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Bialik2010 Apoptosis Spikemodel Lab

About lab

Bialik2010 Apoptosis Spikemodel

This Biosimulant lab wraps Bialik2010 Apoptosis Spikemodel as a runnable systems biology model with a companion visualization module. This model is from the article: Systems biology analysis of programmed cell death Shani Bialik, Einat Zalckvar, Yaara Ber, Assaf D. 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: Bialik2010_Apoptosis_SPIKEmodel. 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 mRNA_XIAP, mRNA_EIF4G2, mRNA_CDK1, mRNA_BIRC2, mRNA_BCL2, and mRNA_APAF1, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, mRNA_XIAP moved from 0 to 0 across 1.0 simulation windows.

Output Visualizations

Bialik2010 Apoptosis Spikemodel - run interpretation

Summary table for Bialik2010 Apoptosis Spikemodel, reporting the scientific question, observed answer, dominant module, and caveat.

Bialik2010 Apoptosis Spikemodel - timeseries visualization

Trajectories of mRNA_XIAP, mRNA_EIF4G2, mRNA_CDK1, mRNA_BIRC2, mRNA_BCL2, and mRNA_APAF1 across the 1.0 simulation. In this run mRNA_XIAP, mRNA_EIF4G2, mRNA_CDK1, mRNA_BIRC2 stayed near their initial values — no observable moved appreciably.

Model Context

  • Core model: models/core
  • Visualization model: models/visualisation
  • Standard: other
  • Upstream source: biomodels_ebi:MODEL1107050000
  • License: CC0

Inputs

InputMaps ToDefaultNotes
Initial MRNA Xiapsystemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.initial_mrna_xiapSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol mRNA_XIAP.
Initial MRNA Eif4 G2systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.initial_mrna_eif4_g2Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol mRNA_EIF4G2.
Initial MRNA Cdk1systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.initial_mrna_cdk1Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol mRNA_CDK1.
Initial MRNA Birc2systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.initial_mrna_birc2Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol mRNA_BIRC2.
Initial MRNA Bcl2systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.initial_mrna_bcl2Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol mRNA_BCL2.
Initial MRNA Apaf1systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.initial_mrna_apaf1Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol mRNA_APAF1.

Outputs

OutputMaps ToRole
statesystemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.stateAvailable to the visualization model and downstream workflows.
summarysystemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.summaryAvailable to the visualization model and downstream workflows.
species_labelssystemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.species_labelsAvailable to the visualization model and downstream workflows.
mrna_xiapsystemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.mrna_xiapAvailable to the visualization model and downstream workflows.
mrna_eif4_g2systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.mrna_eif4_g2Available to the visualization model and downstream workflows.
mrna_cdk1systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.mrna_cdk1Available to the visualization model and downstream workflows.
mrna_birc2systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.mrna_birc2Available to the visualization model and downstream workflows.
mrna_bcl2systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.mrna_bcl2Available to the visualization model and downstream workflows.
mrna_apaf1systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.mrna_apaf1Available to the visualization model and downstream workflows.

Runtime

  • Duration: 1.0
  • Communication step: 0.1

Running Locally

biosimulant labs serve

This model is from the article: Systems biology analysis of programmed cell death Shani Bialik, Einat Zalckvar, Yaara Ber, Assaf D. Rubinstein, Adi Kimchi Trends in Biochemical Sciences Volume 35, Iss.

Runtime

Duration1
Comms Step0.1

Runs

Total0
Completed0
Failed0

Metadata

Packagebialik2010-apoptosis-spikemodel-lab
Created2026-05-17
Updated2026-05-17
systemsbiologysbmlbiomodels_ebifaithfulcuratedvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_mrna_xiap",
        "label": "Initial MRNA Xiap",
        "maps_to": "systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.initial_mrna_xiap",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `mRNA_XIAP`."
      },
      {
        "name": "initial_mrna_eif4_g2",
        "label": "Initial MRNA Eif4 G2",
        "maps_to": "systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.initial_mrna_eif4_g2",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `mRNA_EIF4G2`."
      },
      {
        "name": "initial_mrna_cdk1",
        "label": "Initial MRNA Cdk1",
        "maps_to": "systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.initial_mrna_cdk1",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `mRNA_CDK1`."
      },
      {
        "name": "initial_mrna_birc2",
        "label": "Initial MRNA Birc2",
        "maps_to": "systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.initial_mrna_birc2",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `mRNA_BIRC2`."
      },
      {
        "name": "initial_mrna_bcl2",
        "label": "Initial MRNA Bcl2",
        "maps_to": "systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.initial_mrna_bcl2",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `mRNA_BCL2`."
      },
      {
        "name": "initial_mrna_apaf1",
        "label": "Initial MRNA Apaf1",
        "maps_to": "systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.initial_mrna_apaf1",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `mRNA_APAF1`."
      }
    ],
    "outputs": [
      {
        "name": "state",
        "maps_to": "systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.state"
      },
      {
        "name": "summary",
        "maps_to": "systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.summary"
      },
      {
        "name": "species_labels",
        "maps_to": "systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.species_labels"
      },
      {
        "name": "mrna_xiap",
        "maps_to": "systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.mrna_xiap"
      },
      {
        "name": "mrna_eif4_g2",
        "maps_to": "systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.mrna_eif4_g2"
      },
      {
        "name": "mrna_cdk1",
        "maps_to": "systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.mrna_cdk1"
      },
      {
        "name": "mrna_birc2",
        "maps_to": "systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.mrna_birc2"
      },
      {
        "name": "mrna_bcl2",
        "maps_to": "systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.mrna_bcl2"
      },
      {
        "name": "mrna_apaf1",
        "maps_to": "systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.mrna_apaf1"
      }
    ]
  },
  "tags": [
    "systemsbiology",
    "sbml",
    "biomodels_ebi",
    "faithful",
    "curated"
  ],
  "title": "Bialik2010 Apoptosis Spikemodel Lab",
  "models": [
    {
      "path": "owned/models/systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model",
      "alias": "systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model",
      "provenance": {
        "owned_path": "owned/models/systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model_state"
      ],
      "from": "systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.state"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model_summary"
      ],
      "from": "systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.summary"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model_species_labels"
      ],
      "from": "systemsbiology_sbml_bialik2010_apoptosis_spikemodel_model1107050000_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "This model is from the article: Systems biology analysis of programmed cell death Shani Bialik, Einat Zalckvar, Yaara Ber, Assaf D. Rubinstein, Adi Kimchi Trends in Biochemical Sciences Volume 35, Iss.",
  "schema_version": "2.0"
}

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