A Short DNA Sequence
ATGCATCATGCGCCAT
A short DNA sequence algined to large genome
0 - gi|110640213|ref|NC_008253.1| 148810 ATGGCGCATGATGCAT IIIIIIIIIIIIIIII 0 10:A>G,13:C>G
A Set of polynomial dynamical systems
{
"description": "Polynomial model"",
"fieldCardinality": 2,
"name": "priorModel",
"type": "PolynomialDynamicalSystemSet",
"updateRules": [
{
"functions": [
{
"inputVariables": ["x1","x2"],
"polynomialFunction": "x1*x2"
}
],
"target": "x1"
},
{
"functions": [
{
"inputVariables": ["x1"],
"polynomialFunction": "x1+1"
},
{
"inputVariables": ["x1","x2"],
"polynomialFunction": "x1*x2"
}
],
"target": "x2"
},
{
"functions": [
{
"inputVariables": ["x1","x2","x3"],
"polynomialFunction": "x3^2+x1"
}
],
"target": "x3"
},
{
"functions": [
{
"inputVariables": ["x1","x3"],
"polynomialFunction": "x3^2+x1+x2"
}
],
"target": "x4"
}
]
}
a set of discrete dynamical systems
{
"type": "DiscreteDynamicalSystemSet",
"description": "a description",
"simulationName": "a name",
"updateRules": [
{
"target": "CAP",
"functions": [
{
"inputVariables": ["CAP"],
"transitionTable": [
[[0],0],
[[1],1]
]
}
]
},
{
"target": "mRNA",
"functions": [
{
"inputVariables": ["CAP","LacI","mRNA"],
"transitionTable": [
[[0,0,0],0],
[[0,0,1],1],
[[0,1,0],0],
[[0,1,1],0],
[[0,2,0],0],
[[0,2,1],0],
[[1,0,0],1],
[[1,0,1],0],
[[1,1,0],0],
[[1,1,1],0],
[[1,2,0],0],
[[1,2,1],0]
]
}
]
},
{
"target": "LacY",
"functions": [
{
"inputVariables": ["mRNA","LacY"],
"transitionTable": [
[[0,0],0],
[[0,1],1],
[[1,0],1],
[[1,1],1]
]
}
]
},
{
"target": "LacZ",
"functions": [
{
"inputVariables": ["mRNA","LacZ"],
"transitionTable": [
[[0,0],0],
[[0,1],1],
[[1,0],1],
[[1,1],1]
]
}
]
},
{
"target": "LacI",
"functions": [
{
"inputVariables": ["LacI"],
"transitionTable": [
[[0],0],
[[1],1],
[[2],2]
]
}
]
}
],
"variables": [
{
"id": "CAP",
"states": [0,1],
"speed": 1
},
{
"id": "mRNA",
"states": [0,1],
"speed": 1
},
{
"id": "LacY",
"states": [0,1],
"speed": 1
},
{
"id": "LacZ",
"states": [0,1],
"speed": 1
},
{
"id": "LacI",
"states": [0,1,2],
"speed": 1
}
]
}
a set of boolean dynamical systems
{
"type": "BooleanDynamicalSystemSet",
"description": "Sample Boolean Network",
"parameters": [
{
"id": "k1",
"states": [0,1]
},
{
"id": "k2",
"states": [0,1]
}
],
"updateRules": [
{
"target": "x1",
"functions": [
{
"inputVariables": ["k1","x3"],
"booleanFunction": "k1 & x3"
}
]
},
{
"target": "x2",
"functions": [
{
"inputVariables": ["x1" , "k2"],
"booleanFunction": "x1 | k2"
}
]
},
{
"target": "x3",
"functions": [
{
"inputVariables": ["x4","x2"],
"booleanFunction": "x2 & !x4"
}
]
},
{
"target": "x4",
"functions": [
{
"inputVariables": ["x2","k2"],
"booleanFunction": "x2 & k2"
}
]
}
],
"variables": [
{
"id": "x1",
"states": [0,1]
},
{
"id": "x2",
"states": [0,1]
},
{
"id": "x3",
"states": [0,1]
},
{
"id": "x4",
"states": [0,1]
}
]
}
A set of time series
{
"type": "timeSeriesSet",
"timeSeriesData": [
{
"index": [],
"matrix": [
[1,0,0,0],
[0,1,0,1],
[1,1,0,0]
],
"name": "wildtype experiment 1"
},
{
"index": [],
"matrix": [
[1,1,0,0],
[0,0,0,1],
[1,0,0,0]
],
"name": "wildtype experiment 2"
},
{
"index": [1],
"matrix": [
[0,0,0,0],
[0,0,0,1],
[0,1,0,0],
[0,0,0,1]
],
"name": "knockout experiment 1"
},
{
"index": [3],
"matrix": [
[0,1,0,0],
[0,1,0,1],
[0,1,0,1],
[0,0,0,0]
],
"name": "knockout experiment 2"
},
{
"index": [2],
"matrix": [
[1,0,0,0],
[0,0,0,1],
[1,0,0,1],
[0,0,0,0]
],
"name": "knockout experiment 3"
}
]
}
a directed graph representation
{
"description": "",
"fieldCardinality": 2,
"name": "priorReverseEngineeringNetwork",
"type": "directedGraph",
"edges": [
{
"sources": [
{ "score": 0.5, "source": "x1" },
{ "score": 1, "source": "x2" },
{ "score": 1, "source": "x3" },
{ "score": 1, "source": "x4" }
],
"target": "x1"
},
{
"sources": [
