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Fisher2006 Ca Oscillation Dpdnt Nfat Dynamics Lab

About lab

Fisher2006 Ca Oscillation Dpdnt Nfat Dynamics

This Biosimulant lab wraps Fisher2006 Ca Oscillation Dpdnt Nfat Dynamics as a runnable systems biology model with a companion visualization module. The model reproduces the calcium oscillation dependent activation-deactivation kinetics of nuclear factor of activated T cells (NFAT) as depicted in Fig 4a of the paper. It can be used to explore the configured dynamics and compare scenario outcomes across configurations.

What You'll See

The lab asks: Which immune or inflammatory states dominate the simulated response? Source model: Fisher2006_Ca_Oscillation_dpdnt_NFAT_dynamics. 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 Calcium in Nucleus, Calcium in Cytosol, Inactive Calcineurin in nucleus, Inactive Calcineurin in cytosol, Phosphorylated NFAT in cytosol, and NFAT Calcineurin complex in nucleus, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, Inactive Calcineurin in nucleus moved from 5.56e-15 to 3.24e-15 across 1.0 simulation windows.

Output Visualizations

Fisher2006 Ca Oscillation Dpdnt Nfat Dynamics - run interpretation

Summary table for Fisher2006 Ca Oscillation Dpdnt Nfat Dynamics, reporting the scientific question, observed answer, dominant module, and caveat.

Fisher2006 Ca Oscillation Dpdnt Nfat Dynamics - timeseries visualization

Trajectories of Inactive Calcineurin in nucleus, Inactive Calcineurin in cytosol, Phosphorylated NFAT in cytosol, NFAT Calcineurin complex in nucleus, Calcium in Nucleus, and Calcium in Cytosol across the 1.0 simulation. In this run NFAT Calcineurin complex in nucleus climbed from 1.07e-16 to 1.13e-16 and Inactive Calcineurin in nucleus fell from 5.56e-15 to 3.24e-15 — the largest movements among the focused observables.

Fisher2006 Ca Oscillation Dpdnt Nfat Dynamics - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: Inactive Calcineurin in nucleus = 2.32e-15, Inactive Calcineurin in cytosol = 1.1e-15, Phosphorylated NFAT in cytosol = 3.87e-17, with 1 more observable below.

Fisher2006 Ca Oscillation Dpdnt Nfat Dynamics - endpoint snapshot bar

Endpoint snapshot of the focused observables — final values from the captured run. Top 3 by value: Calcium in Cytosol = 2.69e-13, Calcium in Nucleus = 1.13e-13, Inactive Calcineurin in nucleus = 3.24e-15, with 3 more observables below.

Fisher2006 Ca Oscillation Dpdnt Nfat Dynamics - visualization

Visualization card from the Fisher2006 Ca Oscillation Dpdnt Nfat Dynamics dark-mode run.

Model Context

  • Core model: models/core
  • Visualization model: models/visualisation
  • Standard: other
  • Upstream source: biomodels_ebi:BIOMD0000000122
  • License: CC0

Inputs

InputMaps ToDefaultNotes
Initial Calcium In Nucleussystemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.initial_calcium_in_nucleusSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol Ca_Nuc.
Initial Calcium In Cytosolsystemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.initial_calcium_in_cytosolSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol Ca_Cyt.
Initial Inactive Calcineurin In Nucleussystemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.initial_inactive_calcineurin_in_nucleusSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol Inact_C_Nuc.
Initial Inactive Calcineurin In Cytosolsystemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.initial_inactive_calcineurin_in_cytosolSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol Inact_C_Cyt.
Initial Phosphorylated Nfat In Cytosolsystemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.initial_phosphorylated_nfat_in_cytosolSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol NFAT_Pi_Cyt.
Initial Nfat Calcineurin Complex In Nucleussystemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.initial_nfat_calcineurin_complex_in_nucleusSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol NFAT_Act_C_Nuc.

Outputs

OutputMaps ToRole
statesystemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.stateAvailable to the visualization model and downstream workflows.
summarysystemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.summaryAvailable to the visualization model and downstream workflows.
species_labelssystemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.species_labelsAvailable to the visualization model and downstream workflows.
calcium_in_nucleussystemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.calcium_in_nucleusAvailable to the visualization model and downstream workflows.
calcium_in_cytosolsystemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.calcium_in_cytosolAvailable to the visualization model and downstream workflows.
inactive_calcineurin_in_nucleussystemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.inactive_calcineurin_in_nucleusAvailable to the visualization model and downstream workflows.
inactive_calcineurin_in_cytosolsystemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.inactive_calcineurin_in_cytosolAvailable to the visualization model and downstream workflows.
phosphorylated_nfat_in_cytosolsystemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.phosphorylated_nfat_in_cytosolAvailable to the visualization model and downstream workflows.
nfat_calcineurin_complex_in_nucleussystemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.nfat_calcineurin_complex_in_nucleusAvailable to the visualization model and downstream workflows.

