Sarma2012 - Interaction topologies of MAPK cascade (M2_K2_PSEQ) Lab

About lab

Sarma2012 - Interaction topologies of MAPK cascade (M2_K2_PSEQ)

This Biosimulant lab wraps Sarma2012 - Interaction topologies of MAPK cascade (M2_K2_PSEQ) 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 Sarma2012 - Interaction topologies of MAPK cascade (M2 K2 PSEQ) 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 MAP kinase, MAPK kinase PP, MAP kinase MAPK kinase PP, source-defined MK-P state, MAP kinase P MAPK kinase PP, and source-defined MK-PP state, and related outputs, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, MAP kinase moved from 1200.0 to 1005.0 across 1.0 simulation windows.

Output Visualizations

Sarma2012 - Interaction topologies of MAPK cascade (M2_K2_PSEQ) - run interpretation

Summary table for Sarma2012 - Interaction topologies of MAPK cascade (M2_K2_PSEQ), reporting the scientific question, observed answer, dominant module, and caveat.

Sarma2012 - Interaction topologies of MAPK cascade (M2_K2_PSEQ) - timeseries visualization

Trajectories of MAP kinase, source-defined P2 state, source-defined MK_P2 state, source-defined P1 state, MAPK kinase, and source-defined MKK_P1 state across the 1.0 simulation. In this run source-defined MK_P2 state climbed from 0 to 195.0 and MAP kinase fell from 1200.0 to 1005.0 — the largest movements among the focused observables.

Sarma2012 - Interaction topologies of MAPK cascade (M2_K2_PSEQ) - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: MAPK kinase = 1115.8, MAP kinase = 1005.0, MAPK kinase kinase = 267.6, with 7 more observables below.

Model Context

Core model: models/core
Visualization model: models/visualisation
Standard: other
Upstream source: biomodels_ebi:MODEL1204280022
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 MAP kinase	`signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model.initial_map_kinase`		Initial level of MAP kinase. Maps to SBML symbol `species_1`; exposed as a traceable initial-condition perturbation.

Outputs

Output	Maps To	Role
`mapk_kinase_pp`	`signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model.mapk_kinase_pp`	MAPK kinase PP.
`map_kinase_mapk_kinase_pp`	`signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model.map_kinase_mapk_kinase_pp`	MAP kinase MAPK kinase PP.
`source_defined_mk_p_state`	`signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model.source_defined_mk_p_state`	source-defined MK-P state.
`state`	`signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model.state`	Available to the visualization model and downstream workflows.
`summary`	`signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model.summary`	Available to the visualization model and downstream workflows.
`species_labels`	`signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_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

Packagesarma2012-interaction-topologies-of-mapk-cascade-m2-k2-pseq-lab

Created2026-05-16

Updated2026-05-16

signalingsystemssystems-biologysbmlfaithfulbiomodels_ebimapkvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_map_kinase",
        "label": "Initial MAP kinase",
        "maps_to": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model.initial_map_kinase",
        "description": "Initial level of MAP kinase. Maps to SBML symbol `species_1`; exposed as a traceable initial-condition perturbation."
      }
    ],
    "outputs": [
      {
        "name": "mapk_kinase_pp",
        "label": "MAPK kinase PP",
        "maps_to": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model.mapk_kinase_pp",
        "description": "MAPK kinase PP. Maps to SBML symbol `species_2` and is emitted in native SBML units."
      },
      {
        "name": "map_kinase_mapk_kinase_pp",
        "label": "MAP kinase MAPK kinase PP",
        "maps_to": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model.map_kinase_mapk_kinase_pp",
        "description": "MAP kinase MAPK kinase PP. Maps to SBML symbol `species_3` and is emitted in native SBML units."
      },
      {
        "name": "source_defined_mk_p_state",
        "label": "source-defined MK-P state",
        "maps_to": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model.source_defined_mk_p_state",
        "description": "source-defined MK-P state. Maps to SBML symbol `species_4` and is emitted in native SBML units."
      },
      {
        "name": "state",
        "label": "Observable state",
        "maps_to": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation summary",
        "maps_to": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model.summary"
      },
      {
        "name": "species_labels",
        "label": "Observable labels",
        "maps_to": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model.species_labels"
      }
    ]
  },
  "tags": [
    "signaling",
    "systems",
    "systems-biology",
    "sbml",
    "faithful",
    "biomodels_ebi",
    "mapk"
  ],
  "title": "Sarma2012 - Interaction topologies of MAPK cascade (M2_K2_PSEQ) Lab",
  "models": [
    {
      "path": "owned/models/signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model",
      "alias": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model",
      "provenance": {
        "owned_path": "owned/models/signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model_state"
      ],
      "from": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model.state"
    },
    {
      "to": [
        "visualisation.signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model_summary"
      ],
      "from": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model.summary"
    },
    {
      "to": [
        "visualisation.signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_model_species_labels"
      ],
      "from": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280022_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"
}

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