Ghaffari2019 - Thrombomodulin Gene Expression after Retinoic Acid Treatment for Cancer Patients with Coagulation Disorders Lab

{
  "io": {
    "inputs": [
      {
        "name": "initial_stm",
        "label": "STM",
        "units": "native SBML value",
        "default": 1,
        "maps_to": "oncology_sbml_ghaffari2019_thrombomodulin_gene_expression_afte_model1907140001_model.initial_stm",
        "description": "Initial STM. Sets the initial value of bundled SBML symbol `sTM`."
      },
      {
        "name": "initial_rec1t",
        "label": "REC1t",
        "units": "native SBML value",
        "default": "1e-6",
        "maps_to": "oncology_sbml_ghaffari2019_thrombomodulin_gene_expression_afte_model1907140001_model.initial_rec1t",
        "description": "Initial REC1t. Sets the initial value of bundled SBML symbol `REC1t`."
      },
      {
        "name": "initial_tm_m_rna",
        "label": "TM mRNA",
        "units": "native SBML value",
        "default": 0,
        "maps_to": "oncology_sbml_ghaffari2019_thrombomodulin_gene_expression_afte_model1907140001_model.initial_tm_m_rna",
        "description": "Initial TM mRNA. Sets the initial value of bundled SBML symbol `TM_mRNA`."
      }
    ],
    "outputs": [
      {
        "name": "tm",
        "maps_to": "oncology_sbml_ghaffari2019_thrombomodulin_gene_expression_afte_model1907140001_model.tm",
        "description": "TM observable. Maps to SBML symbol `TM`."
      },
      {
        "name": "ra",
        "maps_to": "oncology_sbml_ghaffari2019_thrombomodulin_gene_expression_afte_model1907140001_model.ra",
        "description": "RA observable. Maps to SBML symbol `RA`."
      },
      {
        "name": "stm",
        "maps_to": "oncology_sbml_ghaffari2019_thrombomodulin_gene_expression_afte_model1907140001_model.stm",
        "description": "STM observable. Maps to SBML symbol `sTM`."
      },
      {
        "name": "rec1t",
        "maps_to": "oncology_sbml_ghaffari2019_thrombomodulin_gene_expression_afte_model1907140001_model.rec1t",
        "description": "REC1t observable. Maps to SBML symbol `REC1t`."
      },
      {
        "name": "tm_m_rna",
        "maps_to": "oncology_sbml_ghaffari2019_thrombomodulin_gene_expression_afte_model1907140001_model.tm_m_rna",
        "description": "TM mRNA observable. Maps to SBML symbol `TM_mRNA`."
      },
      {
        "name": "state",
        "maps_to": "oncology_sbml_ghaffari2019_thrombomodulin_gene_expression_afte_model1907140001_model.state",
        "description": "Full raw SBML observable record for reproducibility and downstream visualisation."
      },
      {
        "name": "summary",
        "maps_to": "oncology_sbml_ghaffari2019_thrombomodulin_gene_expression_afte_model1907140001_model.summary",
        "description": "Change and peak summary across the simulated SBML observables."
      },
      {
        "name": "species_labels",
        "maps_to": "oncology_sbml_ghaffari2019_thrombomodulin_gene_expression_afte_model1907140001_model.species_labels",
        "description": "Mapping from selected raw SBML observable symbols to display labels."
      }
    ]
  },
  "tags": [
    "biomodels_ebi",
    "curated",
    "drug-response",
    "faithful",
    "oncology",
    "pharmacology",
    "physiology",
    "sbml",
    "systemsbiology",
    "tumor-growth"
  ],
  "title": "Ghaffari2019 - Thrombomodulin Gene Expression after Retinoic Acid Treatment for Cancer Patients with Coagulation Disorders Lab",
  "models": [
    {
      "path": "owned/models/oncology_sbml_ghaffari2019_thrombomodulin_gene_expression_afte_model1907140001_model",
      "alias": "oncology_sbml_ghaffari2019_thrombomodulin_gene_expression_afte_model1907140001_model",
      "provenance": {
        "owned_path": "owned/models/oncology_sbml_ghaffari2019_thrombomodulin_gene_expression_afte_model1907140001_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.oncology_sbml_ghaffari2019_thrombomodulin_gene_expression_afte_model1907140001_model_state"
      ],
      "from": "oncology_sbml_ghaffari2019_thrombomodulin_gene_expression_afte_model1907140001_model.state"
    },
    {
      "to": [
        "visualisation.oncology_sbml_ghaffari2019_thrombomodulin_gene_expression_afte_model1907140001_model_summary"
      ],
      "from": "oncology_sbml_ghaffari2019_thrombomodulin_gene_expression_afte_model1907140001_model.summary"
    },
    {
      "to": [
        "visualisation.oncology_sbml_ghaffari2019_thrombomodulin_gene_expression_afte_model1907140001_model_species_labels"
      ],
      "from": "oncology_sbml_ghaffari2019_thrombomodulin_gene_expression_afte_model1907140001_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 10,
    "initial_inputs": {},
    "communication_step": 1
  },
  "description": "Publication includes a mathematical model for how retinoic acid affects thrombomodulin gene and mRNA expression as well as a two-compartment pharmacokinetic model for retinoic acid. It can be used to explore tumor-related dynamics and compare treatment-response behavior across conditions.",
  "schema_version": "2.0"
}