Pokhilko1998 - Intrinsic Activation Kinetics (Dimensional Model) Lab

About lab

Pokhilko1998 - Intrinsic Activation Kinetics (Dimensional Model)

This Biosimulant lab wraps Pokhilko1998 - Intrinsic Activation Kinetics (Dimensional Model) as a runnable signaling model with a companion visualization module. Clean Biosimulant lab for systems signaling model: Pokhilko1998 - Intrinsic Activation Kinetics (Dimensional Model). 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 Pokhilko1998 - Intrinsic Activation Kinetics (Dimensional Model) redistribute cascade activity across source-defined species? 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 response node X, source-defined Y state, source-defined Z state, and source-defined S state, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, source-defined Z state moved from 2.000 to 2.091 across 1.0 simulation windows.

Output Visualizations

Pokhilko1998 - Intrinsic Activation Kinetics (Dimensional Model) - run interpretation

Summary table for Pokhilko1998 - Intrinsic Activation Kinetics (Dimensional Model), reporting the scientific question, observed answer, dominant module, and caveat.

Pokhilko1998 - Intrinsic Activation Kinetics (Dimensional Model) - timeseries visualization

Trajectories of source-defined Z state, response node X, source-defined Y state, and source-defined S state across the 1.0 simulation. In this run source-defined Z state climbed from 2.000 to 2.091 and response node X fell from 0.5000 to 0.4969 — the largest movements among the focused observables.

Pokhilko1998 - Intrinsic Activation Kinetics (Dimensional Model) - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: source-defined S state = 2.600, source-defined Z state = 2.091, source-defined Y state = 0.5002, with 1 more observable below.

Model Context

Core model: models/core
Visualization model: models/visualisation
Standard: other
Upstream source: biomodels_ebi:MODEL1808210003
License: CC0
Visual scope: blood and immune cascade signaling
Caveat: Values are native SBML quantities; equations, parameters, units, and initial values remain in the bundled source file.

Inputs

Input	Maps To	Notes
Initial response node X	`signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model.initial_response_node_x`	Initial level of response node X. Maps to SBML symbol `X`; exposed as a traceable initial-condition perturbation.
Initial source-defined Y state	`signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model.initial_source_defined_y_state`	Initial level of source-defined Y state. Maps to SBML symbol `Y`; exposed as a traceable initial-condition perturbation.
Initial source-defined Z state	`signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model.initial_source_defined_z_state`	Initial level of source-defined Z state. Maps to SBML symbol `Z`; exposed as a traceable initial-condition perturbation.

Outputs

Output	Maps To	Role
`response_node_x`	`signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model.response_node_x`	response node X.
`source_defined_y_state`	`signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model.source_defined_y_state`	source-defined Y state.
`source_defined_z_state`	`signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model.source_defined_z_state`	source-defined Z state.
`state`	`signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model.state`	Available to the visualization model and downstream workflows.
`summary`	`signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model.summary`	Available to the visualization model and downstream workflows.
`species_labels`	`signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_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 systems signaling model: Pokhilko1998 - Intrinsic Activation Kinetics (Dimensional Model). 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

Packagepokhilko1998-intrinsic-activation-kinetics-dimensional-model-lab

Created2026-05-16

Updated2026-05-16

signalingsystemssystems-biologysbmlfaithfulbiomodels_ebicoagulationvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_response_node_x",
        "label": "Initial response node X",
        "maps_to": "signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model.initial_response_node_x",
        "description": "Initial level of response node X. Maps to SBML symbol `X`; exposed as a traceable initial-condition perturbation."
      },
      {
        "name": "initial_source_defined_y_state",
        "label": "Initial source-defined Y state",
        "maps_to": "signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model.initial_source_defined_y_state",
        "description": "Initial level of source-defined Y state. Maps to SBML symbol `Y`; exposed as a traceable initial-condition perturbation."
      },
      {
        "name": "initial_source_defined_z_state",
        "label": "Initial source-defined Z state",
        "maps_to": "signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model.initial_source_defined_z_state",
        "description": "Initial level of source-defined Z state. Maps to SBML symbol `Z`; exposed as a traceable initial-condition perturbation."
      }
    ],
    "outputs": [
      {
        "name": "response_node_x",
        "label": "response node X",
        "maps_to": "signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model.response_node_x",
        "description": "response node X. Maps to SBML symbol `X` and is emitted in native SBML units."
      },
      {
        "name": "source_defined_y_state",
        "label": "source-defined Y state",
        "maps_to": "signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model.source_defined_y_state",
        "description": "source-defined Y state. Maps to SBML symbol `Y` and is emitted in native SBML units."
      },
      {
        "name": "source_defined_z_state",
        "label": "source-defined Z state",
        "maps_to": "signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model.source_defined_z_state",
        "description": "source-defined Z state. Maps to SBML symbol `Z` and is emitted in native SBML units."
      },
      {
        "name": "state",
        "label": "Observable state",
        "maps_to": "signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation summary",
        "maps_to": "signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model.summary"
      },
      {
        "name": "species_labels",
        "label": "Observable labels",
        "maps_to": "signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model.species_labels"
      }
    ]
  },
  "tags": [
    "signaling",
    "systems",
    "systems-biology",
    "sbml",
    "faithful",
    "biomodels_ebi",
    "coagulation"
  ],
  "title": "Pokhilko1998 - Intrinsic Activation Kinetics (Dimensional Model) Lab",
  "models": [
    {
      "path": "owned/models/signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model",
      "alias": "signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model",
      "provenance": {
        "owned_path": "owned/models/signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model_state"
      ],
      "from": "signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model.state"
    },
    {
      "to": [
        "visualisation.signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model_summary"
      ],
      "from": "signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model.summary"
    },
    {
      "to": [
        "visualisation.signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model_species_labels"
      ],
      "from": "signaling_sbml_pokhilko1998_intrinsic_activation_kinetics_dimen_model1808210003_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "Clean Biosimulant lab for systems signaling model: Pokhilko1998 - Intrinsic Activation Kinetics (Dimensional Model). Values are native SBML quantities; equations, parameters, and initial values remain in the bundled source file.",
  "schema_version": "2.0"
}

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