Smith2013 - Regulation of Insulin Signalling by Oxidative Stress Lab

About lab

Smith2013 - Regulation of Insulin Signalling by Oxidative Stress

This Biosimulant lab wraps Smith2013 - Regulation of Insulin Signalling by Oxidative Stress as a runnable signaling model with a companion visualization module. Clean Biosimulant lab for metabolic and hormone-linked 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 does Smith2013 - Regulation of Insulin Signalling by Oxidative Stress shift hormone-linked signaling readouts? 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 INS state, source-defined INR state, Ins In R, Ins In R P, Ins 2 In R P, and Cytoplasm In R, and related outputs, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, PIP2 Mol moved from 2e+08 to 2.01e+08 across 1.0 simulation windows.

Output Visualizations

Smith2013 - Regulation of Insulin Signalling by Oxidative Stress - run interpretation

Summary table for Smith2013 - Regulation of Insulin Signalling by Oxidative Stress, reporting the scientific question, observed answer, dominant module, and caveat.

Smith2013 - Regulation of Insulin Signalling by Oxidative Stress - timeseries visualization

Trajectories of PIP2 Mol, PI345P3 Mol, PTP1B, PTP1B Ox, source-defined PIP2 state, and PI345P3 across the 1.0 simulation. In this run PIP2 Mol climbed from 2e+08 to 2.01e+08 and PI345P3 Mol fell from 1e+06 to 1.85e+05 — the largest movements among the focused observables.

Smith2013 - Regulation of Insulin Signalling by Oxidative Stress - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: PIP2 Mol = 2.01e+08, PP2A = 5e+05, source-defined PIP2 state = 2.01e+05, with 7 more observables below.

Model Context

Core model: models/core
Visualization model: models/visualisation
Standard: other
Upstream source: biomodels_ebi:BIOMD0000000474
License: CC0
Visual scope: metabolic and hormone signaling response
Caveat: Values are native SBML quantities; equations, parameters, units, and initial values remain in the bundled source file.

Inputs

Input	Maps To	Notes
Initial Cytoplasm Foxo1 Tot	`signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model.initial_cytoplasm_foxo1_tot`	Initial level of Cytoplasm Foxo1 Tot. Maps to SBML symbol `cytoplasm_Foxo1_tot`; exposed as a traceable initial-condition perturbation.
Initial Dnabound Foxo1 Tot	`signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model.initial_dnabound_foxo1_tot`	Initial level of Dnabound Foxo1 Tot. Maps to SBML symbol `dnabound_Foxo1_tot`; exposed as a traceable initial-condition perturbation.
Initial DUSP DUSP Ox	`signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model.initial_dusp_dusp_ox`	Initial level of DUSP DUSP Ox. Maps to SBML symbol `DUSP_plus_DUSP_ox`; exposed as a traceable initial-condition perturbation.

Outputs

Output	Maps To	Role
`in_r_active`	`signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model.in_r_active`	In R active.
`akt`	`signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model.akt`	AKT.
`source_defined_akt_p2_state`	`signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model.source_defined_akt_p2_state`	source-defined AKT_P2 state.
`state`	`signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model.state`	Available to the visualization model and downstream workflows.
`summary`	`signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model.summary`	Available to the visualization model and downstream workflows.
`species_labels`	`signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_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 metabolic and hormone-linked 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

Packagesmith2013-regulation-of-insulin-signalling-by-oxidative-stress-l

Created2026-05-16

Updated2026-05-16

signalingsystemssystems-biologysbmlfaithfulbiomodels_ebistress-responsemetabolic-signalinghormone-signalingvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_cytoplasm_foxo1_tot",
        "label": "Initial Cytoplasm Foxo1 Tot",
        "maps_to": "signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model.initial_cytoplasm_foxo1_tot",
        "description": "Initial level of Cytoplasm Foxo1 Tot. Maps to SBML symbol `cytoplasm_Foxo1_tot`; exposed as a traceable initial-condition perturbation."
      },
      {
        "name": "initial_dnabound_foxo1_tot",
        "label": "Initial Dnabound Foxo1 Tot",
        "maps_to": "signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model.initial_dnabound_foxo1_tot",
        "description": "Initial level of Dnabound Foxo1 Tot. Maps to SBML symbol `dnabound_Foxo1_tot`; exposed as a traceable initial-condition perturbation."
      },
      {
        "name": "initial_dusp_dusp_ox",
        "label": "Initial DUSP DUSP Ox",
        "maps_to": "signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model.initial_dusp_dusp_ox",
        "description": "Initial level of DUSP DUSP Ox. Maps to SBML symbol `DUSP_plus_DUSP_ox`; exposed as a traceable initial-condition perturbation."
      }
    ],
    "outputs": [
      {
        "name": "in_r_active",
        "label": "In R active",
        "maps_to": "signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model.in_r_active",
        "description": "In R active. Maps to SBML symbol `InR_active` and is emitted in native SBML units."
      },
      {
        "name": "akt",
        "label": "AKT",
        "maps_to": "signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model.akt",
        "description": "AKT. Maps to SBML symbol `Akt` and is emitted in native SBML units."
      },
      {
        "name": "source_defined_akt_p2_state",
        "label": "source-defined AKT_P2 state",
        "maps_to": "signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model.source_defined_akt_p2_state",
        "description": "source-defined AKT_P2 state. Maps to SBML symbol `Akt_P2` and is emitted in native SBML units."
      },
      {
        "name": "state",
        "label": "Observable state",
        "maps_to": "signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation summary",
        "maps_to": "signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model.summary"
      },
      {
        "name": "species_labels",
        "label": "Observable labels",
        "maps_to": "signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model.species_labels"
      }
    ]
  },
  "tags": [
    "signaling",
    "systems",
    "systems-biology",
    "sbml",
    "faithful",
    "biomodels_ebi",
    "stress-response",
    "metabolic-signaling",
    "hormone-signaling"
  ],
  "title": "Smith2013 - Regulation of Insulin Signalling by Oxidative Stress Lab",
  "models": [
    {
      "path": "owned/models/signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model",
      "alias": "signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model",
      "provenance": {
        "owned_path": "owned/models/signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model_state"
      ],
      "from": "signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model.state"
    },
    {
      "to": [
        "visualisation.signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model_summary"
      ],
      "from": "signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model.summary"
    },
    {
      "to": [
        "visualisation.signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model_species_labels"
      ],
      "from": "signaling_sbml_smith2013_regulation_of_insulin_signalling_by_ox_biomd0000000474_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "Clean Biosimulant lab for metabolic and hormone-linked 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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