Input/Output Types

algorun:DNASequence

Usage: A Short DNA Sequence

Example:

ATGCATCATGCGCCAT

algorun:AlignedDNASequence

Usage: A short DNA sequence algined to large genome

Example:

0   -       gi|110640213|ref|NC_008253.1|   148810  ATGGCGCATGATGCAT        IIIIIIIIIIIIIIII        0       10:A>G,13:C>G

superadam:PolynomialDynamicalSystemSet

Usage: A Set of polynomial dynamical systems

Example:

{
"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"
    }
  ]
  }

superadam:DiscreteDynamicalSystemSet

Usage: a set of discrete dynamical systems

Example:

{
    "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
        }
    ]
}

superadam:BooleanDynamicalSystemSet

Usage: a set of boolean dynamical systems

Example:

{
    "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]
        }
    ]
}

superadam:TimeSeriesSet

Usage: A set of time series

Example:

{
"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"
    }
  ]
}

superadam:DirectedGraph

Usage: a directed graph representation

Example:

{
"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"
    }
]
}

superadam:AnnotatedGraph

Usage: an annotated graph representation

Example:

{
    "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"]
   ]
   }

superadam:SteadyStates

Usage: steady states of boolean dynamical system set

Example:

{
"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]
                    ]
                }
    }