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Moreno2019 - Stochastic model of G1 arrest due to proteostasis decline delimits replicative lifespan in yeast Lab

About lab

Moreno2019 - Stochastic model of G1 arrest due to proteostasis decline delimits replicative lifespan in yeast Lab

Single-model lab wrapper for Moreno2019 - Stochastic model of G1 arrest due to proteostasis decline delimits replicative lifespan in yeast. This model is described within the paper: A G1 arrest due to proteostasis decline delimits replicative lifespan in yeastDavid F. Moreno, Kirsten Jenkins, Sandrine Morlot, Gilles Charvin, Attila Csik\u00e1s.

This lab is a single-model Biosimulant wrapper for a cell-cycle simulation. The captured run uses the lab defaults and renders the model outputs as dark-mode visualizations for quick inspection and README embedding.

Model Context

This model is described within the paper: A G1 arrest due to proteostasis decline delimits replicative lifespan in yeastDavid F. Moreno, Kirsten Jenkins, Sandrine Morlot, Gilles Charvin, Attila Csikás.

  • Core model: Moreno2019 - Stochastic model of G1 arrest due to proteostasis decline delimits replicative lifespan in yeast
  • Runtime used by the lab: duration 10, step 1
  • Controllable inputs: Hsp104
  • Primary outputs: Protein load, Model state YP, Ydj1 chaperone, Prot F, Prot Model state M, Oligomerized proteostasis species, Protein aggregate burden, Ydj1-oligomer aggregate complex, Model state YM, Model state YO, and 5 more
  • Tags: cellcycle, sbml, biomodels_ebi, faithful

Output Visualizations

The images below were generated from a Biosimulant lab run in dark mode. Each capture corresponds to one rendered visualization from the run output panel.

1. Moreno2019 Stochastic Model Of G1 Arrest Due To Proteostasis Decline Delimits Re

G1/S commitment view, focused on the regulatory variables that gate entry into DNA synthesis and cell-cycle progression.

moreno2019 stochastic model of g1 arrest due to proteostasis decline delimits re

2. Moreno2019 Stochastic Model Of G1 Arrest Due To Proteostasis Decline Delimits Re

G1/S commitment view, focused on the regulatory variables that gate entry into DNA synthesis and cell-cycle progression.

moreno2019 stochastic model of g1 arrest due to proteostasis decline delimits re

3. Moreno2019 Stochastic Model Of G1 Arrest Due To Proteostasis Decline Delimits Re

G1/S commitment view, focused on the regulatory variables that gate entry into DNA synthesis and cell-cycle progression.

moreno2019 stochastic model of g1 arrest due to proteostasis decline delimits re

4. Moreno2019 Stochastic Model Of G1 Arrest Due To Proteostasis Decline Delimits Re

G1/S commitment view, focused on the regulatory variables that gate entry into DNA synthesis and cell-cycle progression.

moreno2019 stochastic model of g1 arrest due to proteostasis decline delimits re

5. Moreno2019 Stochastic Model Of G1 Arrest Due To Proteostasis Decline Delimits Re

G1/S commitment view, focused on the regulatory variables that gate entry into DNA synthesis and cell-cycle progression.

moreno2019 stochastic model of g1 arrest due to proteostasis decline delimits re

How to Read This Run

Use the time-course plots to see transient and steady-state behavior, the range or snapshot charts to identify the variables with the strongest response, and any phase-portrait view to inspect coupled regulator movement through the simulated trajectory. For this cell-cycle lab, the most useful comparison is usually between checkpoint, commitment, and mitotic-exit variables because those signals define where the simulated system sits in the cycle.

Inputs

InputContext
Hsp104Controls Hsp104 in the lab model via cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.hsp104.

