Abell2011_CalciumSignaling_WithoutAdaptation Lab

About lab

Abell2011_CalciumSignaling_WithoutAdaptation

This Biosimulant lab wraps Abell2011_CalciumSignaling_WithoutAdaptation as a runnable signaling model with a companion visualization module. Clean Biosimulant lab for calcium and second-messenger signaling. It can be used to explore second-messenger and pathway-signaling dynamics and compare scenario outcomes across configurations.

What You'll See

The lab asks: How do calcium-linked states respond in Abell2011 CalciumSignaling WithoutAdaptation? 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 intracellular calcium, IP3, source-defined G state, extracellular calcium, stored calcium, and calmodulin, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, IP3 moved from 0 to 0.0216 across 1.0 simulation windows.

Output Visualizations

Abell2011_CalciumSignaling_WithoutAdaptation - run interpretation

Summary table for Abell2011_CalciumSignaling_WithoutAdaptation, reporting the scientific question, observed answer, dominant module, and caveat.

Abell2011_CalciumSignaling_WithoutAdaptation - timeseries visualization

Trajectories of IP3, CaS, CaI, CaM, G, and CaO across the 1.0 simulation. In this run IP3 climbed from 0 to 0.0216 and CaS fell from 2.000 to 1.996 — the largest movements among the focused observables.

Abell2011_CalciumSignaling_WithoutAdaptation - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: CaO = 1000.0, CaS = 1.996, CaI = 0.0538, with 3 more observables below.

Model Context

Core model: models/core
Visualization model: models/visualisation
Standard: other
Upstream source: biomodels_ebi:BIOMD0000000354
License: CC0
Visual scope: calcium second-messenger signaling
Caveat: Values are native SBML quantities; equations, parameters, units, and initial values remain in the bundled source file.

Inputs

Input	Maps To	Default	Notes
Initial intracellular calcium	`signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model.initial_intracellular_calcium`		Initial level of intracellular calcium. Maps to SBML symbol `CaI`; exposed as a traceable initial-condition perturbation.

Outputs

Output	Maps To	Role
`intracellular_calcium`	`signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model.intracellular_calcium`	intracellular calcium.
`extracellular_calcium`	`signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model.extracellular_calcium`	extracellular calcium.
`stored_calcium`	`signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model.stored_calcium`	stored calcium.
`state`	`signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model.state`	Available to the visualization model and downstream workflows.
`summary`	`signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model.summary`	Available to the visualization model and downstream workflows.
`species_labels`	`signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model.species_labels`	Available to the visualization model and downstream workflows.

Runtime

Duration: 1.0
Communication step: 0.1

Running Locally

biosimulant labs serve .

Clean Biosimulant lab for calcium and second-messenger signaling. Values are native SBML quantities; equations, parameters, and initial values remain in the bundled source file.

Runtime

Duration1

Comms Step0.1

Runs

Total0

Completed0

Failed0

Metadata

Packageabell2011-calciumsignaling-withoutadaptation-lab

Created2026-05-16

Updated2026-05-16

signalingsystemssystems-biologysbmlfaithfulbiomodels_ebicalcium-signalingvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_intracellular_calcium",
        "label": "Initial intracellular calcium",
        "maps_to": "signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model.initial_intracellular_calcium",
        "description": "Initial level of intracellular calcium. Maps to SBML symbol `CaI`; exposed as a traceable initial-condition perturbation."
      }
    ],
    "outputs": [
      {
        "name": "intracellular_calcium",
        "label": "intracellular calcium",
        "maps_to": "signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model.intracellular_calcium",
        "description": "intracellular calcium. Maps to SBML symbol `CaI` and is emitted in native SBML units."
      },
      {
        "name": "extracellular_calcium",
        "label": "extracellular calcium",
        "maps_to": "signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model.extracellular_calcium",
        "description": "extracellular calcium. Maps to SBML symbol `CaO` and is emitted in native SBML units."
      },
      {
        "name": "stored_calcium",
        "label": "stored calcium",
        "maps_to": "signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model.stored_calcium",
        "description": "stored calcium. Maps to SBML symbol `CaS` and is emitted in native SBML units."
      },
      {
        "name": "state",
        "label": "Observable state",
        "maps_to": "signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation summary",
        "maps_to": "signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model.summary"
      },
      {
        "name": "species_labels",
        "label": "Observable labels",
        "maps_to": "signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model.species_labels"
      }
    ]
  },
  "tags": [
    "signaling",
    "systems",
    "systems-biology",
    "sbml",
    "faithful",
    "biomodels_ebi",
    "calcium-signaling"
  ],
  "title": "Abell2011_CalciumSignaling_WithoutAdaptation Lab",
  "models": [
    {
      "path": "owned/models/signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model",
      "alias": "signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model",
      "provenance": {
        "owned_path": "owned/models/signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model_state"
      ],
      "from": "signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model.state"
    },
    {
      "to": [
        "visualisation.signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model_summary"
      ],
      "from": "signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model.summary"
    },
    {
      "to": [
        "visualisation.signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model_species_labels"
      ],
      "from": "signaling_sbml_abell2011_calciumsignaling_withoutadaptation_biomd0000000354_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "Clean Biosimulant lab for calcium and second-messenger signaling. Values are native SBML quantities; equations, parameters, and initial values remain in the bundled source file.",
  "schema_version": "2.0"
}

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