{ "score": 1, "source": "x2" },
{ "score": 1, "source": "x4" }
],
"target": "x2"
},
{
"sources": [
{ "score": 0.5, "source": "x1" },
{ "score": 0.5, "source": "x2" }
],
"target": "x3"
},
{
"sources": [
{ "score": 0.33, "source": "x2" },
{ "score": 0.66, "source": "x3" }
],
"target": "x4"
}
]
}
an annotated graph representation
{
"type": "AnnotatedGraph",
"description": "Sample Annotated Graph",
"node": [
{
"id" : "node0",
"label": " 0 0 0 0 0"
},
{
"id" : "node1",
"label": " 0 0 0 0 1"
},
{
"id" : "node2",
"label": " 0 0 0 0 2"
},
{
"id" : "node3",
"label": " 0 0 0 1 0"
},
{
"id" : "node4",
"label": " 0 0 0 1 1"
},
{
"id" : "node5",
"label": " 0 0 0 1 2"
},
{
"id" : "node6",
"label": " 0 0 1 0 0"
},
{
"id" : "node7",
"label": " 0 0 1 0 1"
},
{
"id" : "node8",
"label": " 0 0 1 0 2"
},
{
"id" : "node9",
"label": " 0 0 1 1 0"
},
{
"id" : "node10",
"label": " 0 0 1 1 1"
},
{
"id" : "node11",
"label": " 0 0 1 1 2"
},
{
"id" : "node12",
"label": " 0 1 0 0 0"
},
{
"id" : "node13",
"label": " 0 1 0 0 1"
},
{
"id" : "node14",
"label": " 0 1 0 0 2"
},
{
"id" : "node15",
"label": " 0 1 0 1 0"
},
{
"id" : "node16",
"label": " 0 1 0 1 1"
},
{
"id" : "node17",
"label": " 0 1 0 1 2"
},
{
"id" : "node18",
"label": " 0 1 1 0 0"
},
{
"id" : "node19",
"label": " 0 1 1 0 1"
},
{
"id" : "node20",
"label": " 0 1 1 0 2"
},
{
"id" : "node21",
"label": " 0 1 1 1 0"
},
{
"id" : "node22",
"label": " 0 1 1 1 1"
},
{
"id" : "node23",
"label": " 0 1 1 1 2"
},
{
"id" : "node24",
"label": " 1 0 0 0 0"
},
{
"id" : "node25",
"label": " 1 0 0 0 1"
},
{
"id" : "node26",
"label": " 1 0 0 0 2"
},
{
"id" : "node27",
"label": " 1 0 0 1 0"
},
{
"id" : "node28",
"label": " 1 0 0 1 1"
},
{
"id" : "node29",
"label": " 1 0 0 1 2"
},
{
"id" : "node30",
"label": " 1 0 1 0 0"
},
{
"id" : "node31",
"label": " 1 0 1 0 1"
},
{
"id" : "node32",
"label": " 1 0 1 0 2"
},
{
"id" : "node33",
"label": " 1 0 1 1 0"
},
{
"id" : "node34",
"label": " 1 0 1 1 1"
},
{
"id" : "node35",
"label": " 1 0 1 1 2"
},
{
"id" : "node36",
"label": " 1 1 0 0 0"
},
{
"id" : "node37",
"label": " 1 1 0 0 1"
},
{
"id" : "node38",
"label": " 1 1 0 0 2"
},
{
"id" : "node39",
"label": " 1 1 0 1 0"
},
{
"id" : "node40",
"label": " 1 1 0 1 1"
},
{
"id" : "node41",
"label": " 1 1 0 1 2"
},
{
"id" : "node42",
"label": " 1 1 1 0 0"
},
{
"id" : "node43",
"label": " 1 1 1 0 1"
},
{
"id" : "node44",
"label": " 1 1 1 0 2"
},
{
"id" : "node45",
"label": " 1 1 1 1 0"
},
{
"id" : "node46",
"label": " 1 1 1 1 1"
},
{
"id" : "node47",
"label": " 1 1 1 1 2"
}
],
"connection": [
["node0", "node0"],
["node1", "node1"],
["node2","node2"],
["node3","node3"],
["node4","node4"],
["node5","node5"],
["node6","node6"],
["node7","node7"],
["node8","node8"],
["node9","node9"],
["node10","node10"],
["node11","node11"],
["node12","node21"],
["node13","node10"],
["node14","node11"],
["node15","node21"],
["node16","node10"],
["node17","node11"],
["node18","node21"],
["node19","node10"],
["node20","node11"],
["node21","node21"],
["node22","node10"],
["node23","node11"],
["node24","node36"],
["node25","node25"],
["node26","node26"],
["node27","node39"],
["node28","node28"],
["node29","node29"],
["node30","node42"],
["node31","node31"],
["node32","node32"],
["node33","node45"],
["node34","node34"],
["node35","node35"],
["node36","node33"],
["node37","node34"],
["node38","node35"],
["node39","node33"],
["node40","node34"],
["node41","node35"],
["node42","node33"],
["node43","node34"],
["node44","node35"],
["node45","node33"],
["node46","node34"],
["node47","node35"]
]
}
steady states of boolean dynamical system set
{
"type": "SteadyStates",
"description": "steady states of boolean dynamical system set",
"steadystates": {
"idorder": ["x1","x2","x3","x4"],
"value": [
[0,0,0,0],
[1,1,1,0]
]
}
}