Runtime

  • Duration: 1.0
  • Communication step: 0.1

Running Locally

biosimulant labs serve

The model reproduces the calcium oscillation dependent activation-deactivation kinetics of nuclear factor of activated T cells (NFAT) as depicted in Fig 4a of the paper. It can be used to explore systemsbiology fisher2006 ca oscillation dpdnt nfat dynamics and compare simulation behavior across conditions.

Runtime

Duration1
Comms Step0.1

Runs

Total0
Completed0
Failed0

Metadata

Packagefisher2006-ca-oscillation-dpdnt-nfat-dynamics-lab
Created2026-05-17
Updated2026-05-17
immunologyphysiologysystemsbiologysbmlbiomodels_ebifaithfulcuratedvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_calcium_in_nucleus",
        "label": "Initial Calcium In Nucleus",
        "maps_to": "systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.initial_calcium_in_nucleus",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Ca_Nuc`."
      },
      {
        "name": "initial_calcium_in_cytosol",
        "label": "Initial Calcium In Cytosol",
        "maps_to": "systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.initial_calcium_in_cytosol",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Ca_Cyt`."
      },
      {
        "name": "initial_inactive_calcineurin_in_nucleus",
        "label": "Initial Inactive Calcineurin In Nucleus",
        "maps_to": "systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.initial_inactive_calcineurin_in_nucleus",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Inact_C_Nuc`."
      },
      {
        "name": "initial_inactive_calcineurin_in_cytosol",
        "label": "Initial Inactive Calcineurin In Cytosol",
        "maps_to": "systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.initial_inactive_calcineurin_in_cytosol",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Inact_C_Cyt`."
      },
      {
        "name": "initial_phosphorylated_nfat_in_cytosol",
        "label": "Initial Phosphorylated Nfat In Cytosol",
        "maps_to": "systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.initial_phosphorylated_nfat_in_cytosol",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `NFAT_Pi_Cyt`."
      },
      {
        "name": "initial_nfat_calcineurin_complex_in_nucleus",
        "label": "Initial Nfat Calcineurin Complex In Nucleus",
        "maps_to": "systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.initial_nfat_calcineurin_complex_in_nucleus",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `NFAT_Act_C_Nuc`."
      }
    ],
    "outputs": [
      {
        "name": "state",
        "maps_to": "systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.state"
      },
      {
        "name": "summary",
        "maps_to": "systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.summary"
      },
      {
        "name": "species_labels",
        "maps_to": "systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.species_labels"
      },
      {
        "name": "calcium_in_nucleus",
        "maps_to": "systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.calcium_in_nucleus"
      },
      {
        "name": "calcium_in_cytosol",
        "maps_to": "systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.calcium_in_cytosol"
      },
      {
        "name": "inactive_calcineurin_in_nucleus",
        "maps_to": "systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.inactive_calcineurin_in_nucleus"
      },
      {
        "name": "inactive_calcineurin_in_cytosol",
        "maps_to": "systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.inactive_calcineurin_in_cytosol"
      },
      {
        "name": "phosphorylated_nfat_in_cytosol",
        "maps_to": "systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.phosphorylated_nfat_in_cytosol"
      },
      {
        "name": "nfat_calcineurin_complex_in_nucleus",
        "maps_to": "systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.nfat_calcineurin_complex_in_nucleus"
      }
    ]
  },
  "tags": [
    "immunology",
    "physiology",
    "systemsbiology",
    "sbml",
    "biomodels_ebi",
    "faithful",
    "curated"
  ],
  "title": "Fisher2006 Ca Oscillation Dpdnt Nfat Dynamics Lab",
  "models": [
    {
      "path": "owned/models/systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model",
      "alias": "systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model",
      "provenance": {
        "owned_path": "owned/models/systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model_state"
      ],
      "from": "systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.state"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model_summary"
      ],
      "from": "systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.summary"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model_species_labels"
      ],
      "from": "systemsbiology_sbml_fisher2006_ca_oscillation_dpdnt_nfat_dynamics_biomd0000000122_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "The model reproduces the calcium oscillation dependent activation-deactivation kinetics of nuclear factor of activated T cells (NFAT) as depicted in Fig 4a of the paper. It can be used to explore systemsbiology fisher2006 ca oscillation dpdnt nfat dynamics and compare simulation behavior across conditions.",
  "schema_version": "2.0"
}

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