Neumann2010_CD95Stimulation_NFkB_Apoptosis Lab

About lab

Neumann2010_CD95Stimulation_NFkB_Apoptosis

This Biosimulant lab wraps Neumann2010_CD95Stimulation_NFkB_Apoptosis as a runnable signaling model with a companion visualization module. Clean Biosimulant lab for NF-kB pathway signaling. It can be used to explore second-messenger and pathway-signaling dynamics and compare scenario outcomes across configurations.

What You'll See

The lab asks: How does Neumann2010 CD95Stimulation NFkB Apoptosis move NF-kB and inhibitor-linked signaling states? 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 source-defined L state, source-defined L_RF state, source-defined L_RF_C8 state, L RF FL, L RF FS, and P43 P41, and related outputs, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, source-defined L state moved from 113.2 to 21.954 across 1.0 simulation windows.

Output Visualizations

Neumann2010_CD95Stimulation_NFkB_Apoptosis - run interpretation

Summary table for Neumann2010_CD95Stimulation_NFkB_Apoptosis, reporting the scientific question, observed answer, dominant module, and caveat.

Neumann2010_CD95Stimulation_NFkB_Apoptosis - timeseries visualization

Trajectories of source-defined L state, source-defined RF state, source-defined L:RF state, source-defined FL state, source-defined FS state, and L RF FL FS across the 1.0 simulation. In this run source-defined L:RF state climbed from 0 to 83.726 and source-defined L state fell from 113.2 to 21.954 — the largest movements among the focused observables.

Neumann2010_CD95Stimulation_NFkB_Apoptosis - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: source-defined L:RF state = 83.726, source-defined C8 state = 63.763, source-defined L state = 21.954, with 7 more observables below.

Model Context

Core model: models/core
Visualization model: models/visualisation
Standard: other
Upstream source: biomodels_ebi:BIOMD0000000243
License: CC0
Visual scope: NF-kB activation and feedback signaling
Caveat: Values are native SBML quantities; equations, parameters, units, and initial values remain in the bundled source file.

Inputs

Input	Maps To	Default	Notes
Initial source-defined L state	`signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model.initial_source_defined_l_state`		Initial level of source-defined L state. Maps to SBML symbol `L`; exposed as a traceable initial-condition perturbation.

Outputs

Output	Maps To	Role
`nf_k_b_ik_b`	`signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model.nf_k_b_ik_b`	NF K B Ik B.
`nf_k_b_ik_b_p`	`signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model.nf_k_b_ik_b_p`	NF K B Ik B P.
`nfkb`	`signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model.nfkb`	NF-kB.
`state`	`signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model.state`	Available to the visualization model and downstream workflows.
`summary`	`signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model.summary`	Available to the visualization model and downstream workflows.
`species_labels`	`signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model.species_labels`	Available to the visualization model and downstream workflows.

Runtime

Duration: 1.0
Communication step: 0.1

Running Locally

biosimulant labs serve .

Clean Biosimulant lab for NF-kB pathway signaling. Values are native SBML quantities; equations, parameters, and initial values remain in the bundled source file.

Runtime

Duration1

Comms Step0.1

Runs

Total0

Completed0

Failed0

Metadata

Packageneumann2010-cd95stimulation-nfkb-apoptosis-lab

Created2026-05-16

Updated2026-05-16

signalingsystemssystems-biologysbmlfaithfulbiomodels_ebinfkbapoptosisvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_source_defined_l_state",
        "label": "Initial source-defined L state",
        "maps_to": "signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model.initial_source_defined_l_state",
        "description": "Initial level of source-defined L state. Maps to SBML symbol `L`; exposed as a traceable initial-condition perturbation."
      }
    ],
    "outputs": [
      {
        "name": "nf_k_b_ik_b",
        "label": "NF K B Ik B",
        "maps_to": "signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model.nf_k_b_ik_b",
        "description": "NF K B Ik B. Maps to SBML symbol `NF_kB_IkB` and is emitted in native SBML units."
      },
      {
        "name": "nf_k_b_ik_b_p",
        "label": "NF K B Ik B P",
        "maps_to": "signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model.nf_k_b_ik_b_p",
        "description": "NF K B Ik B P. Maps to SBML symbol `NF_kB_IkB_P` and is emitted in native SBML units."
      },
      {
        "name": "nfkb",
        "label": "NF-kB",
        "maps_to": "signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model.nfkb",
        "description": "NF-kB. Maps to SBML symbol `NF_kB_star` and is emitted in native SBML units."
      },
      {
        "name": "state",
        "label": "Observable state",
        "maps_to": "signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation summary",
        "maps_to": "signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model.summary"
      },
      {
        "name": "species_labels",
        "label": "Observable labels",
        "maps_to": "signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model.species_labels"
      }
    ]
  },
  "tags": [
    "signaling",
    "systems",
    "systems-biology",
    "sbml",
    "faithful",
    "biomodels_ebi",
    "nfkb",
    "apoptosis"
  ],
  "title": "Neumann2010_CD95Stimulation_NFkB_Apoptosis Lab",
  "models": [
    {
      "path": "owned/models/signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model",
      "alias": "signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model",
      "provenance": {
        "owned_path": "owned/models/signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model_state"
      ],
      "from": "signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model.state"
    },
    {
      "to": [
        "visualisation.signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model_summary"
      ],
      "from": "signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model.summary"
    },
    {
      "to": [
        "visualisation.signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model_species_labels"
      ],
      "from": "signaling_sbml_neumann2010_cd95stimulation_nfkb_apoptosis_biomd0000000243_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "Clean Biosimulant lab for NF-kB pathway signaling. Values are native SBML quantities; equations, parameters, and initial values remain in the bundled source file.",
  "schema_version": "2.0"
}

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