Conant2007_glycolysis_2C Lab

About lab

Conant2007 glycolysis 2C Lab

Curated microbiology lab for Conant2007_glycolysis_2C. The bundled SBML is executed directly through Tellurium and visualised with conservative, source-traceable labels.

This lab asks: Which glycolytic state changes most strongly in the bundled SBML run?

Model Context

The core model executes the bundled sbml source through Biosimulant and publishes traceable state, summary, and observable ports. The visualisation model turns those ports into dark-mode run cards for quick inspection of microbiology dynamics.

Scope: metabolic pathway dynamics.

Caveat: The bundled SBML is the executable source of truth; labels are conservative where source symbols are ambiguous.

Run Context

Duration: 10
Communication step: 0.01
Initial inputs: lab defaults

Primary Inputs

External Glucose (GLCo)
Fructose 26 Bisphosphate Pool (F26bP)

Primary Outputs

Model state (state)
Simulation summary (summary)
Observable labels (species_labels)
GLCi (GLCi)
ATP (ATP)
G6P (G6P)
ADP (ADP)

Model Wiring

conant2007_glycolysis_2c uses models/core
visualisation uses models/visualisation
conant2007_glycolysis_2c.state -> visualisation.conant2007_glycolysis_2c_state
conant2007_glycolysis_2c.summary -> visualisation.conant2007_glycolysis_2c_summary
conant2007_glycolysis_2c.species_labels -> visualisation.conant2007_glycolysis_2c_species_labels
conant2007_glycolysis_2c.intracellular_glucose -> visualisation.conant2007_glycolysis_2c_intracellular_glucose
conant2007_glycolysis_2c.atp -> visualisation.conant2007_glycolysis_2c_atp
conant2007_glycolysis_2c.glucose_6_phosphate -> visualisation.conant2007_glycolysis_2c_glucose_6_phosphate
conant2007_glycolysis_2c.adp -> visualisation.conant2007_glycolysis_2c_adp

Output Visualizations

visualisation table

The summary table records the numeric run outputs used to answer the lab question: Which glycolytic state changes most strongly in the bundled SBML run?

visualisation table

visualisation timeseries

The time-series view follows GLCi, ATP, G6P, ADP through the simulated run so the transient and final microbial dynamics are visible in one panel.

visualisation timeseries

visualisation bar

The comparison view ranks the headline outputs from this run, making the dominant endpoint responses easy to scan.

visualisation bar

Source and Dependencies

Core model: models/core
Visualisation model: models/visualisation
Upstream source: biomodels_ebi:BIOMD0000000177
Upstream URL: https://www.ebi.ac.uk/biomodels/BIOMD0000000177
License: CC0
Runtime packages: tellurium==2.2.11.2

Running in Biosimulant

Open this folder as a Biosimulant lab, then run the canvas. The screenshots above were captured from the served lab UI in dark mode using the automated README visualisation workflow.

Curated microbiology lab for Conant2007_glycolysis_2C. The bundled SBML is executed directly through Tellurium and visualised with conservative, source-traceable labels.

Runtime

Duration10

Comms Step0.01

Runs

Total0

Completed0

Failed0

Metadata

Packageconant2007-glycolysis-2c-lab

Created2026-05-15

Updated2026-05-15

microbiologysbmlbiomodels_ebifaithfultelluriumvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "external_glucose",
        "maps_to": "conant2007_glycolysis_2c.external_glucose"
      },
      {
        "name": "fructose_26_bisphosphate_pool",
        "maps_to": "conant2007_glycolysis_2c.fructose_26_bisphosphate_pool"
      }
    ],
    "outputs": [
      {
        "name": "state",
        "maps_to": "conant2007_glycolysis_2c.state"
      },
      {
        "name": "summary",
        "maps_to": "conant2007_glycolysis_2c.summary"
      },
      {
        "name": "species_labels",
        "maps_to": "conant2007_glycolysis_2c.species_labels"
      },
      {
        "name": "intracellular_glucose",
        "maps_to": "conant2007_glycolysis_2c.intracellular_glucose"
      },
      {
        "name": "atp",
        "maps_to": "conant2007_glycolysis_2c.atp"
      },
      {
        "name": "glucose_6_phosphate",
        "maps_to": "conant2007_glycolysis_2c.glucose_6_phosphate"
      },
      {
        "name": "adp",
        "maps_to": "conant2007_glycolysis_2c.adp"
      }
    ]
  },
  "title": "Conant2007_glycolysis_2C Lab",
  "models": [
    {
      "path": "owned/models/conant2007_glycolysis_2c",
      "alias": "conant2007_glycolysis_2c",
      "provenance": {
        "owned_path": "owned/models/conant2007_glycolysis_2c"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.conant2007_glycolysis_2c_state"
      ],
      "from": "conant2007_glycolysis_2c.state"
    },
    {
      "to": [
        "visualisation.conant2007_glycolysis_2c_summary"
      ],
      "from": "conant2007_glycolysis_2c.summary"
    },
    {
      "to": [
        "visualisation.conant2007_glycolysis_2c_species_labels"
      ],
      "from": "conant2007_glycolysis_2c.species_labels"
    },
    {
      "to": [
        "visualisation.conant2007_glycolysis_2c_intracellular_glucose"
      ],
      "from": "conant2007_glycolysis_2c.intracellular_glucose"
    },
    {
      "to": [
        "visualisation.conant2007_glycolysis_2c_atp"
      ],
      "from": "conant2007_glycolysis_2c.atp"
    },
    {
      "to": [
        "visualisation.conant2007_glycolysis_2c_glucose_6_phosphate"
      ],
      "from": "conant2007_glycolysis_2c.glucose_6_phosphate"
    },
    {
      "to": [
        "visualisation.conant2007_glycolysis_2c_adp"
      ],
      "from": "conant2007_glycolysis_2c.adp"
    }
  ],
  "runtime": {
    "duration": 10,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "description": "Curated microbiology lab for Conant2007_glycolysis_2C. The bundled SBML is executed directly through Tellurium and visualised with conservative, source-traceable labels.",
  "schema_version": "2.0"
}

Select a run from History to view its results.