{
  "emt": {
    "file": "[id-179]__[var-46]__[in-10]__[MICROENVIRONMENT-CONTROL].aeon",
    "comment": "From Fontanals control paper",
    "vars": 56,
    "inputs": ["v_ROS", "v_IL6", "v_DELTA", "v_TGFB", "v_FAT4_L", "v_EGF", "v_ECM", "v_HGF", "v_RPTL", "v_WNT"],
    "uncontrollable": ["v_AJ_b1","v_AJ_b2","v_FA_b1","v_FA_b2","v_FA_b3"],
    "targets": {
      "epithelial": {
        "v_AJ_b1": true,
        "v_AJ_b2": true,
        "v_FA_b1": false,
        "v_FA_b2": false,
        "v_FA_b3": false
      },
      "hybrid_1": {
        "v_AJ_b1": true,
        "v_AJ_b2": true,
        "v_FA_b1": true,
        "v_FA_b2": false,
        "v_FA_b3": false
      },
      "hybrid_2": {
        "v_AJ_b1": true,
        "v_AJ_b2": false,
        "v_FA_b1": true,
        "v_FA_b2": true,
        "v_FA_b3": false
      },
      "hybrid_3": {
        "v_AJ_b1": true,
        "v_AJ_b2": true,
        "v_FA_b1": true,
        "v_FA_b2": true,
        "v_FA_b3": true
      },
      "mensenchymal_1": {
        "v_AJ_b1": false,
        "v_AJ_b2": false,
        "v_FA_b1": true,
        "v_FA_b2": false,
        "v_FA_b3": false
      },
      "mensenchymal_2": {
        "v_AJ_b1": false,
        "v_AJ_b2": false,
        "v_FA_b1": true,
        "v_FA_b2": true,
        "v_FA_b3": false
      },
      "mensenchymal_3": {
        "v_AJ_b1": false,
        "v_AJ_b2": false,
        "v_FA_b1": true,
        "v_FA_b2": true,
        "v_FA_b3": true
      },
      "undefined": {
        "v_AJ_b1": false,
        "v_AJ_b2": false,
        "v_FA_b1": false,
        "v_FA_b2": false,
        "v_FA_b3": false
      }
    }
  },
  "cardiac": {
    "file": "[id-010]__[var-13]__[in-2]__[CARDIAC-DEVELOPMENT].aeon",
    "vars": 15,
    "comment": "Former benchmarks",
    "inputs": ["v_exogen_CanWnt_I", "v_exogen_BMP2_I"],
    "uncontrollable": ["v_Tbx1", "v_Tbx5"],
    "targets": {
      "FHF": {
        "v_Tbx1": false,
        "v_Tbx5": true
      },
      "SHF": {
        "v_Tbx1": true,
        "v_Tbx5": false
      },
      "None": {
        "v_Tbx1": false,
        "v_Tbx5": false
      }
    }
  },
  "reduced_mapk": {
    "file": "[id-089]__[var-13]__[in-4]__[MAPK-REDUCED-1].aeon",
    "comment": "Experimental based on former benchmarks",
    "vars": 18,
    "inputs": ["v_DNA_damage", "v_EGFR_stimulus", "v_FGFR3_stimulus", "v_TGFBR_stimulus"],
    "uncontrollable": ["v_Apoptosis", "v_Proliferation", "v_Growth_Arrest"],
    "targets": {
      "apoptosis": {
        "v_Apoptosis": true,
        "v_Growth_Arrest": true,
        "v_Proliferation": false
      },
      "proliferation": {
        "v_Apoptosis": false,
        "v_Growth_Arrest": false,
        "v_Proliferation": true
      },
      "no_decision": {
        "v_Apoptosis": false,
        "v_Growth_Arrest": false,
        "v_Proliferation": false
      },
      "growth_arrest": {
        "v_Apoptosis": false,
        "v_Growth_Arrest": true,
        "v_Proliferation": false
      }
    }
  },
  "full_mapk": {
    "file": "[id-070]__[var-49]__[in-4]__[MAPK-CANCER-CELL-FATE].aeon",
    "comment": "Former benchmarks",
    "vars": 53,
    "inputs": ["v_DNA_damage", "v_EGFR_stimulus", "v_FGFR3_stimulus", "v_TGFBR_stimulus"],
    "uncontrollable": ["v_Apoptosis", "v_Proliferation", "v_Growth_Arrest"],
    "targets": {
      "apoptosis": {
        "v_Apoptosis": true,
        "v_Growth_Arrest": true,
        "v_Proliferation": false
      },
      "proliferation": {
        "v_Apoptosis": false,
        "v_Growth_Arrest": false,
        "v_Proliferation": true
      },
      "no_decision": {
        "v_Apoptosis": false,
        "v_Growth_Arrest": false,
        "v_Proliferation": false
      },
      "growth_arrest": {
        "v_Apoptosis": false,
        "v_Growth_Arrest": true,
        "v_Proliferation": false
      }
    }
  },

  "full_mapk_uncertain_DUSP1": {
    "file": "[id-070]__[var-49]__[in-4]__[MAPK-CANCER-CELL-FATE]_uncertain_DUSP1_reg.aeon",
    "comment": "Former benchmarks",
    "vars": 56,
    "inputs": [],
    "uncontrollable": ["v_Apoptosis", "v_Proliferation", "v_Growth_Arrest", "v_p38", "v_JNK"],
    "targets": {
      "apoptosis": {
        "v_Apoptosis": true,
        "v_Growth_Arrest": true,
        "v_Proliferation": false
      },
      "proliferation": {
        "v_Apoptosis": false,
        "v_Growth_Arrest": false,
        "v_Proliferation": true
      },
      "no_decision": {
        "v_Apoptosis": false,
        "v_Growth_Arrest": false,
        "v_Proliferation": false
      },
      "growth_arrest": {
