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BIOMD0000000524 Variant Kallenberger2014 Cd95l Induced Apoptosis Initiated By Caspase 8 Wild Type H Lab

About lab

Kallenberger2014 Cd95l Induced Apoptosis Initiated By Caspase 8 Wild Type H (BIOMD0000000524)

This Biosimulant lab wraps BIOMD0000000524 Kallenberger2014 Cd95l Induced Apoptosis Initiated By Caspase 8 Wild Type H as a runnable systems biology model with a companion visualization module. Kallenberger2014 - CD95L induced apoptosis initiated by caspase-8, wild-type HeLa cells (cis/trans variant) The paper describes a new approach that combines single cell and population data in the same. It can be used to explore the configured dynamics and compare scenario outcomes across configurations.

What You'll See

The lab asks: Which source-defined system states dominate this SBML model trajectory? Source model: Kallenberger2014 - CD95L induced apoptosis initiated by caspase-8, wild-type HeLa cells (cis/trans variant). 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 PrER_mGFP, PrNES_mCherry, p55free, tBid, p43, and p30, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, p55free moved from 127.0 to 127.0 across 1.0 simulation windows.

Output Visualizations

Kallenberger2014 Cd95l Induced Apoptosis Initiated By Caspase 8 Wild Type H - run interpretation

Summary table for Kallenberger2014 Cd95l Induced Apoptosis Initiated By Caspase 8 Wild Type H, reporting the scientific question, observed answer, dominant module, and caveat.

Kallenberger2014 Cd95l Induced Apoptosis Initiated By Caspase 8 Wild Type H - timeseries visualization

Trajectories of p55free, p30, p43, PrNES_mCherry, tBid, and PrER_mGFP across the 1.0 simulation. In this run p30 climbed from 0 to 3.05e-05 and p55free fell from 127.0 to 127.0 — the largest movements among the focused observables.

Kallenberger2014 Cd95l Induced Apoptosis Initiated By Caspase 8 Wild Type H - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: p55free = 0.00887, p30 = 3.05e-05, p43 = 6.34e-09, with 3 more observables below.

Kallenberger2014 Cd95l Induced Apoptosis Initiated By Caspase 8 Wild Type H - endpoint snapshot bar

Endpoint snapshot of the focused observables — final values from the captured run. Top 3 by value: PrER_mGFP = 3316.0, PrNES_mCherry = 1909.0, p55free = 127.0, with 3 more observables below.

Kallenberger2014 Cd95l Induced Apoptosis Initiated By Caspase 8 Wild Type H - visualization

Visualization card from the Kallenberger2014 Cd95l Induced Apoptosis Initiated By Caspase 8 Wild Type H dark-mode run.

Model Context

  • Core model: models/core
  • Visualization model: models/visualisation
  • Standard: other
  • Upstream source: biomodels_ebi:BIOMD0000000524
  • License: CC0

Inputs

InputMaps ToDefaultNotes
Initial Pr Er M Gfpsystemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.initial_pr_er_m_gfpSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol PrER_mGFP.
Initial Pr Nes M Cherrysystemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.initial_pr_nes_m_cherrySource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol PrNES_mCherry.
Initial P55freesystemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.initial_p55freeSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol p55free.
Initial T Bidsystemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.initial_t_bidSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol tBid.
Initial Model State P43systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.initial_model_state_p43Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol p43.
Initial Model State P30systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.initial_model_state_p30Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol p30.

Outputs

OutputMaps ToRole
statesystemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.stateAvailable to the visualization model and downstream workflows.
summarysystemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.summaryAvailable to the visualization model and downstream workflows.
species_labelssystemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.species_labelsAvailable to the visualization model and downstream workflows.
pr_er_m_gfpsystemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.pr_er_m_gfpAvailable to the visualization model and downstream workflows.
pr_nes_m_cherrysystemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.pr_nes_m_cherryAvailable to the visualization model and downstream workflows.
p55freesystemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.p55freeAvailable to the visualization model and downstream workflows.
t_bidsystemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.t_bidAvailable to the visualization model and downstream workflows.
p43systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.p43Available to the visualization model and downstream workflows.
p30systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.p30Available to the visualization model and downstream workflows.

