simulation部分接口

[cairijun]

simulation部分需要进行编译。
编译依赖：boost（只需要boost::numeric::odeint）、Cython、支持C++11的C++编译器。
运行./setup.py build_ext -i即可编译。

进行模拟前需要先把设计方案发送到后端进行预处理，生成调控关系等信息，然后再进行模拟。

• POST /simulation/preprocess

  请求：

  [
      {
          "inputs": [
              {"id": 8, "receptor_id": 12, "promoter_id": 1}, 
              {"id": 9, "receptor_id": 13, "promoter_id": 17}
          ], 
          "logics": [16], 
          "outputs": [1]
      },
      {
          "inputs": [
              {"id": 3, "receptor_id": 4, "promoter_id": 9}, 
              {"id": 4, "receptor_id": 5, "promoter_id": 20}
          ], 
          "logics": [12], 
          "outputs": [2]
      }
  ]

  响应：

  {
    "output_RBS": {  /* 每个output对应的RBS，output包括中间产物，用户可以更换RBS */
      "BBa_C0079": "BBa_B0034", 
      "RFP": "BBa_B0034", 
      "T7ptag": "BBa_B0034", 
      "ZntR": "BBa_B0034", 
      "supD": "BBa_B0034"
    }, 
    "reactants": [  /* 参与反应的物质列表，请勿修改 */
      "RFP", "aTc", "BBa_C0079", "ZntR", "Arsenic ions", 
      "YFP", "Zinc ions", "PAI", "supD", "T7ptag"
    ], 
    "relationships": [  /* 调控关系，请勿修改 */
      {
        "K": 0.001, "from": "PAI", "gamma": 0.002, 
        "n": 1.0, "to": "supD", "type": "PROMOTE"
      }, 
      {
        "K": 0.0021, "from": "Zinc ions", "gamma": 0.122, 
        "n": 1.2, "to": "T7ptag", "type": "PROMOTE"
      }, 
      {
        "K": 1.0, "from_1": "supD", "from_2": "T7ptag", "gamma": 0.0, 
        "n": 1.0, "to": "RFP", "type": "BIPROMOTE"
      }, 
      {
        "K": 0.0056, "from": "aTc", "gamma": 0.07, 
        "n": 3.0, "to": "ZntR", "type": "PROMOTE"
      }, 
      {
        "K": 0.0056, "from": "BBa_C0079", "gamma": 0.07, 
        "n": 3.0, "to": "ZntR", "type": "REPRESS"
      }, 
      {
        "K": 6.8e-05, "from": "Arsenic ions", "gamma": 0.0023, 
        "n": 1.0, "to": "BBa_C0079", "type": "PROMOTE"
      }, 
      {
        "K": 6.8e-05, "from": "ZntR", "gamma": 0.0023, 
        "n": 1.0, "to": "BBa_C0079", "type": "REPRESS"
      }, 
      {
        "from": "BBa_C0079", "to": "YFP", "type": "SIMPLE"
      }
    ]
  }

• POST /simulation/simulate

  请求：

  {
    "output_RBS": {/* ... */},
    "reactants": [/* ... */],
    "relationships": [/* ... */],
    "x0": {  /* 部分反应物的初始浓度，其余为0 */
      "Arsenic ions": 0.003, "aTc": 0.001, "Zinc ions": 0.01, "PAI": 0.004
    },
    "t": 200  /* 反应时间 */
  }

  响应：

  {
    "t": [0.0, 0.0011698867286399487, 0.0023397734572798974, ..., 200.0],  /* 时间刻度 */
    "c": [
      [0.0, ..., 5.902561416597707],  /* 第一种反应物的浓度变化 */
      [0.0, ..., 4.096369890704216],  /* 第二种反应物的浓度变化 */
    ]
  }

更多例子请参考/tests/test_simulation.py中的单元测试。