Chen2004 - Cell Cycle Regulation Lab

{
  "io": {
    "inputs": [
      {
        "name": "cdc15i",
        "label": "CDC15i",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.cdc15i",
        "description": "Controls CDC15i in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.cdc15i`."
      },
      {
        "name": "model_state_ie",
        "label": "Model state IE",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.model_state_ie",
        "description": "Controls Model state IE in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.model_state_ie`."
      },
      {
        "name": "model_state_pe",
        "label": "Model state PE",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.model_state_pe",
        "description": "Controls Model state PE in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.model_state_pe`."
      },
      {
        "name": "phosphorylated_tem1gd",
        "label": "Phosphorylated TEM1GD",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_tem1gd",
        "description": "Controls Phosphorylated TEM1GD in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_tem1gd`."
      }
    ],
    "outputs": [
      {
        "name": "bub2",
        "label": "Bub2",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.bub2",
        "description": "Tracks Bub2 in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.bub2`."
      },
      {
        "name": "budding_index",
        "label": "Budding index",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.budding_index",
        "description": "Tracks Budding index in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.budding_index`."
      },
      {
        "name": "model_state_c2_c2",
        "label": "Model state C2 (C2)",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.model_state_c2_c2",
        "description": "Tracks Model state C2 (C2) in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.model_state_c2_c2`."
      },
      {
        "name": "phosphorylated_model_state_c2",
        "label": "Phosphorylated Model state C2",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_model_state_c2",
        "description": "Tracks Phosphorylated Model state C2 in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_model_state_c2`."
      },
      {
        "name": "model_state_c5_c5",
        "label": "Model state C5 (C5)",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.model_state_c5_c5",
        "description": "Tracks Model state C5 (C5) in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.model_state_c5_c5`."
      },
      {
        "name": "phosphorylated_model_state_c5",
        "label": "Phosphorylated Model state C5",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_model_state_c5",
        "description": "Tracks Phosphorylated Model state C5 in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_model_state_c5`."
      },
      {
        "name": "cdc14_phosphatase",
        "label": "Cdc14 phosphatase",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.cdc14_phosphatase",
        "description": "Tracks Cdc14 phosphatase in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.cdc14_phosphatase`."
      },
      {
        "name": "cdc15_mitotic_exit_kinase",
        "label": "Cdc15 mitotic exit kinase",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.cdc15_mitotic_exit_kinase",
        "description": "Tracks Cdc15 mitotic exit kinase in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.cdc15_mitotic_exit_kinase`."
      },
      {
        "name": "cdc20",
        "label": "Cdc20",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.cdc20",
        "description": "Tracks Cdc20 in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.cdc20`."
      },
      {
        "name": "inactive_cdc20",
        "label": "Inactive Cdc20",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.inactive_cdc20",
        "description": "Tracks Inactive Cdc20 in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.inactive_cdc20`."
      },
      {
        "name": "cdc6_replication_licensing_factor",
        "label": "Cdc6 replication licensing factor",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.cdc6_replication_licensing_factor",
        "description": "Tracks Cdc6 replication licensing factor in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.cdc6_replication_licensing_factor`."
      },
      {
        "name": "phosphorylated_cdc6",
        "label": "Phosphorylated CDC6",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_cdc6",
        "description": "Tracks Phosphorylated CDC6 in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_cdc6`."
      },
      {
        "name": "cdh1_apc_c_activator",
        "label": "Cdh1 APC/C activator",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.cdh1_apc_c_activator",
        "description": "Tracks Cdh1 APC/C activator in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.cdh1_apc_c_activator`."
      },
      {
        "name": "inactive_cdh1",
        "label": "Inactive Cdh1",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.inactive_cdh1",
        "description": "Tracks Inactive Cdh1 in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.inactive_cdh1`."
      },
      {
        "name": "clb2_mitotic_cyclin",
        "label": "Clb2 mitotic cyclin",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.clb2_mitotic_cyclin",
        "description": "Tracks Clb2 mitotic cyclin in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.clb2_mitotic_cyclin`."
      },
      {
        "name": "clb5_s_phase_cyclin",
        "label": "Clb5 S-phase cyclin",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.clb5_s_phase_cyclin",
        "description": "Tracks Clb5 S-phase cyclin in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.clb5_s_phase_cyclin`."
