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Chickarmane2008 Stem Cell Lineage Determination Lab

About lab

Chickarmane2008 Stem Cell Lineage Determination

This Biosimulant lab wraps Chickarmane2008 Stem Cell Lineage Determination as a runnable systems biology model with a companion visualization module. Chickarmane2008 - Stem cell lineage determination In this work, a dynamical model of lineage determination based upon a minimal circuit, as discussed in PMID: 17215298 , which contains the Oct4/Sox2/N. 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: Chickarmane2008 - Stem cell lineage determination. 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 TargetGene, SOX2 Gene, Protein, OCT4 Gene, NANOG Gene, and GCNF Gene, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, TargetGene moved from 0.0100 to 0.0100 across 1.0 simulation windows.

Output Visualizations

Chickarmane2008 Stem Cell Lineage Determination - run interpretation

Summary table for Chickarmane2008 Stem Cell Lineage Determination, reporting the scientific question, observed answer, dominant module, and caveat.

Chickarmane2008 Stem Cell Lineage Determination - timeseries visualization

Trajectories of TargetGene, SOX2 Gene, Protein, OCT4 Gene, NANOG Gene, and GCNF Gene across the 1.0 simulation. In this run TargetGene, SOX2 Gene, Protein, OCT4 Gene stayed near their initial values — no observable moved appreciably.

Chickarmane2008 Stem Cell Lineage Determination - endpoint snapshot bar

Endpoint snapshot of the focused observables — final values from the captured run. Top 1 by value: TargetGene = 0.0100.

Model Context

  • Core model: models/core
  • Visualization model: models/visualisation
  • Standard: other
  • Upstream source: biomodels_ebi:BIOMD0000000209
  • License: CC0

Inputs

InputMaps ToDefaultNotes
Initial Target Genesystemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.initial_target_geneSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol targetGene.
Initial Sox2 Genesystemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.initial_sox2_geneSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol SOX2_Gene.
Initial Proteinsystemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.initial_proteinSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol Protein.
Initial Oct4 Genesystemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.initial_oct4_geneSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol OCT4_Gene.
Initial Nanog Genesystemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.initial_nanog_geneSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol NANOG_Gene.
Initial Gcnf Genesystemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.initial_gcnf_geneSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol GCNF_Gene.

Outputs

OutputMaps ToRole
statesystemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.stateAvailable to the visualization model and downstream workflows.
summarysystemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.summaryAvailable to the visualization model and downstream workflows.
species_labelssystemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.species_labelsAvailable to the visualization model and downstream workflows.
target_genesystemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.target_geneAvailable to the visualization model and downstream workflows.
sox2_genesystemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.sox2_geneAvailable to the visualization model and downstream workflows.
proteinsystemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.proteinAvailable to the visualization model and downstream workflows.
oct4_genesystemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.oct4_geneAvailable to the visualization model and downstream workflows.
nanog_genesystemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.nanog_geneAvailable to the visualization model and downstream workflows.
gcnf_genesystemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.gcnf_geneAvailable to the visualization model and downstream workflows.

Runtime

  • Duration: 1.0
  • Communication step: 0.1

Running Locally

biosimulant labs serve

Chickarmane2008 - Stem cell lineage determination In this work, a dynamical model of lineage determination based upon a minimal circuit, as discussed in PMID: 17215298 , which contains the Oct4/Sox2/N. It can be used to explore systemsbiology chickarmane2008 stem cell lineage determination dynamics and compare simulation behavior across conditions.

Runtime

Duration1
Comms Step0.1

Runs

Total0
Completed0
Failed0

Metadata

Packagechickarmane2008-stem-cell-lineage-determination-lab
Created2026-05-17
Updated2026-05-17
developmentsystemsbiologysbmlbiomodels_ebifaithfulcuratedvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_target_gene",
        "label": "Initial Target Gene",
        "maps_to": "systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.initial_target_gene",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `targetGene`."
      },
      {
        "name": "initial_sox2_gene",
        "label": "Initial Sox2 Gene",
        "maps_to": "systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.initial_sox2_gene",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `SOX2_Gene`."
      },
      {
        "name": "initial_protein",
        "label": "Initial Protein",
        "maps_to": "systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.initial_protein",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Protein`."
      },
      {
        "name": "initial_oct4_gene",
        "label": "Initial Oct4 Gene",
        "maps_to": "systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.initial_oct4_gene",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `OCT4_Gene`."
      },
      {
        "name": "initial_nanog_gene",
        "label": "Initial Nanog Gene",
        "maps_to": "systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.initial_nanog_gene",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `NANOG_Gene`."
      },
      {
        "name": "initial_gcnf_gene",
        "label": "Initial Gcnf Gene",
        "maps_to": "systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.initial_gcnf_gene",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `GCNF_Gene`."
      }
    ],
    "outputs": [
      {
        "name": "state",
        "maps_to": "systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.state"
      },
      {
        "name": "summary",
        "maps_to": "systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.summary"
      },
      {
        "name": "species_labels",
        "maps_to": "systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.species_labels"
      },
      {
        "name": "target_gene",
        "maps_to": "systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.target_gene"
      },
      {
        "name": "sox2_gene",
        "maps_to": "systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.sox2_gene"
      },
      {
        "name": "protein",
        "maps_to": "systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.protein"
      },
      {
        "name": "oct4_gene",
        "maps_to": "systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.oct4_gene"
      },
      {
        "name": "nanog_gene",
        "maps_to": "systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.nanog_gene"
      },
      {
        "name": "gcnf_gene",
        "maps_to": "systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.gcnf_gene"
      }
    ]
  },
  "tags": [
    "development",
    "systemsbiology",
    "sbml",
    "biomodels_ebi",
    "faithful",
    "curated"
  ],
  "title": "Chickarmane2008 Stem Cell Lineage Determination Lab",
  "models": [
    {
      "path": "owned/models/systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model",
      "alias": "systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model",
      "provenance": {
        "owned_path": "owned/models/systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model_state"
      ],
      "from": "systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.state"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model_summary"
      ],
      "from": "systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.summary"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model_species_labels"
      ],
      "from": "systemsbiology_sbml_chickarmane2008_stem_cell_lineage_determination_biomd0000000209_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "Chickarmane2008 - Stem cell lineage determination In this work, a dynamical model of lineage determination based upon a minimal circuit, as discussed in PMID: 17215298 , which contains the Oct4/Sox2/N. It can be used to explore systemsbiology chickarmane2008 stem cell lineage determination dynamics and compare simulation behavior across conditions.",
  "schema_version": "2.0"
}

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