 = "Insufficient memory has been allocated to store reactions in the Multistate Complexes."
86 = "The reaction identifier [?] has not been recognised.";
87 = "An error has occurred while initialising reaction [?] for a Multistate Complex."
88 = "Two effects of a reaction attempt to change the same state flag of the Multistate Complex."
89 = "An unrecognised symbol has been found in the reaction effect [?]."
90 = "The relative rate for a reaction is greater than one. All relative rates must be less than or equal to one."
91 = "The state [?] in Rapid Equilibrium [?] has not been recognised."
92 = "The probabilities for Rapid Equilibrium [?] of a Multistate Complex Type are not valid."
93 = "An attempt has been made to redefine Rapid Equilibrium [?] of a Multistate Complex Type."
94 = "There are insufficient free Multistate Complexes to create a new Multistate Complex with a particular state."
95 = "There are free Multistate Complexes whose initial states have not been set."
96 = "An error has occurred while initialising the Storage Variables for Complex Type: [?]."
97 = "An error has occurred while initialising the Storage Variables."
98 = "An error has occurred while initialising the Display Variables."
99 = "Insufficient memory has been allocated to store Display Variables."
100 = "Insufficient memory has been allocated to store states in the Display Variable [?]."
101 = "An unrecognised binary digit was found in the binary string [?]."
102 = "The display interval specified in the INI file is too small."
103 = "The store interval specified in the INI file is too small."
104 = "The number of iterations specified in the INI file is too small."
105 = "An unrecognised character has been found within the wildcard binary string [?]."
106 = "An attempt was made to redefine the probability for the state [?]."
107 = "The wildcard binary string [?] is invalid."
108 = "An attempt was made to redefine the concentration for the state [?]."
109 = "An error has occurred while initialising the Display Variables for Complex Type: [?]."
110 = "An attempt was made to redefine the rapid equilibrium probability for the state [?]."
111 = "Insufficient memory has been allocated to store events."
112 = "An error has occurred while initialising the Event Manager."
113 = "An error has occurred while initialising the reaction rates at different times for reaction number [?]."
114 = "The value at time [?] is invalid."
115 = "An error has occurred while initialising the reaction rates at different times for the state [?]."
116 = "There are too many events."
117 = "The number of values specified at time [?] is incorrect."
118 = "An error has occurred while initialising the rapid equilibrium probabilities at different times for Rapid Equilibrium [?]."
119 = "Shutting down reaction system..."
120 = "Shut down complete"
121 = "The value [?] has been changed in iteration [?]."
122 = "A default [?] of [?] has been assigned to [?] states of multistate complex type [?]."
123 = "A default rate of [?] has been assigned to [?] states of multistate complex type [?] for [?]."
124 = "An error has occurred while initialising Complex Arrays."
125 = "The number of requested complexes for array [?] exceeds the number of available complexes."
126 = "The insertion of a complex into address ([?],[?]) of Complex Array [?] has failed."
127 = "An error has occurred while initialising the Storage Variables for Complex Array: [?]."
128 = "Insufficient memory has been allocated to store Array Snapshot Variables."
129 = "Illegal insertion of Complex Type '[?]' was attempted in Array '[?]'."
130 = "An error has occurred while initialising the Array Storage Variables."
131 = "An error has occurred while initialising the Array: [?]."
132 = "A NULL complex has been detected at coordinate ([?],[?]) of the Array: [?]."
133 = "An error occurred while filling the Complex Array [?] with complexes (Address.nX: [?], Address.nY: [?])."
134 = "An error has occurred while trying to save specific coordinate values for Array Output Variable: [?]."
135 = "An error has occurred while trying to parse the value of the parameter '[?]' in section '[?]' of file '[?]'."
136 = "The probabilities for Rapid Equilibrium [?] of a Neighbour-Sensitive Complex Type are not valid."
137 = "Not all of the probabilities for Rapid Equilibrium [?] of a Neighbour-Sensitive Complex Type could be found in the INI file."
138 = "An invalid value has been assigned for the parameter '[?]' in Array '[?]'."
139 = "The value '[?]' is invalid as a Coupled_States specifier (Must include wildcard characters)."
140 = "An error has occurred while initialising Neighbour-Sensitive Complexes."
141 = "The value [?] is invalid as an interval for averaged Snapshot Variable [?] (must be in the range 0 < AverageInterval <= StoreInterval)."
142 = "Warning: Averaging buffer overflow has occurred for output variable [?]. The value of this variable is unreliable at best!!"
143 = "Output of complex type levels will be averaged."
144 = "The sample interval specified in the INI file is too large."
