Chassagnole2001 Threonine Synthesis Lab

About lab

Chassagnole2001 Threonine Synthesis

This Biosimulant lab wraps Chassagnole2001 Threonine Synthesis as a runnable systems biology model with a companion visualization module. . It can be used to explore the configured dynamics and compare scenario outcomes across configurations.

What You'll See

The lab asks: Which source-defined system states dominate this SBML model trajectory? Source model: Chassagnole2001_Threonine Synthesis. 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 NADPH, NADP, ATP, ADP, Threonine, and Aspartate, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, ADP moved from 0 to 0.0339 across 1.0 simulation windows.

Output Visualizations

Chassagnole2001 Threonine Synthesis - run interpretation

Summary table for Chassagnole2001 Threonine Synthesis, reporting the scientific question, observed answer, dominant module, and caveat.

Chassagnole2001 Threonine Synthesis - timeseries visualization

Trajectories of ADP, ATP, NADPH, NADP, Aspartate, and Threonine across the 1.0 simulation. In this run ADP climbed from 0 to 0.0339 and ATP fell from 10.000 to 9.966 — the largest movements among the focused observables.

Chassagnole2001 Threonine Synthesis - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: ADP = 0.0339, ATP = 0.0339, NADPH = 0.0280, with 3 more observables below.

Chassagnole2001 Threonine Synthesis - endpoint snapshot bar

Endpoint snapshot of the focused observables — final values from the captured run. Top 3 by value: ATP = 9.966, Threonine = 2.000, Aspartate = 1.974, with 3 more observables below.

Chassagnole2001 Threonine Synthesis - visualization

Visualization card from the Chassagnole2001 Threonine Synthesis dark-mode run.

Model Context

Core model: models/core
Visualization model: models/visualisation
Standard: other
Upstream source: biomodels_ebi:BIOMD0000000066
License: CC0

Inputs

Input	Maps To	Notes
Initial Nadph	`systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.initial_nadph`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `nadph`.
Initial Nadp	`systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.initial_nadp`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `nadp`.
Initial Model State ATP	`systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.initial_model_state_atp`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `atp`.
Initial Model State ADP	`systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.initial_model_state_adp`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `adp`.
Initial Threonine	`systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.initial_threonine`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `thr`.
Initial Aspartate	`systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.initial_aspartate`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `asp`.

Outputs

Output	Maps To	Role
`state`	`systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.state`	Available to the visualization model and downstream workflows.
`summary`	`systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.summary`	Available to the visualization model and downstream workflows.
`species_labels`	`systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.species_labels`	Available to the visualization model and downstream workflows.
`nadph`	`systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.nadph`	Available to the visualization model and downstream workflows.
`nadp`	`systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.nadp`	Available to the visualization model and downstream workflows.
`atp`	`systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.atp`	Available to the visualization model and downstream workflows.
`adp`	`systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.adp`	Available to the visualization model and downstream workflows.
`threonine`	`systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.threonine`	Available to the visualization model and downstream workflows.
`aspartate`	`systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.aspartate`	Available to the visualization model and downstream workflows.

Runtime

Duration: 1.0
Communication step: 0.1

Running Locally

biosimulant labs serve

. It can be used to explore systemsbiology chassagnole2001 threonine synthesis BioModels0000000066 dynamics and compare simulation behavior across conditions.

Runtime

Duration1

Comms Step0.1

Runs

Total0

Completed0

Failed0

Metadata

Packagechassagnole2001-threonine-synthesis-lab

Created2026-05-17

Updated2026-05-17

systemsbiologysbmlbiomodels_ebifaithfulcuratedvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_nadph",
        "label": "Initial Nadph",
        "maps_to": "systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.initial_nadph",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `nadph`."
      },
      {
        "name": "initial_nadp",
        "label": "Initial Nadp",
        "maps_to": "systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.initial_nadp",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `nadp`."
      },
      {
        "name": "initial_model_state_atp",
        "label": "Initial Model State ATP",
        "maps_to": "systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.initial_model_state_atp",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `atp`."
      },
      {
        "name": "initial_model_state_adp",
        "label": "Initial Model State ADP",
        "maps_to": "systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.initial_model_state_adp",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `adp`."
      },
      {
        "name": "initial_threonine",
        "label": "Initial Threonine",
        "maps_to": "systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.initial_threonine",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `thr`."
      },
      {
        "name": "initial_aspartate",
        "label": "Initial Aspartate",
        "maps_to": "systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.initial_aspartate",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `asp`."
      }
    ],
    "outputs": [
      {
        "name": "state",
        "maps_to": "systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.state"
      },
      {
        "name": "summary",
        "maps_to": "systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.summary"
      },
      {
        "name": "species_labels",
        "maps_to": "systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.species_labels"
      },
      {
        "name": "nadph",
        "maps_to": "systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.nadph"
      },
      {
        "name": "nadp",
        "maps_to": "systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.nadp"
      },
      {
        "name": "atp",
        "maps_to": "systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.atp"
      },
      {
        "name": "adp",
        "maps_to": "systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.adp"
      },
      {
        "name": "threonine",
        "maps_to": "systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.threonine"
      },
      {
        "name": "aspartate",
        "maps_to": "systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.aspartate"
      }
    ]
  },
  "tags": [
    "systemsbiology",
    "sbml",
    "biomodels_ebi",
    "faithful",
    "curated"
  ],
  "title": "Chassagnole2001 Threonine Synthesis Lab",
  "models": [
    {
      "path": "owned/models/systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model",
      "alias": "systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model",
      "provenance": {
        "owned_path": "owned/models/systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model_state"
      ],
      "from": "systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.state"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model_summary"
      ],
      "from": "systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.summary"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model_species_labels"
      ],
      "from": "systemsbiology_sbml_chassagnole2001_threonine_synthesis_biomd0000000066_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": ". It can be used to explore systemsbiology chassagnole2001 threonine synthesis BioModels0000000066 dynamics and compare simulation behavior across conditions.",
  "schema_version": "2.0"
}

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