Spike config file mode // - line comment /* - block comment */ // Import - exactly one model import: { from: "path/to/file.andl" sbml: { net: "CPN" boundary: false reversible: false } as: "ModelName" // optional - If not present or empty try to get name from model checksum: a5s7w6e7w // optional – for checking version of the model !!! Not in use yet !!! } configuration: { // configuration of the model model: { // name: "confModel1"// name of configuration !!! Not in use yet !!! // set constants (for coloured models - before unfolding) constants: { all: { // name of a group C01: 2 // constantName:value // if constant does not exists then it’ll be created and can be used in configuration e.g. defining place markings M: "D/2 + 1" } } // set markings (for coloured models - before unfolding) places: { place1: 1 //placeName:value P: "1000`(M,M)" // example of use of newly created constant P_2_2: 500 } observers: { place: { OP01: { function: "P_1_1 + P_2_3" } // override (if observer is already defined in andl file then override its value) OP1: { "function": "(P_1_1 + P_2_3) / 2" } } transition: { OT01: { function: "t3_1_1_1_2 / 4" } } // defining observers which can observe mixed values mixed: { M01: { function: "t3_1_1_1_2 + P_1_1" // transition + place } M02: { function: "P2 + M" // place + constant } } } } // configuration of the simulation SIM01 simulation : { name: "SIM01" // Name of the simulation type: continuous // [continuous, stochastic, hybrid] solver: BDF // [BDF, classic, direct, delta-leaping, static, staticAcc] threads: 1 // 0 - try to get the number of concurrent threads supported by the hardware interval: 1:1:1000// start:step:end (startTimePoint:intervalSize:endTimePoint) // runs: 1000000 // Applicable only for stochastic simulation // configuration for continues simulation iniStep: 0.1 linSolver: CVDense //[CVDense, CVSpgmr, CVDiag, CVSpbcg, and CVSptfqmr] relTol: 1.0e-5 absTol: 1.0e-10 // Export results to the file export: { // Array of places to save, including coloured places like P in this example (if empty export all) places: ["P_1_1", "OP01", "Grid.*", "D", "P"] // Array of transitions to save, including coloured transitions (if empty export all) transitions: ["t3_1_1_1_2", "t3", "t3" ] observers: ["M01", "OT01"] // Array of observers to save (if empty export all) to: "sim01-file01.csv" } export: { places: ["P2", "P", "P_2_2"] places: ["P2", "P_1_1", "P"] transitions: ["t3"] observers: ["M01", "M02"] to: "sim01-file02 .csv" } export: { places: ["P_1_.*","P_2_.*","P_3_.*"] // Array of places to save (if empty export all) to: "sim01-file03.csv" } } // the next simulation will start when previous will end, in the future this behaviour will change // configuration of the simulation SIM02 simulation : { name: "SIM02" // Name of the simulation type: stochastic // [continuous, stochastic, hybrid] solver: direct // [BDF, classic, direct, delta-leaping, static, staticAcc] threads: 100 // 0 - try to get the number of concurrent threads supported by the hardware interval: 1:1:1000// start:step:end (startTimePoint:intervalSize:endTimePoint) runs: 1000000 // Applicable only for stochastic simulation // Export results to the file export: { // Array of places to save, including coloured places like P in this example (if empty export all) places: ["P_1_1", "OP01", "Grid.*", "D", "P"] // Array of transitions to save, including coloured transitions (if empty export all) transitions: ["t3_1_1_1_2", "t3", "t3" ] observers: ["M01", "OT01"] // Array of observers to save (if empty export all) to: "sim02-file01.csv" } export: { places: ["P2", "P", "P_2_2"] places: ["P2", "P_1_1", "P"] transitions: ["t3"] observers: ["M01", "M02"] to: "sim02-file02 .csv" } export: { places: ["P_1_.*","P_2_.*","P_3_.*"] // Array of places to save (if empty export all) to: "sim02-file03.csv" } } } MIME types defined: application/x-spike