145 = "The store interval specified in the INI file is too small."
146 = "The Neighbour ID [?] specified for the neighbour-sensitive reaction [?] is invalid for the current array geometry."
147 = "An invalid Reaction ID [?] has been specified in the file [?].\n(Note: The Reaction IDs in a Neighbour-Sensitive Complex INI file must be compatible with those specified in the associated Neighbour-Sensitive Complex INI file."
148 = "A default rate of [?] has been assigned to [?] states of neighbour-sensitive complex type [?] for [?]."
149 = "An error has occurred while initialising reaction [?] for a Neighbour-Sensitive Complex."
150 = "StochSim completed the simulation successfully."
151 = "An error has occurred while initialising spatial extensions."
152 = "An invalid value [?] has been assigned for the parameter [?] in section [?] of the system configuration file."
153 = "An invalid value [?] has been assigned for the parameter [?] in section [?] of file [?]."
154 = "An error has occurred while initialising the output manager."
155 = "Using spatial extensions."
156 = "Created [?] x [?] [?] Complex Array '[?]' with complex type [?] and boundary condition [?]."
157 = Variable values will be stored every [?] iterations ([?] simulation seconds)."
158 = "An error has occurred while initialising the Snapshot Variables for Complex Array: [?]."
159 = "An error has occurred while initialising the Output Managers."
160 = "An error has occurred while initialising the Output Manager for Complex Arrays."
161 = "An error has occurred while initialising Snapshot Variable [?]."
162 = "Insufficient memory has been allocated to store Array Dump Variables."
163 = "Insufficient memory has been allocated to store states in the Snapshot Variable [?]."
164 = "Using the default store interval ([?] s) for Snapshot Variable [?]."
165 = "Output averaging will not be performed for Snapshot Variable [?], because the specified averaging interval is 0."
166 = "The value [?] is invalid as a sampling interval for averaged Snapshot Variable [?] (must be in the range 0 < SampleInterval <= AverageInterval).".
167 = "An error has occurred while initialising Array Dump Variable [?]."
168 = "An error has occurred while initialising the application."
169 = "An error has occurred while trying to create Complex Array '[?]'."
170 = "The number of neighbours specified ([?]) for the neighbour-sensitive Complex Type [?] does not match the geometry '[?]' of Complex Array [?]."
171 = "YDimension = [?] for the Complex Array [?] is not compatible with a [?] geometry (must be an even number)."
172 = "An error has occured while trying to set neighbour [?] of complex ([?], [?])."
173 = "An error has occurred while initialising reaction [?] for a Neighbour-sensitive Complex."
174 = "Reading initial state of Complex Array [?] from complex array dump file [?] (using the last frame at Time [?])..."
175 = "An error has occured while trying to retrieve the state of the complex at the array coordinate ([?],[?]) in the dump file [?]."
176 = "The state of the Complex Array [?] at the specified time ([?]) could not be found in the dump file [?]."
177 = "Reading initial state of Complex Array [?] from complex array dump file [?] at time [?]..."
178 = "Optimising the reaction matrix..."
179 = "The geometry of the Complex Array [?] does not match the geometry of its initial state specification file [?]."
180 = "The dimensions of the Complex Array [?] do not match the dimensions of its initial state specification file [?]."
181 = "There was an error while parsing the initial state specification file [?] for the Complex Array [?]."
182 = "The interval between Complex Type level dump times specified in the INI file is too large."
183 = "Complex Type levels will be dumped every [?] iterations ([?] simulation seconds)."
184 = "Complex Type levels will be dumped only at the beginning and end of the simulation."
185 = "Not enough instances of Complex Type [?] in state '[?]' are present to initialise the Complex Array '[?]' according to the file [?] (only [?] instances are present)."
186 = "The Complex Type [?] appearing in the file [?] does not exist in this simulation."
187 = "The concentration of the Complex Type [?] was not found in the file [?] at time [?]."
188 = "Reading Complex Type levels from the file [?]..."
189 = "Using system snapshot from time [?]...."
190 = "The number of state flags for the complex type [?], as specified in column [?] of file [?] does not match."
191 = "Reading complex type levels from the dump file [?]. (The [[?]] section of [?] will be ignored.)"
192 = "Reading the initial state levels for the multistate complex type [?] from the dump file [?]. (The [[?]] section of [?] will be ignored.)"
193 = "Not enough instances of Complex Type [?] in state '[?]' are present to initialise the Complex Array '[?]' (only [?] instances are present)."
194 = "Not enough instances of Complex Type [?] are remaining to initialise the Complex Array '[?]' (only [?] instances remaining to fill [?] coordinates)."