        "v_Apoptosis": false,
        "v_Growth_Arrest": true,
        "v_Proliferation": false
      }
    }
  },
  "full_mapk_uncertain_FRS2": {
    "file": "[id-070]__[var-49]__[in-4]__[MAPK-CANCER-CELL-FATE]_uncertain_FRS2.aeon",
    "comment": "Former benchmarks",
    "vars": 56,
    "inputs": [],
    "uncontrollable": ["v_Apoptosis", "v_Proliferation", "v_Growth_Arrest", "v_FRS2"],
    "targets": {
      "apoptosis": {
        "v_Apoptosis": true,
        "v_Growth_Arrest": true,
        "v_Proliferation": false
      },
      "proliferation": {
        "v_Apoptosis": false,
        "v_Growth_Arrest": false,
        "v_Proliferation": true
      },
      "no_decision": {
        "v_Apoptosis": false,
        "v_Growth_Arrest": false,
        "v_Proliferation": false
      },
      "growth_arrest": {
        "v_Apoptosis": false,
        "v_Growth_Arrest": true,
        "v_Proliferation": false
      }
    }
  },
  "full_mapk_uncertain_MEK1_2": {
    "file": "[id-070]__[var-49]__[in-4]__[MAPK-CANCER-CELL-FATE]_uncertain_MEK1_2.aeon",
    "comment": "Former benchmarks",
    "vars": 56,
    "inputs": [],
    "uncontrollable": ["v_Apoptosis", "v_Proliferation", "v_Growth_Arrest", "MEK1_2"],
    "targets": {
      "apoptosis": {
        "v_Apoptosis": true,
        "v_Growth_Arrest": true,
        "v_Proliferation": false
      },
      "proliferation": {
        "v_Apoptosis": false,
        "v_Growth_Arrest": false,
        "v_Proliferation": true
      },
      "no_decision": {
        "v_Apoptosis": false,
        "v_Growth_Arrest": false,
        "v_Proliferation": false
      },
      "growth_arrest": {
        "v_Apoptosis": false,
        "v_Growth_Arrest": true,
        "v_Proliferation": false
      }
    }
  },
  "t_lgl": {
    "file": "[id-014]__[var-54]__[in-7]__[T-LGL-SURVIVAL-NETWORK-2008].aeon",
    "comment": "From Fontanals control paper",
    "vars": 61,
    "inputs": ["v_Stimuli", "v_Stimuli2", "v_CD45", "v_IL15", "v_IFNG", "v_PDGF", "v_TAX"],
    "uncontrollable": ["v_Apoptosis", "v_Proliferation", "v_Cytoskeleton_signaling"],
    "targets": {
      "apoptosis": {
        "v_Apoptosis": true,
        "v_Proliferation": false
      },
      "proliferation": {
        "v_Apoptosis": false,
        "v_Proliferation": true
      }
    }
  },
  "cell_fate": {
    "file": "[id-150]__[var-31]__[in-2]__[CELL-FATE-DECISION-MULTISCALE].aeon",
    "comment": "From Fontanals control paper",
    "inputs": ["v_FASL", "v_FADD"],
    "uncontrollable": ["v_Apoptosis", "v_Survival", "v_NonACD", "v_DEATH", "v_DIVISION"],
    "vars": 33,
    "targets": {
      "naive": {
        "v_NonACD": false,
        "v_Apoptosis": false,
        "v_Survival": false
      },
      "apoptosis": {
        "v_NonACD": false,
        "v_Apoptosis": true,
        "v_Survival": false
      },
      "survival": {
        "v_NonACD": false,
        "v_Apoptosis": false,
        "v_Survival": true
      },
      "necrosis": {
        "v_NonACD": true,
        "v_Apoptosis": false,
        "v_Survival": false
      }
    }
  },
  "erbb": {
    "file": "[id-096]__[var-19]__[in-1]__[ERBB-REGULATED-G1-S-TRANSITION].aeon",
    "comment": "Former benchmark",
    "vars": 20,
    "inputs": ["v_EGF"],
    "uncontrollable": ["v_pRB1"],
    "targets": {
      "phosporilation": {
        "v_pRB1": true
      },
      "non_phosporilation": {
        "v_pRB1": false
      }
    }
  },
  "tumour": {
    "file": "[id-065]__[var-30]__[in-2]__[TUMOUR-CELL-INVASION-AND-MIGRATION].aeon",
    "comment": "Former benchmark",
    "uncontrollable":["v_Apoptosis", "v_CellCycleArrest", "v_Invasion", "v_Migration", "v_EMT", "v_Metastasis"],
    "inputs": ["v_DNAdamage", "v_ECM"],
    "vars": 32,
    "targets": {
      "hybrid": {
        "v_Apoptosis": false,
        "v_CellCycleArrest": false,
        "v_Invasion": false,
        "v_Migration": false,
        "v_EMT": false,
        "v_Metastasis": false
      },
      "apoptosis": {
        "v_Apoptosis": true,
        "v_CellCycleArrest": true,
        "v_Invasion": false,
        "v_Migration": false,
        "v_EMT": false,
        "v_Metastasis": false
      },
      "emt": {
        "v_Apoptosis": false,
        "v_CellCycleArrest": true,
        "v_Invasion": false,
        "v_Migration": false,
        "v_EMT": true,
        "v_Metastasis": false
      },
      "metastasis": {
        "v_Apoptosis": false,
        "v_CellCycleArrest": true,
        "v_Invasion": true,
        "v_Migration": true,
        "v_EMT": true,
        "v_Metastasis": true
      }
    }
  }
}