Nakakuki2010_CellFateDecision_Core Lab

About lab

Nakakuki2010_CellFateDecision_Core

This Biosimulant lab wraps Nakakuki2010_CellFateDecision_Core as a runnable signaling model with a companion visualization module. Clean Biosimulant lab for MAPK/ERK receptor 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 Nakakuki2010 CellFateDecision Core propagate receptor or RAS/ERK pathway activity? 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 X1 state, source-defined X2 state, Pp ERK Nucleus, source-defined DUSP state, P Rskn, and C FOS Pre RNA, and related outputs, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, source-defined X1 state moved from 0 to 0.2770 across 1.0 simulation windows.

Output Visualizations

Nakakuki2010_CellFateDecision_Core - run interpretation

Summary table for Nakakuki2010_CellFateDecision_Core, reporting the scientific question, observed answer, dominant module, and caveat.

Nakakuki2010_CellFateDecision_Core - timeseries visualization

Trajectories of source-defined X1 state, Pp ERK Cytosol, Pp ERK Nucleus, source-defined DUSP state, source-defined X2 state, and P Rskn across the 1.0 simulation. In this run source-defined X1 state climbed from 0 to 0.2770 — the largest movements among the focused observables.

Nakakuki2010_CellFateDecision_Core - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: source-defined X1 state = 0.2770, Pp ERK Cytosol = 0.2715, Pp ERK Nucleus = 0.0791, with 7 more observables below.

Model Context

Core model: models/core
Visualization model: models/visualisation
Standard: other
Upstream source: biomodels_ebi:BIOMD0000000251
License: CC0
Visual scope: receptor-to-MAPK cascade 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 Pp ERK Cytosol	`signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model.initial_pp_erk_cytosol`		Initial level of Pp ERK Cytosol. Maps to SBML symbol `ppERKc`; exposed as a traceable initial-condition perturbation.

Outputs

Output	Maps To	Role
`pp_erk_nucleus`	`signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model.pp_erk_nucleus`	Pp ERK Nucleus.
`pp_erk_cytosol`	`signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model.pp_erk_cytosol`	Pp ERK Cytosol.
`source_defined_dusp_state`	`signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model.source_defined_dusp_state`	source-defined DUSP state.
`state`	`signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model.state`	Available to the visualization model and downstream workflows.
`summary`	`signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model.summary`	Available to the visualization model and downstream workflows.
`species_labels`	`signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_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 MAPK/ERK receptor 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

Packagenakakuki2010-cellfatedecision-core-lab

Created2026-05-16

Updated2026-05-16

signalingsystemssystems-biologysbmlfaithfulbiomodels_ebimapkvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_pp_erk_cytosol",
        "label": "Initial Pp ERK Cytosol",
        "maps_to": "signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model.initial_pp_erk_cytosol",
        "description": "Initial level of Pp ERK Cytosol. Maps to SBML symbol `ppERKc`; exposed as a traceable initial-condition perturbation."
      }
    ],
    "outputs": [
      {
        "name": "pp_erk_nucleus",
        "label": "Pp ERK Nucleus",
        "maps_to": "signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model.pp_erk_nucleus",
        "description": "Pp ERK Nucleus. Maps to SBML symbol `ppERKn` and is emitted in native SBML units."
      },
      {
        "name": "pp_erk_cytosol",
        "label": "Pp ERK Cytosol",
        "maps_to": "signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model.pp_erk_cytosol",
        "description": "Pp ERK Cytosol. Maps to SBML symbol `ppERKc` and is emitted in native SBML units."
      },
      {
        "name": "source_defined_dusp_state",
        "label": "source-defined DUSP state",
        "maps_to": "signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model.source_defined_dusp_state",
        "description": "source-defined DUSP state. Maps to SBML symbol `DUSP` and is emitted in native SBML units."
      },
      {
        "name": "state",
        "label": "Observable state",
        "maps_to": "signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation summary",
        "maps_to": "signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model.summary"
      },
      {
        "name": "species_labels",
        "label": "Observable labels",
        "maps_to": "signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model.species_labels"
      }
    ]
  },
  "tags": [
    "signaling",
    "systems",
    "systems-biology",
    "sbml",
    "faithful",
    "biomodels_ebi",
    "mapk"
  ],
  "title": "Nakakuki2010_CellFateDecision_Core Lab",
  "models": [
    {
      "path": "owned/models/signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model",
      "alias": "signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model",
      "provenance": {
        "owned_path": "owned/models/signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model_state"
      ],
      "from": "signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model.state"
    },
    {
      "to": [
        "visualisation.signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model_summary"
      ],
      "from": "signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model.summary"
    },
    {
      "to": [
        "visualisation.signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model_species_labels"
      ],
      "from": "signaling_sbml_nakakuki2010_cellfatedecision_core_biomd0000000251_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "Clean Biosimulant lab for MAPK/ERK receptor signaling. Values are native SBML quantities; equations, parameters, and initial values remain in the bundled source file.",
  "schema_version": "2.0"
}

Select a run from History to view its results.