Schmitz2014 Rna Triplex Formation Lab

About lab

Schmitz2014 Rna Triplex Formation

This Biosimulant lab wraps Schmitz2014 Rna Triplex Formation as a runnable systems biology model with a companion visualization module. Schmitz2014 - RNA triplex formation The model is parameterized using theparameters for gene CCDC3 from Supplementary Table S1. It can be used to explore the configured dynamics and compare scenario outcomes across configurations.

What You'll See

The lab asks: Which gene-regulatory states dominate the source model trajectory? Source model: Schmitz2014 - RNA triplex formation. 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 protein, mRNA, TF_miRNA_2, TF_miRNA_1, TF_mRNA, and triplex, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, mRNA moved from 1.000 to 0.9223 across 1.0 simulation windows.

Output Visualizations

Schmitz2014 Rna Triplex Formation - run interpretation

Summary table for Schmitz2014 Rna Triplex Formation, reporting the scientific question, observed answer, dominant module, and caveat.

Schmitz2014 Rna Triplex Formation - timeseries visualization

Trajectories of mRNA, triplex, protein, TF_miRNA_2, TF_miRNA_1, and TF_mRNA across the 1.0 simulation. In this run triplex climbed from 0 to 0.0776 and mRNA fell from 1.000 to 0.9223 — the largest movements among the focused observables.

Schmitz2014 Rna Triplex Formation - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: mRNA = 0.0777, triplex = 0.0776, protein = 0.0187.

Schmitz2014 Rna Triplex Formation - endpoint snapshot bar

Endpoint snapshot of the focused observables — final values from the captured run. Top 3 by value: TF_miRNA_2 = 1.000, TF_miRNA_1 = 1.000, TF_mRNA = 1.000, with 3 more observables below.

Schmitz2014 Rna Triplex Formation - visualization

Visualization card from the Schmitz2014 Rna Triplex Formation dark-mode run.

Model Context

Core model: models/core
Visualization model: models/visualisation
Standard: other
Upstream source: biomodels_ebi:BIOMD0000000530
License: CC0

Inputs

Input	Maps To	Notes
Initial Protein	`systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.initial_protein`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_10`.
Initial MRNA	`systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.initial_mrna`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_1`.
Initial Tf Mi RNA 2	`systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.initial_tf_mi_rna_2`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_9`.
Initial Tf Mi RNA 1	`systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.initial_tf_mi_rna_1`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_8`.
Initial Tf MRNA	`systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.initial_tf_mrna`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_7`.
Initial Triplex	`systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.initial_triplex`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_6`.

Outputs

Output	Maps To	Role
`state`	`systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.state`	Available to the visualization model and downstream workflows.
`summary`	`systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.summary`	Available to the visualization model and downstream workflows.
`species_labels`	`systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.species_labels`	Available to the visualization model and downstream workflows.
`protein`	`systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.protein`	Available to the visualization model and downstream workflows.
`mrna`	`systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.mrna`	Available to the visualization model and downstream workflows.
`tf_mi_rna_2`	`systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.tf_mi_rna_2`	Available to the visualization model and downstream workflows.
`tf_mi_rna_1`	`systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.tf_mi_rna_1`	Available to the visualization model and downstream workflows.
`tf_mrna`	`systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.tf_mrna`	Available to the visualization model and downstream workflows.
`triplex`	`systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.triplex`	Available to the visualization model and downstream workflows.

Runtime

Duration: 1.0
Communication step: 0.1

Running Locally

biosimulant labs serve

Schmitz2014 - RNA triplex formation The model is parameterized using theparameters for gene CCDC3 from Supplementary Table S1. It can be used to explore systemsbiology schmitz2014 rna triplex formation BioModels0000000530 dynamics and compare simulation behavior across conditions.

Runtime

Duration1

Comms Step0.1

Runs

Total0

Completed0

Failed0

Metadata

Packageschmitz2014-rna-triplex-formation-lab

Created2026-05-17

Updated2026-05-17

generegulationsystemsbiologysbmlbiomodels_ebifaithfulcuratedvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_protein",
        "label": "Initial Protein",
        "maps_to": "systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_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 `species_10`."
      },
      {
        "name": "initial_mrna",
        "label": "Initial MRNA",
        "maps_to": "systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.initial_mrna",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_1`."
      },
      {
        "name": "initial_tf_mi_rna_2",
        "label": "Initial Tf Mi RNA 2",
        "maps_to": "systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.initial_tf_mi_rna_2",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_9`."
      },
      {
        "name": "initial_tf_mi_rna_1",
        "label": "Initial Tf Mi RNA 1",
        "maps_to": "systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.initial_tf_mi_rna_1",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_8`."
      },
      {
        "name": "initial_tf_mrna",
        "label": "Initial Tf MRNA",
        "maps_to": "systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.initial_tf_mrna",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_7`."
      },
      {
        "name": "initial_triplex",
        "label": "Initial Triplex",
        "maps_to": "systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.initial_triplex",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_6`."
      }
    ],
    "outputs": [
      {
        "name": "state",
        "maps_to": "systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.state"
      },
      {
        "name": "summary",
        "maps_to": "systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.summary"
      },
      {
        "name": "species_labels",
        "maps_to": "systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.species_labels"
      },
      {
        "name": "protein",
        "maps_to": "systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.protein"
      },
      {
        "name": "mrna",
        "maps_to": "systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.mrna"
      },
      {
        "name": "tf_mi_rna_2",
        "maps_to": "systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.tf_mi_rna_2"
      },
      {
        "name": "tf_mi_rna_1",
        "maps_to": "systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.tf_mi_rna_1"
      },
      {
        "name": "tf_mrna",
        "maps_to": "systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.tf_mrna"
      },
      {
        "name": "triplex",
        "maps_to": "systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.triplex"
      }
    ]
  },
  "tags": [
    "generegulation",
    "systemsbiology",
    "sbml",
    "biomodels_ebi",
    "faithful",
    "curated"
  ],
  "title": "Schmitz2014 Rna Triplex Formation Lab",
  "models": [
    {
      "path": "owned/models/systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model",
      "alias": "systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model",
      "provenance": {
        "owned_path": "owned/models/systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model_state"
      ],
      "from": "systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.state"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model_summary"
      ],
      "from": "systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.summary"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model_species_labels"
      ],
      "from": "systemsbiology_sbml_schmitz2014_rna_triplex_formation_biomd0000000530_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "Schmitz2014 - RNA triplex formation The model is parameterized using theparameters for gene CCDC3 from Supplementary Table S1. It can be used to explore systemsbiology schmitz2014 rna triplex formation BioModels0000000530 dynamics and compare simulation behavior across conditions.",
  "schema_version": "2.0"
}

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