195 = "The INI file [?] requests [?] Array Snapshot Variables, but only [?] were created. Ensure that all Snapshot Variables are correctly defined and rerun StochSim."
; section MS_1.INI
; This file contains details for the multistate complex type CaMKII
[General]
Description =
StateFlags = open,P286,P306,calm,ha
NumRapidEqm = 2
Reactions = 1F,2F,3F,4F,5F,5R,6F,6R
NumDisplayVariables = 6
[Initial States]
00000 = 360
Wildcards =
[Rapid Equilibrium 1]
Flag = open
?0??0 = 0.002
?0??1 = 1
?1??0 = 1
?1??1 = 1
Wildcards =?0??0,?0??1,?1??0,?1??1
[Rapid Equilibrium 2]
Flag = ha
1??1? = 0.99999
Wildcards = 1??1?
[Reaction 1F]
Effect =
10??? = 1
Wildcards = 10???
[Reaction 2F]
Effect = -P286
?1??? = 1
Wildcards = ?1???
[Reaction 3F]
Effect = +P306
1?00? = 1
Wildcards = 1?00?
[Reaction 4F]
Effect = -P306
??1?? = 1
Wildcards = ??1??
[Reaction 5F]
Effect = +calm
??000 = 1
Wildcards = ??000
[Reaction 5R]
Effect = -calm
???10 = 1
Wildcards = ???10
[Reaction 6F]
Effect = +calm,+ha
1?000 = 1
Wildcards = 1?000
[Reaction 6R]
Effect = -calm,-ha
???11 = 1
Wildcards = ???11
[Display Variable 1]
Name = open
States = 1????
[Display Variable 2]
Name = P286
States = ?1???
[Display Variable 3]
Name = P306
States = ??1??
[Display Variable 4]
Name = calm_bound_high_affinity
States = ????1
[Display Variable 5]
Name = calm_bound_low_affinity
States = ???10
[Display Variable 6]
Name = calm_bound_total
States = ???1?
; section NS_1.INI
[General]
Description =
NumNeighbours = 2
NumRapidEqm = 0
Reactions = 1F
[Reaction 1F]
1???? = 1
EffectOnNeighbour = +P286
ReactNeighbourID = 1
Wildcards = 1????;
; section REACTION.INI
[General]
NumberOfReactions = 6
[Reaction 1]
Description = CaMKII is phosphorylated at residue 286
Substrates = CaMKII
Products = CaMKII
kf = 30
kr = 0
[Reaction 2]
Description = CaMKII is dephosphorylated at residue 286
Substrates = CaMKII,PP1
Products = CaMKII,PP1
kf = 1.6e-7
kr = 0
[Reaction 3]
Description = CaMKII is phosphorylated at residue 306
Substrates = CaMKII
Products = CaMKII
kf = 0.55
kr = 0
[Reaction 4]
Description = CaMKII is dephosphorylated at residue 306
Substrates = CaMKII,PP1
Products = CaMKII,PP1
kf = 1.6e-7
kr = 0
[Reaction 5]
Description = CaMKII binds to calmodulin (low-affinity site)
Substrates = CaMKII,calm
Products = CaMKII
kf = 4.2e6@actcalm
kr = 24.8
[Reaction 6]
Description = CaMKII binds to calmodulin (high-affinity site)
Substrates = CaMKII,calm
Products = CaMKII
kf = 4.2e6@actcalm
kr = 2.5e-4
; section STCHSTC.INI
;; CaMKII hexamer - try to reproduce trapping experiment in Meyer1992 - wildtype
;; Same as trapping_10, but with better parameter values
[Simulation Parameters]
DisplayInterval = 0.001
StoreInterval = 0.001
TimeIncrement = 1e-8
SimulationDuration = 300
ReactionVolume = 5e-14
MaximumNumberComplexes = 5000
[Options]
AbortOnResolutionErr = 1
DisplayAllLevels = 0
OptimiseTimeIncrement = 1
RandomNumberGenerator = 3
TimeUnits = 1
CreateDumpFile = 0
UseSpatialExtensions = 1
[File Names]
ComplexINIFile = COMPLEX.INI
DumpOut = ../Output/DUMP.OUT
DynamicValues = DYNAMIC.INI
LogFile = ../Output/LOG.OUT
MessageINIFile = MESSAGE.INI
ReactionMatrixOut = ../Output/R_MATRIX.OUT
ReactionINIFile = REACTION.INI
SeedsIn =
SeedsOut = ../Output/SEED.OUT
VariablesOut = ../Output/VAR.OUT
ArrayINIFile = ARRAY.INI
ArrayOutPrefix = ../Output/