Kok2020 - IFNalpha-induced signaling in Huh7.5 cells Lab

About lab

Kok2020 - IFNalpha-induced signaling in Huh7.5 cells

This Biosimulant lab wraps Kok2020 - IFNalpha-induced signaling in Huh7.5 cells as a runnable signaling model with a companion visualization module. Clean Biosimulant lab for systems signaling model: Kok2020 - IFNalpha-induced signaling in Huh7.5 cells. 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 Kok2020 - IFNalpha-induced signaling in Huh7.5 cells route receptor activity into cAMP/PKA-linked readouts? 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 REC state, source-defined SOCS1 state, source-defined IFNA state, A Rec Ifna, USP18, and Stat1c, and related outputs, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, STAT1c moved from 4.86e+05 to 4.48e+05 across 1.0 simulation windows.

Output Visualizations

Kok2020 - IFNalpha-induced signaling in Huh7.5 cells - run interpretation

Summary table for Kok2020 - IFNalpha-induced signaling in Huh7.5 cells, reporting the scientific question, observed answer, dominant module, and caveat.

Kok2020 - IFNalpha-induced signaling in Huh7.5 cells - timeseries visualization

Trajectories of STAT1c, STAT2c, phospho-STAT1pSTAT2c, STAT1 LC 1, STAT1n, and phospho-STAT1pSTAT2n across the 1.0 simulation. In this run phospho-STAT1pSTAT2c climbed from 0 to 2.76e+04 and STAT1c fell from 4.86e+05 to 4.48e+05 — the largest movements among the focused observables.

Kok2020 - IFNalpha-induced signaling in Huh7.5 cells - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: STAT1 LC 1 = 4.83e+05, STAT1 LC 2 = 4.63e+05, STAT1 LC 3 = 4.61e+05, with 7 more observables below.

Model Context

Core model: models/core
Visualization model: models/visualisation
Standard: other
Upstream source: biomodels_ebi:BIOMD0000000959
License: CC0
Visual scope: GPCR and cAMP/PKA signaling
Caveat: Values are native SBML quantities; equations, parameters, units, and initial values remain in the bundled source file.

Inputs

Input	Maps To	Notes
Bind IFN	`signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model.initial_bind_ifn_level`	Bind IFN source parameter. Maps to SBML symbol `BindIFN` and preserves the bundled default.
Dega Rec Ifnby SOCS	`signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model.initial_dega_rec_ifnby_socs_level`	Dega Rec Ifnby SOCS source parameter. Maps to SBML symbol `degaRecIFNBySOCS` and preserves the bundled default.
Initial A Rec Ifna	`signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model.initial_a_rec_ifna`	Initial level of A Rec Ifna. Maps to SBML symbol `aRecIFN`; exposed as a traceable initial-condition perturbation.

Outputs

Output	Maps To	Role
`stat1c`	`signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model.stat1c`	Stat1c.
`stat2c`	`signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model.stat2c`	Stat2c.
`p_stat1p_stat2c`	`signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model.p_stat1p_stat2c`	P Stat1p Stat2c.
`state`	`signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model.state`	Available to the visualization model and downstream workflows.
`summary`	`signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model.summary`	Available to the visualization model and downstream workflows.
`species_labels`	`signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_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 systems signaling model: Kok2020 - IFNalpha-induced signaling in Huh7.5 cells. 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

Packagekok2020-ifnalpha-induced-signaling-in-huh7-5-cells-lab

Created2026-05-16

Updated2026-05-16

signalingsystemssystems-biologysbmlfaithfulbiomodels_ebicytokine-signalinginterferon-signalinggpcrvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_bind_ifn_level",
        "label": "Bind IFN",
        "maps_to": "signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model.initial_bind_ifn_level",
        "description": "Bind IFN source parameter. Maps to SBML symbol `BindIFN` and preserves the bundled default."
      },
      {
        "name": "initial_dega_rec_ifnby_socs_level",
        "label": "Dega Rec Ifnby SOCS",
        "maps_to": "signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model.initial_dega_rec_ifnby_socs_level",
        "description": "Dega Rec Ifnby SOCS source parameter. Maps to SBML symbol `degaRecIFNBySOCS` and preserves the bundled default."
      },
      {
        "name": "initial_a_rec_ifna",
        "label": "Initial A Rec Ifna",
        "maps_to": "signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model.initial_a_rec_ifna",
        "description": "Initial level of A Rec Ifna. Maps to SBML symbol `aRecIFN`; exposed as a traceable initial-condition perturbation."
      }
    ],
    "outputs": [
      {
        "name": "stat1c",
        "label": "Stat1c",
        "maps_to": "signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model.stat1c",
        "description": "Stat1c. Maps to SBML symbol `STAT1c` and is emitted in native SBML units."
      },
      {
        "name": "stat2c",
        "label": "Stat2c",
        "maps_to": "signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model.stat2c",
        "description": "Stat2c. Maps to SBML symbol `STAT2c` and is emitted in native SBML units."
      },
      {
        "name": "p_stat1p_stat2c",
        "label": "P Stat1p Stat2c",
        "maps_to": "signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model.p_stat1p_stat2c",
        "description": "P Stat1p Stat2c. Maps to SBML symbol `pSTAT1pSTAT2c` and is emitted in native SBML units."
      },
      {
        "name": "state",
        "label": "Observable state",
        "maps_to": "signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation summary",
        "maps_to": "signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model.summary"
      },
      {
        "name": "species_labels",
        "label": "Observable labels",
        "maps_to": "signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model.species_labels"
      }
    ]
  },
  "tags": [
    "signaling",
    "systems",
    "systems-biology",
    "sbml",
    "faithful",
    "biomodels_ebi",
    "cytokine-signaling",
    "interferon-signaling",
    "gpcr"
  ],
  "title": "Kok2020 - IFNalpha-induced signaling in Huh7.5 cells Lab",
  "models": [
    {
      "path": "owned/models/signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model",
      "alias": "signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model",
      "provenance": {
        "owned_path": "owned/models/signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model_state"
      ],
      "from": "signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model.state"
    },
    {
      "to": [
        "visualisation.signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model_summary"
      ],
      "from": "signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model.summary"
    },
    {
      "to": [
        "visualisation.signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model_species_labels"
      ],
      "from": "signaling_sbml_kok2020_ifnalpha_induced_signaling_in_huh7_5_cel_biomd0000000959_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "Clean Biosimulant lab for systems signaling model: Kok2020 - IFNalpha-induced signaling in Huh7.5 cells. Values are native SBML quantities; equations, parameters, and initial values remain in the bundled source file.",
  "schema_version": "2.0"
}

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