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Mouse Iron Distribution Deficient Iron Diet Lab

About lab

Mouse Iron Distribution Deficient Iron Diet

This Biosimulant lab wraps Mouse Iron Distribution Deficient Iron Diet as a runnable systems biology model with a companion visualization module. Mouse Iron Distribution Dynamics Dynamic model of iron distribution in mice. It can be used to explore the configured dynamics and compare scenario outcomes across configurations.

What You'll See

The lab asks: Which source-defined system states dominate this SBML model trajectory? Source model: Mouse Iron Distribution - Deficient iron diet (No Tracer). 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 FeLiver, FeRBC, FeDuo, FeSpleen, FeBM, and FeRest, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, FeDuo moved from 4.52e-07 to 3.18e-07 across 1.0 simulation windows.

Output Visualizations

Mouse Iron Distribution Deficient Iron Diet - run interpretation

Summary table for Mouse Iron Distribution Deficient Iron Diet, reporting the scientific question, observed answer, dominant module, and caveat.

Mouse Iron Distribution Deficient Iron Diet - timeseries visualization

Trajectories of FeDuo, FeSpleen, FeBM, FeRBC, FeLiver, and FeRest across the 1.0 simulation. In this run FeBM climbed from 6.51e-07 to 6.94e-07 and FeDuo fell from 4.52e-07 to 3.18e-07 — the largest movements among the focused observables.

Mouse Iron Distribution Deficient Iron Diet - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: FeDuo = 1.35e-07, FeSpleen = 5.25e-08, FeBM = 4.3e-08, with 3 more observables below.

Mouse Iron Distribution Deficient Iron Diet - endpoint snapshot bar

Endpoint snapshot of the focused observables — final values from the captured run. Top 3 by value: FeRBC = 3e-05, FeRest = 5.65e-06, FeLiver = 2.32e-06, with 3 more observables below.

Mouse Iron Distribution Deficient Iron Diet - visualization

Visualization card from the Mouse Iron Distribution Deficient Iron Diet dark-mode run.

Model Context

  • Core model: models/core
  • Visualization model: models/visualisation
  • Standard: other
  • Upstream source: biomodels_ebi:BIOMD0000000737
  • License: CC0

Inputs

InputMaps ToDefaultNotes
Initial Fe Liversystemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.initial_fe_liverSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol FeLiver.
Initial Fe Rbcsystemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.initial_fe_rbcSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol FeRBC.
Initial Fe Duosystemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.initial_fe_duoSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol FeDuo.
Initial Fe Spleensystemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.initial_fe_spleenSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol FeSpleen.
Initial Fe Bmsystemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.initial_fe_bmSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol FeBM.
Initial Fe Restsystemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.initial_fe_restSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol FeRest.

Outputs

OutputMaps ToRole
statesystemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.stateAvailable to the visualization model and downstream workflows.
summarysystemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.summaryAvailable to the visualization model and downstream workflows.
species_labelssystemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.species_labelsAvailable to the visualization model and downstream workflows.
fe_liversystemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.fe_liverAvailable to the visualization model and downstream workflows.
fe_rbcsystemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.fe_rbcAvailable to the visualization model and downstream workflows.
fe_duosystemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.fe_duoAvailable to the visualization model and downstream workflows.
fe_spleensystemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.fe_spleenAvailable to the visualization model and downstream workflows.
fe_bmsystemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.fe_bmAvailable to the visualization model and downstream workflows.
fe_restsystemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.fe_restAvailable to the visualization model and downstream workflows.

Runtime

  • Duration: 1.0
  • Communication step: 0.1

Running Locally

biosimulant labs serve

Mouse Iron Distribution Dynamics Dynamic model of iron distribution in mice. This model includes only normal iron with the parameters that fit the data from Lopes et al.

Runtime

Duration1
Comms Step0.1

Runs

Total0
Completed0
Failed0

Metadata

Packagemouse-iron-distribution-deficient-iron-diet-lab
Created2026-05-17
Updated2026-05-17
systemsbiologysbmlbiomodels_ebifaithfulcuratedvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_fe_liver",
        "label": "Initial Fe Liver",
        "maps_to": "systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.initial_fe_liver",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `FeLiver`."
      },
      {
        "name": "initial_fe_rbc",
        "label": "Initial Fe Rbc",
        "maps_to": "systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.initial_fe_rbc",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `FeRBC`."
      },
      {
        "name": "initial_fe_duo",
        "label": "Initial Fe Duo",
        "maps_to": "systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.initial_fe_duo",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `FeDuo`."
      },
      {
        "name": "initial_fe_spleen",
        "label": "Initial Fe Spleen",
        "maps_to": "systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.initial_fe_spleen",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `FeSpleen`."
      },
      {
        "name": "initial_fe_bm",
        "label": "Initial Fe Bm",
        "maps_to": "systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.initial_fe_bm",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `FeBM`."
      },
      {
        "name": "initial_fe_rest",
        "label": "Initial Fe Rest",
        "maps_to": "systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.initial_fe_rest",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `FeRest`."
      }
    ],
    "outputs": [
      {
        "name": "state",
        "maps_to": "systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.state"
      },
      {
        "name": "summary",
        "maps_to": "systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.summary"
      },
      {
        "name": "species_labels",
        "maps_to": "systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.species_labels"
      },
      {
        "name": "fe_liver",
        "maps_to": "systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.fe_liver"
      },
      {
        "name": "fe_rbc",
        "maps_to": "systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.fe_rbc"
      },
      {
        "name": "fe_duo",
        "maps_to": "systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.fe_duo"
      },
      {
        "name": "fe_spleen",
        "maps_to": "systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.fe_spleen"
      },
      {
        "name": "fe_bm",
        "maps_to": "systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.fe_bm"
      },
      {
        "name": "fe_rest",
        "maps_to": "systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.fe_rest"
      }
    ]
  },
  "tags": [
    "systemsbiology",
    "sbml",
    "biomodels_ebi",
    "faithful",
    "curated"
  ],
  "title": "Mouse Iron Distribution Deficient Iron Diet Lab",
  "models": [
    {
      "path": "owned/models/systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model",
      "alias": "systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model",
      "provenance": {
        "owned_path": "owned/models/systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model_state"
      ],
      "from": "systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.state"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model_summary"
      ],
      "from": "systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.summary"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model_species_labels"
      ],
      "from": "systemsbiology_sbml_mouse_iron_distribution_deficient_iron_diet_no_t_biomd0000000737_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "Mouse Iron Distribution Dynamics Dynamic model of iron distribution in mice. This model includes only normal iron with the parameters that fit the data from Lopes et al.",
  "schema_version": "2.0"
}

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