; 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/