Yao2016_Calcium_Signaling Lab

About lab

Yao2016_Calcium_Signaling

This Biosimulant lab wraps Yao2016_Calcium_Signaling 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 Yao2016 Calcium Signaling? 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 Source Defined PLC State, IP3, Source Defined H State, and Calcium, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, Source Defined PLC State moved from 0 to 5.379 across 1.0 simulation windows.

Output Visualizations

Yao2016_Calcium_Signaling - run interpretation

Summary table for Yao2016_Calcium_Signaling, reporting the scientific question, observed answer, dominant module, and caveat.

Yao2016_Calcium_Signaling - timeseries visualization

Trajectories of Source Defined PLC State, IP3, Calcium, and Source Defined H State across the 1.0 simulation. In this run Source Defined PLC State climbed from 0 to 5.379 — the largest movements among the focused observables.

Yao2016_Calcium_Signaling - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: Source Defined PLC State = 5.379, Source Defined H State = 0.7112, IP3 = 0.5073, with 1 more observable below.

Model Context

Core model: models/core
Visualization model: models/visualisation
Standard: other
Upstream source: biomodels_ebi:MODEL1611150001
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 source-defined PLC state	`signaling_sbml_yao2016_calcium_signaling_model1611150001_model.initial_source_defined_plc_state`		Initial level of source-defined PLC state. Maps to SBML symbol `PLC`; exposed as a traceable initial-condition perturbation.

Outputs

Output	Maps To	Role
`calcium`	`signaling_sbml_yao2016_calcium_signaling_model1611150001_model.calcium`	Calcium.
`source_defined_plc_state`	`signaling_sbml_yao2016_calcium_signaling_model1611150001_model.source_defined_plc_state`	Source Defined PLC State.
`ip3`	`signaling_sbml_yao2016_calcium_signaling_model1611150001_model.ip3`	IP3.
`state`	`signaling_sbml_yao2016_calcium_signaling_model1611150001_model.state`	Available to the visualization model and downstream workflows.
`summary`	`signaling_sbml_yao2016_calcium_signaling_model1611150001_model.summary`	Available to the visualization model and downstream workflows.
`species_labels`	`signaling_sbml_yao2016_calcium_signaling_model1611150001_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

Packageyao2016-calcium-signaling-lab

Created2026-05-16

Updated2026-05-16

signalingsystemssystems-biologysbmlfaithfulbiomodels_ebicalcium-signalingvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_source_defined_plc_state",
        "label": "Initial source-defined PLC state",
        "maps_to": "signaling_sbml_yao2016_calcium_signaling_model1611150001_model.initial_source_defined_plc_state",
        "description": "Initial level of source-defined PLC state. Maps to SBML symbol `PLC`; exposed as a traceable initial-condition perturbation."
      }
    ],
    "outputs": [
      {
        "name": "calcium",
        "label": "Calcium",
        "maps_to": "signaling_sbml_yao2016_calcium_signaling_model1611150001_model.calcium",
        "description": "Calcium. Maps to SBML symbol `ca` and is emitted in native SBML units."
      },
      {
        "name": "source_defined_plc_state",
        "label": "Source Defined PLC State",
        "maps_to": "signaling_sbml_yao2016_calcium_signaling_model1611150001_model.source_defined_plc_state",
        "description": "Source Defined PLC State. Maps to SBML symbol `PLC` and is emitted in native SBML units."
      },
      {
        "name": "ip3",
        "label": "IP3",
        "maps_to": "signaling_sbml_yao2016_calcium_signaling_model1611150001_model.ip3",
        "description": "IP3. Maps to SBML symbol `IP3` and is emitted in native SBML units."
      },
      {
        "name": "state",
        "label": "Observable state",
        "maps_to": "signaling_sbml_yao2016_calcium_signaling_model1611150001_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation summary",
        "maps_to": "signaling_sbml_yao2016_calcium_signaling_model1611150001_model.summary"
      },
      {
        "name": "species_labels",
        "label": "Observable labels",
        "maps_to": "signaling_sbml_yao2016_calcium_signaling_model1611150001_model.species_labels"
      }
    ]
  },
  "tags": [
    "signaling",
    "systems",
    "systems-biology",
    "sbml",
    "faithful",
    "biomodels_ebi",
    "calcium-signaling"
  ],
  "title": "Yao2016_Calcium_Signaling Lab",
  "models": [
    {
      "path": "owned/models/signaling_sbml_yao2016_calcium_signaling_model1611150001_model",
      "alias": "signaling_sbml_yao2016_calcium_signaling_model1611150001_model",
      "provenance": {
        "owned_path": "owned/models/signaling_sbml_yao2016_calcium_signaling_model1611150001_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.signaling_sbml_yao2016_calcium_signaling_model1611150001_model_state"
      ],
      "from": "signaling_sbml_yao2016_calcium_signaling_model1611150001_model.state"
    },
    {
      "to": [
        "visualisation.signaling_sbml_yao2016_calcium_signaling_model1611150001_model_summary"
      ],
      "from": "signaling_sbml_yao2016_calcium_signaling_model1611150001_model.summary"
    },
    {
      "to": [
        "visualisation.signaling_sbml_yao2016_calcium_signaling_model1611150001_model_species_labels"
      ],
      "from": "signaling_sbml_yao2016_calcium_signaling_model1611150001_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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