Outputs

OutputContext
Protein loadTracks Protein load in the lab model via cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.protein_load.
Model state YPTracks Model state YP in the lab model via cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.model_state_yp.
Ydj1 chaperoneTracks Ydj1 chaperone in the lab model via cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.ydj1_chaperone.
Prot FTracks Prot F in the lab model via cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.prot_f.
Prot Model state MTracks Prot Model state M in the lab model via cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.prot_model_state_m.
Oligomerized proteostasis speciesTracks Oligomerized proteostasis species in the lab model via cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.oligomerized_proteostasis_species.
Protein aggregate burdenTracks Protein aggregate burden in the lab model via cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.protein_aggregate_burden.
Ydj1-oligomer aggregate complexTracks Ydj1-oligomer aggregate complex in the lab model via cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.ydj1_oligomer_aggregate_complex.
Model state YMTracks Model state YM in the lab model via cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.model_state_ym.
Model state YOTracks Model state YO in the lab model via cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.model_state_yo.
Cln3 Start cyclinTracks Cln3 Start cyclin in the lab model via cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.cln3_start_cyclin.
Model state YCTracks Model state YC in the lab model via cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.model_state_yc.
Folded Cln3 Start cyclinTracks Folded Cln3 Start cyclin in the lab model via cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.folded_cln3_start_cyclin.
Whi5 Start inhibitorTracks Whi5 Start inhibitor in the lab model via cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.whi5_start_inhibitor.
Inactive Whi5 Start inhibitorTracks Inactive Whi5 Start inhibitor in the lab model via cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.inactive_whi5_start_inhibitor.

Lab Files

  • lab.yaml defines the Biosimulant lab wrapper, exposed inputs, outputs, and runtime settings.
  • wiring-layout.json stores the canvas layout used by the lab UI.
  • models/core/model.yaml contains the wrapped simulation model metadata.
  • models/core/README.md contains the source model notes and provenance.
  • models/visualisation/model.yaml defines the visualization model used to render the run outputs.
  • assets/ contains the generated dark-mode visualization captures embedded above.

Single-model lab wrapper for Moreno2019 - Stochastic model of G1 arrest due to proteostasis decline delimits replicative lifespan in yeast. This model is described within the paper: A G1 arrest due to proteostasis decline delimits replicative lifespan in yeastDavid F. Moreno, Kirsten Jenkins, Sandrine Morlot, Gilles Charvin, Attila Csik\u00e1s.

