Zymomonas ED Pathway Lab

About lab

Zymomonas ED Pathway

This Biosimulant lab wraps Zymomonas ED Pathway as a runnable signaling model with a companion visualization module. Clean Biosimulant lab for systems signaling model: Zymomonas ED Pathway. 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 Zymomonas ED Pathway shift hormone-linked signaling 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 Ethanolex, Glucex, Pyrex, Acetper, Acetex, and Co2per, and related outputs, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, Ethanolex moved from 0.2400 to 0.2482 across 1.0 simulation windows.

Output Visualizations

Zymomonas ED Pathway - run interpretation

Summary table for Zymomonas ED Pathway, reporting the scientific question, observed answer, dominant module, and caveat.

Zymomonas ED Pathway - timeseries visualization

Trajectories of Ethanolex, Co2per, Pyrcy, Acetcy, GLUC6P, and PGLACTON across the 1.0 simulation. In this run Ethanolex climbed from 0.2400 to 0.2482 and Co2per fell from 0.0182 to 0.0146 — the largest movements among the focused observables.

Zymomonas ED Pathway - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: Glucex = 33.600, Co2ex = 8.684, Acetper = 4.590, with 7 more observables below.

Model Context

Core model: models/core
Visualization model: models/visualisation
Standard: other
Upstream source: biomodels_ebi:MODEL2008060001
License: CC0
Visual scope: metabolic and hormone signaling response
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 Co2ex	`signaling_sbml_zymomonas_ed_pathway_model2008060001_model.initial_co2ex`		Initial level of Co2ex. Maps to SBML symbol `CO2ex`; exposed as a traceable initial-condition perturbation.
Initial Glucex	`signaling_sbml_zymomonas_ed_pathway_model2008060001_model.initial_glucex`		Initial level of Glucex. Maps to SBML symbol `GLUCex`; exposed as a traceable initial-condition perturbation.

Outputs

Output	Maps To	Role
`ethanolex`	`signaling_sbml_zymomonas_ed_pathway_model2008060001_model.ethanolex`	Ethanolex.
`glucex`	`signaling_sbml_zymomonas_ed_pathway_model2008060001_model.glucex`	Glucex.
`pyrex`	`signaling_sbml_zymomonas_ed_pathway_model2008060001_model.pyrex`	Pyrex.
`state`	`signaling_sbml_zymomonas_ed_pathway_model2008060001_model.state`	Available to the visualization model and downstream workflows.
`summary`	`signaling_sbml_zymomonas_ed_pathway_model2008060001_model.summary`	Available to the visualization model and downstream workflows.
`species_labels`	`signaling_sbml_zymomonas_ed_pathway_model2008060001_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: Zymomonas ED Pathway. 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

Packagezymomonas-ed-pathway-lab

Created2026-05-16

Updated2026-05-16

signalingsystemssystems-biologysbmlfaithfulbiomodels_ebicellular-signalingvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_co2ex",
        "label": "Initial Co2ex",
        "maps_to": "signaling_sbml_zymomonas_ed_pathway_model2008060001_model.initial_co2ex",
        "description": "Initial level of Co2ex. Maps to SBML symbol `CO2ex`; exposed as a traceable initial-condition perturbation."
      },
      {
        "name": "initial_glucex",
        "label": "Initial Glucex",
        "maps_to": "signaling_sbml_zymomonas_ed_pathway_model2008060001_model.initial_glucex",
        "description": "Initial level of Glucex. Maps to SBML symbol `GLUCex`; exposed as a traceable initial-condition perturbation."
      }
    ],
    "outputs": [
      {
        "name": "ethanolex",
        "label": "Ethanolex",
        "maps_to": "signaling_sbml_zymomonas_ed_pathway_model2008060001_model.ethanolex",
        "description": "Ethanolex. Maps to SBML symbol `ETHANOLex` and is emitted in native SBML units."
      },
      {
        "name": "glucex",
        "label": "Glucex",
        "maps_to": "signaling_sbml_zymomonas_ed_pathway_model2008060001_model.glucex",
        "description": "Glucex. Maps to SBML symbol `GLUCex` and is emitted in native SBML units."
      },
      {
        "name": "pyrex",
        "label": "Pyrex",
        "maps_to": "signaling_sbml_zymomonas_ed_pathway_model2008060001_model.pyrex",
        "description": "Pyrex. Maps to SBML symbol `PYRex` and is emitted in native SBML units."
      },
      {
        "name": "state",
        "label": "Observable state",
        "maps_to": "signaling_sbml_zymomonas_ed_pathway_model2008060001_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation summary",
        "maps_to": "signaling_sbml_zymomonas_ed_pathway_model2008060001_model.summary"
      },
      {
        "name": "species_labels",
        "label": "Observable labels",
        "maps_to": "signaling_sbml_zymomonas_ed_pathway_model2008060001_model.species_labels"
      }
    ]
  },
  "tags": [
    "signaling",
    "systems",
    "systems-biology",
    "sbml",
    "faithful",
    "biomodels_ebi",
    "cellular-signaling"
  ],
  "title": "Zymomonas ED Pathway Lab",
  "models": [
    {
      "path": "owned/models/signaling_sbml_zymomonas_ed_pathway_model2008060001_model",
      "alias": "signaling_sbml_zymomonas_ed_pathway_model2008060001_model",
      "provenance": {
        "owned_path": "owned/models/signaling_sbml_zymomonas_ed_pathway_model2008060001_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.signaling_sbml_zymomonas_ed_pathway_model2008060001_model_state"
      ],
      "from": "signaling_sbml_zymomonas_ed_pathway_model2008060001_model.state"
    },
    {
      "to": [
        "visualisation.signaling_sbml_zymomonas_ed_pathway_model2008060001_model_summary"
      ],
      "from": "signaling_sbml_zymomonas_ed_pathway_model2008060001_model.summary"
    },
    {
      "to": [
        "visualisation.signaling_sbml_zymomonas_ed_pathway_model2008060001_model_species_labels"
      ],
      "from": "signaling_sbml_zymomonas_ed_pathway_model2008060001_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "Clean Biosimulant lab for systems signaling model: Zymomonas ED Pathway. Values are native SBML quantities; equations, parameters, and initial values remain in the bundled source file.",
  "schema_version": "2.0"
}

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