Vinod2011_MitoticExit Lab

About lab

Vinod2011 MitoticExit Lab

Curated microbiology lab for Vinod2011_MitoticExit. The bundled SBML is executed directly through Tellurium and visualised with conservative, source-traceable labels.

This lab asks: Which mitotic-exit regulator changes most over the simulated window?

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: yeast cell-cycle state dynamics.

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

Run Context

Duration: 2
Communication step: 0.01
Initial inputs: lab defaults

Primary Inputs

Initial Total Clb2 Cyclin (Clb2T_1)
Initial Total Clb5 Cyclin (Clb5T_1)

Primary Outputs

Model state (state)
Simulation summary (summary)
Observable labels (species_labels)
Clb2T (Clb2T_1)
Clb5T (Clb5T_1)
Cln (Cln_1)
Cdc20 (Cdc20_1)

Model Wiring

vinod2011_budding_yeast_mitotic_exit uses models/core
visualisation uses models/visualisation
vinod2011_budding_yeast_mitotic_exit.state -> visualisation.vinod2011_budding_yeast_mitotic_exit_state
vinod2011_budding_yeast_mitotic_exit.summary -> visualisation.vinod2011_budding_yeast_mitotic_exit_summary
vinod2011_budding_yeast_mitotic_exit.species_labels -> visualisation.vinod2011_budding_yeast_mitotic_exit_species_labels
vinod2011_budding_yeast_mitotic_exit.total_clb2_cyclin -> visualisation.vinod2011_budding_yeast_mitotic_exit_total_clb2_cyclin
vinod2011_budding_yeast_mitotic_exit.total_clb5_cyclin -> visualisation.vinod2011_budding_yeast_mitotic_exit_total_clb5_cyclin
vinod2011_budding_yeast_mitotic_exit.cln_cyclin -> visualisation.vinod2011_budding_yeast_mitotic_exit_cln_cyclin
vinod2011_budding_yeast_mitotic_exit.cdc20_activator -> visualisation.vinod2011_budding_yeast_mitotic_exit_cdc20_activator

Output Visualizations

visualisation table

The summary table records the numeric run outputs used to answer the lab question: Which mitotic-exit regulator changes most over the simulated window?

visualisation table

visualisation timeseries

The time-series view follows Clb2T, Clb5T, Cln, Cdc20 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:BIOMD0000000370
Upstream URL: https://www.ebi.ac.uk/biomodels/BIOMD0000000370
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 Vinod2011_MitoticExit. The bundled SBML is executed directly through Tellurium and visualised with conservative, source-traceable labels.

Runtime

Duration2

Comms Step0.01

Runs

Total0

Completed0

Failed0

Metadata

Packagevinod2011-mitoticexit-lab

Created2026-05-15

Updated2026-05-15

microbiologysbmlbiomodels_ebifaithfultelluriumvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_total_clb2_cyclin",
        "maps_to": "vinod2011_budding_yeast_mitotic_exit.initial_total_clb2_cyclin"
      },
      {
        "name": "initial_total_clb5_cyclin",
        "maps_to": "vinod2011_budding_yeast_mitotic_exit.initial_total_clb5_cyclin"
      }
    ],
    "outputs": [
      {
        "name": "state",
        "maps_to": "vinod2011_budding_yeast_mitotic_exit.state"
      },
      {
        "name": "summary",
        "maps_to": "vinod2011_budding_yeast_mitotic_exit.summary"
      },
      {
        "name": "species_labels",
        "maps_to": "vinod2011_budding_yeast_mitotic_exit.species_labels"
      },
      {
        "name": "total_clb2_cyclin",
        "maps_to": "vinod2011_budding_yeast_mitotic_exit.total_clb2_cyclin"
      },
      {
        "name": "total_clb5_cyclin",
        "maps_to": "vinod2011_budding_yeast_mitotic_exit.total_clb5_cyclin"
      },
      {
        "name": "cln_cyclin",
        "maps_to": "vinod2011_budding_yeast_mitotic_exit.cln_cyclin"
      },
      {
        "name": "cdc20_activator",
        "maps_to": "vinod2011_budding_yeast_mitotic_exit.cdc20_activator"
      }
    ]
  },
  "title": "Vinod2011_MitoticExit Lab",
  "models": [
    {
      "path": "owned/models/vinod2011_budding_yeast_mitotic_exit",
      "alias": "vinod2011_budding_yeast_mitotic_exit",
      "provenance": {
        "owned_path": "owned/models/vinod2011_budding_yeast_mitotic_exit"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.vinod2011_budding_yeast_mitotic_exit_state"
      ],
      "from": "vinod2011_budding_yeast_mitotic_exit.state"
    },
    {
      "to": [
        "visualisation.vinod2011_budding_yeast_mitotic_exit_summary"
      ],
      "from": "vinod2011_budding_yeast_mitotic_exit.summary"
    },
    {
      "to": [
        "visualisation.vinod2011_budding_yeast_mitotic_exit_species_labels"
      ],
      "from": "vinod2011_budding_yeast_mitotic_exit.species_labels"
    },
    {
      "to": [
        "visualisation.vinod2011_budding_yeast_mitotic_exit_total_clb2_cyclin"
      ],
      "from": "vinod2011_budding_yeast_mitotic_exit.total_clb2_cyclin"
    },
    {
      "to": [
        "visualisation.vinod2011_budding_yeast_mitotic_exit_total_clb5_cyclin"
      ],
      "from": "vinod2011_budding_yeast_mitotic_exit.total_clb5_cyclin"
    },
    {
      "to": [
        "visualisation.vinod2011_budding_yeast_mitotic_exit_cln_cyclin"
      ],
      "from": "vinod2011_budding_yeast_mitotic_exit.cln_cyclin"
    },
    {
      "to": [
        "visualisation.vinod2011_budding_yeast_mitotic_exit_cdc20_activator"
      ],
      "from": "vinod2011_budding_yeast_mitotic_exit.cdc20_activator"
    }
  ],
  "runtime": {
    "duration": 2,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "description": "Curated microbiology lab for Vinod2011_MitoticExit. 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.