Ralser2007 - Dynamic Rerouting Carbohydrate Flux Ralserwamelink Lab

About lab

Ralser2007 - Dynamic Rerouting Carbohydrate Flux Ralserwamelink Lab

Scientific Source

Source type: PhysioMe CellML
Upstream ID: physiome:ralser_wamelink_kowald_gerisch_heeren_struys_klipp_jakobs_breitenbach_lehrach_krobitsch_2007
Original URL: https://models.physiomeproject.org/workspace/ralser_wamelink_kowald_gerisch_heeren_struys_klipp_jakobs_breitenbach_lehrach_krobitsch_2007
Bundled artifact: data/ralser_2007.cellml

The bundled CellML/SBML artifact remains the scientific source of truth. This cleanup does not rewrite equations, parameters, units, or initial values; it exposes selected source symbols with conservative user-facing names.

Public Interface

Source-backed inputs:

initial_nadp (Nadp) maps to source symbol NADP; units: mM; evidence: source symbol, component, or units provide a direct public name.
initial_nadph (Nadph) maps to source symbol NADPH; units: mM; evidence: source symbol, component, or units provide a direct public name.
The simulator still uses an internal integration_step parameter from the model manifest; it is not exposed as a biological lab input.

Selected outputs:

state, summary, trajectory, and variable_labels remain available for traceability.
nadp (Nadp) maps to source symbol NADP; units: mM; evidence: source symbol, component, or units provide a direct public name.
nadph (Nadph) maps to source symbol NADPH; units: mM; evidence: source symbol, component, or units provide a direct public name.
ci_pfkatp (Ci Pfkatp) maps to source symbol CiPFKATP; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
cpfkatp (Cpfkatp) maps to source symbol CPFKATP; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
katpase (Katpase) maps to source symbol KATPASE; units: per_min; evidence: source symbol, component, or units provide a direct public name.
keq_ak (Keq Ak) maps to source symbol KeqAK; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.

Ambiguous source symbols are intentionally given conservative names such as model_state_*, cell_population_*, or rate_constant_* rather than unsupported biological interpretations.

Visualisations

Visual scope: Selected source-variable trajectories; final observable ranking; source/runtime evidence table; scientific Q/A.

The visualisation renders a scientific Q/A table, selected source-variable trajectories, final observable values, and source/runtime evidence. The cards use runtime outputs from the core wrapper and suppress empty data.

Output Visualizations

01-ralser2007-dynamic-rerouting-carbohydrate-flux-ralserwamelink-lab-physiology-run

02-selected-physiology-trajectories

03-selected-final-observable-values

04-source-and-runtime-evidence

Caveat

This validates source-faithful execution and Biosimulant wiring for source-model physiology; it does not claim clinical safety or full reproduction of every upstream figure.

Source-faithful physiology lab for Ralser at el. 2007. Public controls and outputs are mapped to real source symbols for source-model physiology.

Runtime

Duration0.01

Comms Step0.01

Settle Steps1

Runs

Total0

Completed0

Failed0

Metadata

Packageralser2007-dynamic-rerouting-carbohydrate-flux-ralserwamelink-la

Created2026-05-23

Updated2026-05-23

physiologycellmlphysiomefaithfulvisualisationother

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_nadp",
        "label": "Initial Nadp",
        "maps_to": "physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model.initial_nadp",
        "description": "Initial value for Nadp. Maps to source symbol `NADP`. Units: mM. Naming evidence: source symbol, component, or units provide a direct public name.",
        "accepted_units": [
          "mM"
        ]
      },
      {
        "name": "initial_nadph",
        "label": "Initial Nadph",
        "maps_to": "physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model.initial_nadph",
        "description": "Initial value for Nadph. Maps to source symbol `NADPH`. Units: mM. Naming evidence: source symbol, component, or units provide a direct public name.",
        "accepted_units": [
          "mM"
        ]
      }
    ],
    "outputs": [
      {
        "name": "state",
        "label": "Selected Source State",
        "maps_to": "physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation Summary",
        "maps_to": "physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model.summary"
      },
      {
        "name": "trajectory",
        "label": "Source Trajectory",
        "maps_to": "physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model.trajectory"
      },
      {
        "name": "variable_labels",
        "label": "Observable Labels",
        "maps_to": "physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model.variable_labels"
      },
      {
        "name": "nadp",
        "label": "Nadp",
        "maps_to": "physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model.nadp",
        "description": "Nadp. Maps to source symbol `NADP`. Units: mM. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "nadph",
        "label": "Nadph",
        "maps_to": "physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model.nadph",
        "description": "Nadph. Maps to source symbol `NADPH`. Units: mM. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "ci_pfkatp",
        "label": "Ci Pfkatp",
        "maps_to": "physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model.ci_pfkatp",
        "description": "Ci Pfkatp. Maps to source symbol `CiPFKATP`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "cpfkatp",
        "label": "Cpfkatp",
        "maps_to": "physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model.cpfkatp",
        "description": "Cpfkatp. Maps to source symbol `CPFKATP`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "katpase",
        "label": "Katpase",
        "maps_to": "physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model.katpase",
        "description": "Katpase. Maps to source symbol `KATPASE`. Units: per_min. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "keq_ak",
        "label": "Keq Ak",
        "maps_to": "physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model.keq_ak",
        "description": "Keq Ak. Maps to source symbol `KeqAK`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      }
    ]
  },
  "title": "Ralser2007 - Dynamic Rerouting Carbohydrate Flux Ralserwamelink Lab",
  "models": [
    {
      "path": "owned/models/physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model",
      "alias": "physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model",
      "parameters": {
        "model_path": "data/ralser_2007.cellml",
        "integration_step": 0.01
      },
      "provenance": {
        "owned_path": "owned/models/physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model_state"
      ],
      "from": "physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model.state"
    },
    {
      "to": [
        "visualisation.physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model_summary"
      ],
      "from": "physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model.summary"
    },
    {
      "to": [
        "visualisation.physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model_trajectory"
      ],
      "from": "physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model.trajectory"
    },
    {
      "to": [
        "visualisation.physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model_variable_labels"
      ],
      "from": "physiology_cellml_ralser_at_el_2007_ralserwamelinkkowaldgerischheerenstruysklippjakobsbreitenbachlehrachkrobitsch2007_model.variable_labels"
    }
  ],
  "runtime": {
    "duration": 0.01,
    "settle_steps": 1,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "description": "Source-faithful physiology lab for Ralser at el. 2007. Public controls and outputs are mapped to real source symbols for source-model physiology.",
  "schema_version": "2.0"
}

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