Runtime

Duration10
Comms Step1

Runs

Total0
Completed0
Failed0

Metadata

Packagemoreno2019-stochastic-model-of-g1-arrest-due-to-proteostasis-dec
Created2026-05-15
Updated2026-05-15
cellcyclesbmlbiomodels_ebifaithfulvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "hsp104",
        "label": "Hsp104",
        "maps_to": "cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.hsp104",
        "description": "Controls Hsp104 in the lab model via `cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.hsp104`."
      }
    ],
    "outputs": [
      {
        "name": "protein_load",
        "label": "Protein load",
        "maps_to": "cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.protein_load",
        "description": "Tracks Protein load in the lab model via `cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.protein_load`."
      },
      {
        "name": "model_state_yp",
        "label": "Model state YP",
        "maps_to": "cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.model_state_yp",
        "description": "Tracks Model state YP in the lab model via `cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.model_state_yp`."
      },
      {
        "name": "ydj1_chaperone",
        "label": "Ydj1 chaperone",
        "maps_to": "cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.ydj1_chaperone",
        "description": "Tracks Ydj1 chaperone in the lab model via `cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.ydj1_chaperone`."
      },
      {
        "name": "prot_f",
        "label": "Prot F",
        "maps_to": "cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.prot_f",
        "description": "Tracks Prot F in the lab model via `cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.prot_f`."
      },
      {
        "name": "prot_model_state_m",
        "label": "Prot Model state M",
        "maps_to": "cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.prot_model_state_m",
        "description": "Tracks Prot Model state M in the lab model via `cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.prot_model_state_m`."
      },
      {
        "name": "oligomerized_proteostasis_species",
        "label": "Oligomerized proteostasis species",
        "maps_to": "cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.oligomerized_proteostasis_species",
        "description": "Tracks Oligomerized proteostasis species in the lab model via `cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.oligomerized_proteostasis_species`."
      },
      {
        "name": "protein_aggregate_burden",
        "label": "Protein aggregate burden",
        "maps_to": "cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.protein_aggregate_burden",
        "description": "Tracks Protein aggregate burden in the lab model via `cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.protein_aggregate_burden`."
      },
      {
        "name": "ydj1_oligomer_aggregate_complex",
        "label": "Ydj1-oligomer aggregate complex",
        "maps_to": "cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.ydj1_oligomer_aggregate_complex",
        "description": "Tracks Ydj1-oligomer aggregate complex in the lab model via `cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.ydj1_oligomer_aggregate_complex`."
      },
      {
        "name": "model_state_ym",
        "label": "Model state YM",
        "maps_to": "cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.model_state_ym",
        "description": "Tracks Model state YM in the lab model via `cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.model_state_ym`."
      },
      {
        "name": "model_state_yo",
        "label": "Model state YO",
        "maps_to": "cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.model_state_yo",
        "description": "Tracks Model state YO in the lab model via `cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.model_state_yo`."
      },
      {
        "name": "cln3_start_cyclin",
        "label": "Cln3 Start cyclin",
        "maps_to": "cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.cln3_start_cyclin",
        "description": "Tracks Cln3 Start cyclin in the lab model via `cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.cln3_start_cyclin`."
      },
      {
        "name": "model_state_yc",
        "label": "Model state YC",
        "maps_to": "cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.model_state_yc",
        "description": "Tracks Model state YC in the lab model via `cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.model_state_yc`."
      },
      {
        "name": "folded_cln3_start_cyclin",
        "label": "Folded Cln3 Start cyclin",
        "maps_to": "cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.folded_cln3_start_cyclin",
        "description": "Tracks Folded Cln3 Start cyclin in the lab model via `cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.folded_cln3_start_cyclin`."
      },
      {
        "name": "whi5_start_inhibitor",
        "label": "Whi5 Start inhibitor",
        "maps_to": "cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.whi5_start_inhibitor",
        "description": "Tracks Whi5 Start inhibitor in the lab model via `cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.whi5_start_inhibitor`."
      },
      {
        "name": "inactive_whi5_start_inhibitor",
        "label": "Inactive Whi5 Start inhibitor",
        "maps_to": "cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.inactive_whi5_start_inhibitor",
        "description": "Tracks Inactive Whi5 Start inhibitor in the lab model via `cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.inactive_whi5_start_inhibitor`."
      }
    ]
  },
  "title": "Moreno2019 - Stochastic model of G1 arrest due to proteostasis decline delimits replicative lifespan in yeast Lab",
  "models": [
    {
      "path": "owned/models/cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model",
      "alias": "cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model",
      "provenance": {
        "owned_path": "owned/models/cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model_state"
      ],
      "from": "cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.state"
    },
    {
      "to": [
        "visualisation.cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model_summary"
      ],
      "from": "cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.summary"
    },
    {
      "to": [
        "visualisation.cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model_species_labels"
      ],
      "from": "cellcycle_sbml_moreno2019_stochastic_model_of_g1_arrest_due_to_model1901210001_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 10,
    "initial_inputs": {},
    "communication_step": 1
  },
  "description": "Single-model lab wrapper for Moreno2019 - Stochastic model of G1 arrest due to proteostasis decline delimits replicative lifespan in yeast. This model is described within the paper: A G1 arrest due to proteostasis decline delimits replicative lifespan in yeastDavid F. Moreno, Kirsten Jenkins, Sandrine Morlot, Gilles Charvin, Attila Csik\\u00e1s.",
  "schema_version": "2.0"
}

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