Runtime

  • Duration: 1.0
  • Communication step: 0.1

Running Locally

biosimulant labs serve

Kallenberger2014 - CD95L induced apoptosis initiated by caspase-8, wild-type HeLa cells (cis/trans variant) The paper describes a new approach that combines single cell and population data in the same. It can be used to explore systemsbiology kallenberger2014 cd95l induced apoptosis initiat dynamics and compare simulation behavior across conditions.

Runtime

Duration1
Comms Step0.1

Runs

Total0
Completed0
Failed0

Metadata

Packagebiomd0000000524-kallenberger2014-cd95l-induced-apoptosis-initiat
Created2026-05-17
Updated2026-05-17
systemsbiologysbmlbiomodels_ebifaithfulcuratedvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_pr_er_m_gfp",
        "label": "Initial Pr Er M Gfp",
        "maps_to": "systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.initial_pr_er_m_gfp",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `PrER_mGFP`."
      },
      {
        "name": "initial_pr_nes_m_cherry",
        "label": "Initial Pr Nes M Cherry",
        "maps_to": "systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.initial_pr_nes_m_cherry",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `PrNES_mCherry`."
      },
      {
        "name": "initial_p55free",
        "label": "Initial P55free",
        "maps_to": "systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.initial_p55free",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `p55free`."
      },
      {
        "name": "initial_t_bid",
        "label": "Initial T Bid",
        "maps_to": "systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.initial_t_bid",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `tBid`."
      },
      {
        "name": "initial_model_state_p43",
        "label": "Initial Model State P43",
        "maps_to": "systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.initial_model_state_p43",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `p43`."
      },
      {
        "name": "initial_model_state_p30",
        "label": "Initial Model State P30",
        "maps_to": "systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.initial_model_state_p30",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `p30`."
      }
    ],
    "outputs": [
      {
        "name": "state",
        "maps_to": "systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.state"
      },
      {
        "name": "summary",
        "maps_to": "systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.summary"
      },
      {
        "name": "species_labels",
        "maps_to": "systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.species_labels"
      },
      {
        "name": "pr_er_m_gfp",
        "maps_to": "systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.pr_er_m_gfp"
      },
      {
        "name": "pr_nes_m_cherry",
        "maps_to": "systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.pr_nes_m_cherry"
      },
      {
        "name": "p55free",
        "maps_to": "systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.p55free"
      },
      {
        "name": "t_bid",
        "maps_to": "systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.t_bid"
      },
      {
        "name": "p43",
        "maps_to": "systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.p43"
      },
      {
        "name": "p30",
        "maps_to": "systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.p30"
      }
    ]
  },
  "tags": [
    "systemsbiology",
    "sbml",
    "biomodels_ebi",
    "faithful",
    "curated"
  ],
  "title": "BIOMD0000000524 Variant Kallenberger2014 Cd95l Induced Apoptosis Initiated By Caspase 8 Wild Type H Lab",
  "models": [
    {
      "path": "owned/models/systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model",
      "alias": "systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model",
      "provenance": {
        "owned_path": "owned/models/systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model_state"
      ],
      "from": "systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.state"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model_summary"
      ],
      "from": "systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.summary"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model_species_labels"
      ],
      "from": "systemsbiology_sbml_kallenberger2014_cd95l_induced_apoptosis_initiat_biomd0000000524_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "Kallenberger2014 - CD95L induced apoptosis initiated by caspase-8, wild-type HeLa cells (cis/trans variant) The paper describes a new approach that combines single cell and population data in the same. It can be used to explore systemsbiology kallenberger2014 cd95l induced apoptosis initiat dynamics and compare simulation behavior across conditions.",
  "schema_version": "2.0"
}

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