Koivumaki2009 Sercaatpase Long Lab

About lab

Koivumaki2009 Sercaatpase Long

This Biosimulant lab wraps Koivumaki2009 Sercaatpase Long as a runnable systems biology model with a companion visualization module. This a model from the article: Modelling sarcoplasmic reticulum calcium ATPase and its regulation in cardiacmyocytes. It can be used to explore the configured dynamics and compare scenario outcomes across configurations.

What You'll See

The lab asks: Which cardiovascular or blood-state variables dominate the simulated response? Source model: Koivumaki2009_SERCAATPase_long. 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 PLB Dephosph, LTRPN, Ca Serca, and Ca Cyt, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, PLB Dephosph moved from 0.1000 to 0.5678 across 1.0 simulation windows.

Output Visualizations

Koivumaki2009 Sercaatpase Long - run interpretation

Summary table for Koivumaki2009 Sercaatpase Long, reporting the scientific question, observed answer, dominant module, and caveat.

Koivumaki2009 Sercaatpase Long - timeseries visualization

Trajectories of PLB Dephosph, Ca Serca, LTRPN, and Ca Cyt across the 1.0 simulation. In this run PLB Dephosph climbed from 0.1000 to 0.5678 and Ca Serca fell from 5.000 to 4.795 — the largest movements among the focused observables.

Koivumaki2009 Sercaatpase Long - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: PLB Dephosph = 0.4678, Ca Serca = 0.2058, LTRPN = 0.0255, with 1 more observable below.

Koivumaki2009 Sercaatpase Long - endpoint snapshot bar

Endpoint snapshot of the focused observables — final values from the captured run. Top 3 by value: LTRPN = 10.982, Ca Serca = 4.795, PLB Dephosph = 0.5678, with 1 more observable below.

Koivumaki2009 Sercaatpase Long - visualization

Visualization card from the Koivumaki2009 Sercaatpase Long dark-mode run.

Model Context

Core model: models/core
Visualization model: models/visualisation
Standard: other
Upstream source: biomodels_ebi:MODEL1006230105
License: CC0

Inputs

Input	Maps To	Notes
Initial Plb Dephosph	`systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.initial_plb_dephosph`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `PLB_dephosph`.
Initial Ltrpn	`systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.initial_ltrpn`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `LTRPN`.
Initial Ca Serca	`systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.initial_ca_serca`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Ca_serca`.
Initial Ca Cyt	`systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.initial_ca_cyt`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Ca_cyt`.

Outputs

Output	Maps To	Role
`state`	`systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.state`	Available to the visualization model and downstream workflows.
`summary`	`systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.summary`	Available to the visualization model and downstream workflows.
`species_labels`	`systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.species_labels`	Available to the visualization model and downstream workflows.
`plb_dephosph`	`systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.plb_dephosph`	Available to the visualization model and downstream workflows.
`ltrpn`	`systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.ltrpn`	Available to the visualization model and downstream workflows.
`ca_serca`	`systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.ca_serca`	Available to the visualization model and downstream workflows.
`ca_cyt`	`systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.ca_cyt`	Available to the visualization model and downstream workflows.

Runtime

Duration: 1.0
Communication step: 0.1

Running Locally

biosimulant labs serve

This a model from the article: Modelling sarcoplasmic reticulum calcium ATPase and its regulation in cardiacmyocytes. Koivumaki JT, Takalo J, Korhonen T, Tavi P, Weckstrom M.

Runtime

Duration1

Comms Step0.1

Runs

Total0

Completed0

Failed0

Metadata

Packagekoivumaki2009-sercaatpase-long-lab

Created2026-05-17

Updated2026-05-17

cardiovascularmetabolismphysiologysystemsbiologysbmlbiomodels_ebifaithfulcuratedvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_plb_dephosph",
        "label": "Initial Plb Dephosph",
        "maps_to": "systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.initial_plb_dephosph",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `PLB_dephosph`."
      },
      {
        "name": "initial_ltrpn",
        "label": "Initial Ltrpn",
        "maps_to": "systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.initial_ltrpn",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `LTRPN`."
      },
      {
        "name": "initial_ca_serca",
        "label": "Initial Ca Serca",
        "maps_to": "systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.initial_ca_serca",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Ca_serca`."
      },
      {
        "name": "initial_ca_cyt",
        "label": "Initial Ca Cyt",
        "maps_to": "systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.initial_ca_cyt",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Ca_cyt`."
      }
    ],
    "outputs": [
      {
        "name": "state",
        "maps_to": "systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.state"
      },
      {
        "name": "summary",
        "maps_to": "systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.summary"
      },
      {
        "name": "species_labels",
        "maps_to": "systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.species_labels"
      },
      {
        "name": "plb_dephosph",
        "maps_to": "systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.plb_dephosph"
      },
      {
        "name": "ltrpn",
        "maps_to": "systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.ltrpn"
      },
      {
        "name": "ca_serca",
        "maps_to": "systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.ca_serca"
      },
      {
        "name": "ca_cyt",
        "maps_to": "systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.ca_cyt"
      }
    ]
  },
  "tags": [
    "cardiovascular",
    "metabolism",
    "physiology",
    "systemsbiology",
    "sbml",
    "biomodels_ebi",
    "faithful",
    "curated"
  ],
  "title": "Koivumaki2009 Sercaatpase Long Lab",
  "models": [
    {
      "path": "owned/models/systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model",
      "alias": "systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model",
      "provenance": {
        "owned_path": "owned/models/systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model_state"
      ],
      "from": "systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.state"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model_summary"
      ],
      "from": "systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.summary"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model_species_labels"
      ],
      "from": "systemsbiology_sbml_koivumaki2009_sercaatpase_long_model1006230105_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "This a model from the article: Modelling sarcoplasmic reticulum calcium ATPase and its regulation in cardiacmyocytes. Koivumaki JT, Takalo J, Korhonen T, Tavi P, Weckstrom M.",
  "schema_version": "2.0"
}

Select a run from History to view its results.