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Lever2014 Phenotypic Models Of T Cell Activation Lab

About lab

Lever2014 Phenotypic Models Of T Cell Activation

This Biosimulant lab wraps Lever2014 Phenotypic Models Of T Cell Activation as a runnable systems biology model with a companion visualization module. This is a phenotypic model of a kinetic proofreading mechanism used to describe dynamics governing interactions between T cell receptors and peptide-MHC complexes. 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: Lever2014 - Phenotypic models of T cell activation.. 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 C0, C9, C8, C7, C6, and C5, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, C0 moved from 3e+04 to 2.39e+04 across 1.0 simulation windows.

Output Visualizations

Lever2014 Phenotypic Models Of T Cell Activation - run interpretation

Summary table for Lever2014 Phenotypic Models Of T Cell Activation, reporting the scientific question, observed answer, dominant module, and caveat.

Lever2014 Phenotypic Models Of T Cell Activation - timeseries visualization

Trajectories of C0, C5, C6, C7, C8, and C9 across the 1.0 simulation. In this run C5 climbed from 0 to 0.1195 and C0 fell from 3e+04 to 2.39e+04 — the largest movements among the focused observables.

Lever2014 Phenotypic Models Of T Cell Activation - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: C0 = 6109.1, C5 = 0.1195, C6 = 0.00452, with 3 more observables below.

Lever2014 Phenotypic Models Of T Cell Activation - endpoint snapshot bar

Endpoint snapshot of the focused observables — final values from the captured run. Top 3 by value: C0 = 2.39e+04, C5 = 0.1195, C6 = 0.00452, with 3 more observables below.

Lever2014 Phenotypic Models Of T Cell Activation - visualization

Visualization card from the Lever2014 Phenotypic Models Of T Cell Activation dark-mode run.

Model Context

  • Core model: models/core
  • Visualization model: models/visualisation
  • Standard: other
  • Upstream source: biomodels_ebi:MODEL1907260003
  • License: CC0

Inputs

InputMaps ToDefaultNotes
Initial Model State C0systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.initial_model_state_c0Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol C0.
Initial Model State C9systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.initial_model_state_c9Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol C9.
Initial Model State C8systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.initial_model_state_c8Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol C8.
Initial Model State C7systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.initial_model_state_c7Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol C7.
Initial Model State C6systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.initial_model_state_c6Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol C6.
Initial Model State C5systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.initial_model_state_c5Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol C5.

Outputs

OutputMaps ToRole
statesystemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.stateAvailable to the visualization model and downstream workflows.
summarysystemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.summaryAvailable to the visualization model and downstream workflows.
species_labelssystemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.species_labelsAvailable to the visualization model and downstream workflows.
model_state_c0systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.model_state_c0Available to the visualization model and downstream workflows.
model_state_c9systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.model_state_c9Available to the visualization model and downstream workflows.
model_state_c8systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.model_state_c8Available to the visualization model and downstream workflows.
model_state_c7systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.model_state_c7Available to the visualization model and downstream workflows.
model_state_c6systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.model_state_c6Available to the visualization model and downstream workflows.
model_state_c5systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.model_state_c5Available to the visualization model and downstream workflows.

Runtime

  • Duration: 1.0
  • Communication step: 0.1

Running Locally

biosimulant labs serve

This is a phenotypic model of a kinetic proofreading mechanism used to describe dynamics governing interactions between T cell receptors and peptide-MHC complexes. It can be used to explore systemsbiology lever2014 phenotypic of t cell dynamics and compare simulation behavior across conditions.

Runtime

Duration1
Comms Step0.1

Runs

Total0
Completed0
Failed0

Metadata

Packagelever2014-phenotypic-models-of-t-cell-activation-lab
Created2026-05-17
Updated2026-05-17
immunologysystemsbiologysbmlbiomodels_ebifaithfulcuratedvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_model_state_c0",
        "label": "Initial Model State C0",
        "maps_to": "systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.initial_model_state_c0",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `C0`."
      },
      {
        "name": "initial_model_state_c9",
        "label": "Initial Model State C9",
        "maps_to": "systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.initial_model_state_c9",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `C9`."
      },
      {
        "name": "initial_model_state_c8",
        "label": "Initial Model State C8",
        "maps_to": "systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.initial_model_state_c8",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `C8`."
      },
      {
        "name": "initial_model_state_c7",
        "label": "Initial Model State C7",
        "maps_to": "systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.initial_model_state_c7",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `C7`."
      },
      {
        "name": "initial_model_state_c6",
        "label": "Initial Model State C6",
        "maps_to": "systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.initial_model_state_c6",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `C6`."
      },
      {
        "name": "initial_model_state_c5",
        "label": "Initial Model State C5",
        "maps_to": "systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.initial_model_state_c5",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `C5`."
      }
    ],
    "outputs": [
      {
        "name": "state",
        "maps_to": "systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.state"
      },
      {
        "name": "summary",
        "maps_to": "systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.summary"
      },
      {
        "name": "species_labels",
        "maps_to": "systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.species_labels"
      },
      {
        "name": "model_state_c0",
        "maps_to": "systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.model_state_c0"
      },
      {
        "name": "model_state_c9",
        "maps_to": "systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.model_state_c9"
      },
      {
        "name": "model_state_c8",
        "maps_to": "systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.model_state_c8"
      },
      {
        "name": "model_state_c7",
        "maps_to": "systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.model_state_c7"
      },
      {
        "name": "model_state_c6",
        "maps_to": "systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.model_state_c6"
      },
      {
        "name": "model_state_c5",
        "maps_to": "systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.model_state_c5"
      }
    ]
  },
  "tags": [
    "immunology",
    "systemsbiology",
    "sbml",
    "biomodels_ebi",
    "faithful",
    "curated"
  ],
  "title": "Lever2014 Phenotypic Models Of T Cell Activation Lab",
  "models": [
    {
      "path": "owned/models/systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model",
      "alias": "systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model",
      "provenance": {
        "owned_path": "owned/models/systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model_state"
      ],
      "from": "systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.state"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model_summary"
      ],
      "from": "systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.summary"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model_species_labels"
      ],
      "from": "systemsbiology_sbml_lever2014_phenotypic_models_of_t_cell_activation_model1907260003_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "This is a phenotypic model of a kinetic proofreading mechanism used to describe dynamics governing interactions between T cell receptors and peptide-MHC complexes. It can be used to explore systemsbiology lever2014 phenotypic of t cell dynamics and compare simulation behavior across conditions.",
  "schema_version": "2.0"
}

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