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Dunster2016 Nondimensional Coagulation Lab

About lab

Dunster2016 Nondimensional Coagulation

This Biosimulant lab wraps Dunster2016 Nondimensional Coagulation as a runnable systems biology model with a companion visualization module. We undertake a mathematical investigation of a model for the generation of thrombin, an enzyme central to haemostatic blood coagulation, as well as to thrombotic disorders, that is the end product of. It can be used to explore the configured dynamics and compare scenario outcomes across configurations.

What You'll See

The lab asks: Which gene-regulatory states dominate the source model trajectory? Source model: Dunster2016 - Nondimensional Coagulation Model. It runs for 1.0 time units with a communication step of 0.1. The run uses the model defaults declared by the curated SBML wrapper. The generated visualizations focus on Prothrombin (II), Xa:L, Va:Xa:L, Thrombin (IIa), Prothrombinase (Va:Xa), and Inactive protein C, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, Prothrombin (II) moved from 17.000 to 6.561 across 1.0 simulation windows.

Output Visualizations

Dunster2016 Nondimensional Coagulation - run interpretation

Summary table for Dunster2016 Nondimensional Coagulation, reporting the scientific question, observed answer, dominant module, and caveat.

Dunster2016 Nondimensional Coagulation - timeseries visualization

Trajectories of Prothrombin (II), Thrombin (IIa), Xa:L, Prothrombinase (Va:Xa), Va:Xa:L, and Inactive protein C across the 1.0 simulation. In this run Thrombin (IIa) climbed from 0 to 7.993 and Prothrombin (II) fell from 17.000 to 6.561 — the largest movements among the focused observables.

Dunster2016 Nondimensional Coagulation - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: Prothrombin (II) = 10.439, Thrombin (IIa) = 7.993, Xa:L = 0.6385, with 3 more observables below.

Dunster2016 Nondimensional Coagulation - endpoint snapshot bar

Endpoint snapshot of the focused observables — final values from the captured run. Top 3 by value: Thrombin (IIa) = 7.993, Prothrombin (II) = 6.561, Prothrombinase (Va:Xa) = 0.4464, with 3 more observables below.

Dunster2016 Nondimensional Coagulation - visualization

Visualization card from the Dunster2016 Nondimensional Coagulation dark-mode run.

Model Context

  • Core model: models/core
  • Visualization model: models/visualisation
  • Standard: other
  • Upstream source: biomodels_ebi:BIOMD0000000925
  • License: CC0

Inputs

InputMaps ToDefaultNotes
Initial Prothrombin Iisystemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.initial_prothrombin_iiSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol Prothrombin__II.
Initial Xa Lsystemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.initial_xa_lSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol Xa_L.
Initial Va Xa Lsystemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.initial_va_xa_lSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol Va_Xa_L.
Initial Thrombin I Iasystemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.initial_thrombin_i_iaSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol Thrombin__IIa.
Initial Prothrombinase Va Xasystemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.initial_prothrombinase_va_xaSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol Prothrombinase__Va_Xa.
Initial Inactive Protein Csystemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.initial_inactive_protein_cSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol Inactive_protein_C.

Outputs

OutputMaps ToRole
statesystemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.stateAvailable to the visualization model and downstream workflows.
summarysystemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.summaryAvailable to the visualization model and downstream workflows.
species_labelssystemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.species_labelsAvailable to the visualization model and downstream workflows.
prothrombin_iisystemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.prothrombin_iiAvailable to the visualization model and downstream workflows.
xa_lsystemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.xa_lAvailable to the visualization model and downstream workflows.
va_xa_lsystemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.va_xa_lAvailable to the visualization model and downstream workflows.
thrombin_i_iasystemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.thrombin_i_iaAvailable to the visualization model and downstream workflows.
prothrombinase_va_xasystemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.prothrombinase_va_xaAvailable to the visualization model and downstream workflows.
inactive_protein_csystemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.inactive_protein_cAvailable to the visualization model and downstream workflows.

Runtime

  • Duration: 1.0
  • Communication step: 0.1

Running Locally

biosimulant labs serve

We undertake a mathematical investigation of a model for the generation of thrombin, an enzyme central to haemostatic blood coagulation, as well as to thrombotic disorders, that is the end product of. It can be used to explore systemsbiology dunster2016 nondimensional coagulation BioModels0000000925 dynamics and compare simulation behavior across conditions.

Runtime

Duration1
Comms Step0.1

Runs

Total0
Completed0
Failed0

Metadata

Packagedunster2016-nondimensional-coagulation-lab
Created2026-05-17
Updated2026-05-17
generegulationsystemsbiologysbmlbiomodels_ebifaithfulcuratedvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_prothrombin_ii",
        "label": "Initial Prothrombin Ii",
        "maps_to": "systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.initial_prothrombin_ii",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Prothrombin__II`."
      },
      {
        "name": "initial_xa_l",
        "label": "Initial Xa L",
        "maps_to": "systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.initial_xa_l",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Xa_L`."
      },
      {
        "name": "initial_va_xa_l",
        "label": "Initial Va Xa L",
        "maps_to": "systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.initial_va_xa_l",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Va_Xa_L`."
      },
      {
        "name": "initial_thrombin_i_ia",
        "label": "Initial Thrombin I Ia",
        "maps_to": "systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.initial_thrombin_i_ia",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Thrombin__IIa`."
      },
      {
        "name": "initial_prothrombinase_va_xa",
        "label": "Initial Prothrombinase Va Xa",
        "maps_to": "systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.initial_prothrombinase_va_xa",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Prothrombinase__Va_Xa`."
      },
      {
        "name": "initial_inactive_protein_c",
        "label": "Initial Inactive Protein C",
        "maps_to": "systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.initial_inactive_protein_c",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Inactive_protein_C`."
      }
    ],
    "outputs": [
      {
        "name": "state",
        "maps_to": "systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.state"
      },
      {
        "name": "summary",
        "maps_to": "systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.summary"
      },
      {
        "name": "species_labels",
        "maps_to": "systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.species_labels"
      },
      {
        "name": "prothrombin_ii",
        "maps_to": "systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.prothrombin_ii"
      },
      {
        "name": "xa_l",
        "maps_to": "systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.xa_l"
      },
      {
        "name": "va_xa_l",
        "maps_to": "systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.va_xa_l"
      },
      {
        "name": "thrombin_i_ia",
        "maps_to": "systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.thrombin_i_ia"
      },
      {
        "name": "prothrombinase_va_xa",
        "maps_to": "systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.prothrombinase_va_xa"
      },
      {
        "name": "inactive_protein_c",
        "maps_to": "systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.inactive_protein_c"
      }
    ]
  },
  "tags": [
    "generegulation",
    "systemsbiology",
    "sbml",
    "biomodels_ebi",
    "faithful",
    "curated"
  ],
  "title": "Dunster2016 Nondimensional Coagulation Lab",
  "models": [
    {
      "path": "owned/models/systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model",
      "alias": "systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model",
      "provenance": {
        "owned_path": "owned/models/systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model_state"
      ],
      "from": "systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.state"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model_summary"
      ],
      "from": "systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.summary"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model_species_labels"
      ],
      "from": "systemsbiology_sbml_dunster2016_nondimensional_coagulation_model_biomd0000000925_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "We undertake a mathematical investigation of a model for the generation of thrombin, an enzyme central to haemostatic blood coagulation, as well as to thrombotic disorders, that is the end product of. It can be used to explore systemsbiology dunster2016 nondimensional coagulation BioModels0000000925 dynamics and compare simulation behavior across conditions.",
  "schema_version": "2.0"
}

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