      },
      {
        "name": "cln2_g1_cyclin",
        "label": "Cln2 G1 cyclin",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.cln2_g1_cyclin",
        "description": "Tracks Cln2 G1 cyclin in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.cln2_g1_cyclin`."
      },
      {
        "name": "esp1_separase",
        "label": "Esp1 separase",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.esp1_separase",
        "description": "Tracks Esp1 separase in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.esp1_separase`."
      },
      {
        "name": "model_state_f2",
        "label": "Model state F2",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.model_state_f2",
        "description": "Tracks Model state F2 in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.model_state_f2`."
      },
      {
        "name": "phosphorylated_f2",
        "label": "Phosphorylated F2",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_f2",
        "description": "Tracks Phosphorylated F2 in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_f2`."
      },
      {
        "name": "model_state_f5",
        "label": "Model state F5",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.model_state_f5",
        "description": "Tracks Model state F5 in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.model_state_f5`."
      },
      {
        "name": "phosphorylated_f5",
        "label": "Phosphorylated F5",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_f5",
        "description": "Tracks Phosphorylated F5 in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_f5`."
      },
      {
        "name": "phosphorylated_ie",
        "label": "Phosphorylated IE",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_ie",
        "description": "Tracks Phosphorylated IE in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_ie`."
      },
      {
        "name": "lte1_mitotic_exit_regulator",
        "label": "Lte1 mitotic exit regulator",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.lte1_mitotic_exit_regulator",
        "description": "Tracks Lte1 mitotic exit regulator in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.lte1_mitotic_exit_regulator`."
      },
      {
        "name": "mad2_spindle_checkpoint_protein",
        "label": "Mad2 spindle checkpoint protein",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.mad2_spindle_checkpoint_protein",
        "description": "Tracks Mad2 spindle checkpoint protein in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.mad2_spindle_checkpoint_protein`."
      },
      {
        "name": "cell_mass",
        "label": "Cell mass",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.cell_mass",
        "description": "Tracks Cell mass in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.cell_mass`."
      },
      {
        "name": "net1_nucleolar_cdc14_anchor",
        "label": "Net1 nucleolar Cdc14 anchor",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.net1_nucleolar_cdc14_anchor",
        "description": "Tracks Net1 nucleolar Cdc14 anchor in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.net1_nucleolar_cdc14_anchor`."
      },
      {
        "name": "phosphorylated_net1",
        "label": "Phosphorylated NET1",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_net1",
        "description": "Tracks Phosphorylated NET1 in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_net1`."
      },
      {
        "name": "replication_origin_state",
        "label": "Replication origin state",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.replication_origin_state",
        "description": "Tracks Replication origin state in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.replication_origin_state`."
      },
      {
        "name": "pds1_securin",
        "label": "Pds1 securin",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.pds1_securin",
        "description": "Tracks Pds1 securin in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.pds1_securin`."
      },
      {
        "name": "ppx_phosphatase",
        "label": "PPX phosphatase",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.ppx_phosphatase",
        "description": "Tracks PPX phosphatase in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.ppx_phosphatase`."
      },
      {
        "name": "rent_cdc14_sequestration_complex",
        "label": "RENT Cdc14 sequestration complex",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.rent_cdc14_sequestration_complex",
        "description": "Tracks RENT Cdc14 sequestration complex in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.rent_cdc14_sequestration_complex`."
      },
      {
        "name": "phosphorylated_rent",
        "label": "Phosphorylated RENT",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_rent",
        "description": "Tracks Phosphorylated RENT in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_rent`."
      },
      {
        "name": "sic1",
        "label": "Sic1",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.sic1",
        "description": "Tracks Sic1 in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.sic1`."
      },
      {
        "name": "phosphorylated_sic1",
        "label": "Phosphorylated Sic1",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_sic1",
        "description": "Tracks Phosphorylated Sic1 in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_sic1`."
      },
      {
        "name": "spindle_state",
        "label": "Spindle state",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.spindle_state",
        "description": "Tracks Spindle state in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.spindle_state`."
      },
      {
        "name": "swi5_transcription_factor",
        "label": "Swi5 transcription factor",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.swi5_transcription_factor",
        "description": "Tracks Swi5 transcription factor in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.swi5_transcription_factor`."
      },
      {
        "name": "phosphorylated_swi5",
        "label": "Phosphorylated SWI5",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_swi5",
        "description": "Tracks Phosphorylated SWI5 in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_swi5`."
      },
      {
        "name": "phosphorylated_tem1gt",
        "label": "Phosphorylated TEM1GT",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_tem1gt",
        "description": "Tracks Phosphorylated TEM1GT in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.phosphorylated_tem1gt`."
      },
      {
        "name": "bck2_g1_regulator",
        "label": "Bck2 G1 regulator",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.bck2_g1_regulator",
        "description": "Tracks Bck2 G1 regulator in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.bck2_g1_regulator`."
      },
      {
        "name": "total_cdc14_phosphatase",
        "label": "Total Cdc14 phosphatase",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.total_cdc14_phosphatase",
        "description": "Tracks Total Cdc14 phosphatase in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.total_cdc14_phosphatase`."
      },
      {
        "name": "total_cdc6_replication_licensing_factor",
        "label": "Total Cdc6 replication licensing factor",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.total_cdc6_replication_licensing_factor",
        "description": "Tracks Total Cdc6 replication licensing factor in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.total_cdc6_replication_licensing_factor`."
      },
      {
        "name": "total_cyclin_dependent_kinase_inhibitor",
        "label": "Total cyclin-dependent kinase inhibitor",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.total_cyclin_dependent_kinase_inhibitor",
        "description": "Tracks Total cyclin-dependent kinase inhibitor in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.total_cyclin_dependent_kinase_inhibitor`."
      },
      {
        "name": "total_clb2_mitotic_cyclin",
        "label": "Total Clb2 mitotic cyclin",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.total_clb2_mitotic_cyclin",
        "description": "Tracks Total Clb2 mitotic cyclin in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.total_clb2_mitotic_cyclin`."
      },
      {
        "name": "total_clb5_s_phase_cyclin",
        "label": "Total Clb5 S-phase cyclin",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.total_clb5_s_phase_cyclin",
        "description": "Tracks Total Clb5 S-phase cyclin in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.total_clb5_s_phase_cyclin`."
      },
      {
        "name": "cln3_start_cyclin",
        "label": "Cln3 Start cyclin",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.cln3_start_cyclin",
        "description": "Tracks Cln3 Start cyclin in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.cln3_start_cyclin`."
      },
      {
        "name": "mcm1",
        "label": "Mcm1",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.mcm1",
        "description": "Tracks Mcm1 in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.mcm1`."
      },
      {
        "name": "total_net1_nucleolar_cdc14_anchor",
        "label": "Total Net1 nucleolar Cdc14 anchor",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.total_net1_nucleolar_cdc14_anchor",
        "description": "Tracks Total Net1 nucleolar Cdc14 anchor in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.total_net1_nucleolar_cdc14_anchor`."
      },
      {
        "name": "sbf_transcription_factor",
        "label": "SBF transcription factor",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.sbf_transcription_factor",
        "description": "Tracks SBF transcription factor in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.sbf_transcription_factor`."
      },
      {
        "name": "total_sic1_cdk_inhibitor",
        "label": "Total Sic1 CDK inhibitor",
        "maps_to": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.total_sic1_cdk_inhibitor",
        "description": "Tracks Total Sic1 CDK inhibitor in the lab model via `cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.total_sic1_cdk_inhibitor`."
      }
    ]
  },
  "title": "Chen2004 - Cell Cycle Regulation Lab",
  "models": [
    {
      "path": "models/core",
      "alias": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model"
    },
    {
      "path": "models/visualisation",
      "alias": "visualisation"
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model_state"
      ],
      "from": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.state"
    },
    {
      "to": [
        "visualisation.cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model_summary"
      ],
      "from": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.summary"
    },
    {
      "to": [
        "visualisation.cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model_species_labels"
      ],
      "from": "cellcycle_sbml_chen2004_cell_cycle_regulation_biomd0000000056_model.species_labels"
    }
  ],
  "package": "chen2004-budding-yeast-cell-cycle",
  "runtime": {
    "duration": 10,
    "initial_inputs": {},
    "communication_step": 1
  },
  "version": "1.0.0",
  "description": "Single-model lab wrapper for Chen2004 - Cell Cycle Regulation. Chen2004 - Cell Cycle Regulation This is a hypothetical model of cell cycle that describes the molecular mechanism for regulating DNA synthesis, bud emergence, mitosis, and cell division in budding ye. It can be used to explore cell-cycle regulation dynamics and compare checkpoint behavior across conditions.",
  "schema_version": "2.0"
}