MODEL2001080001 - Martinez-Guimera2017 - Generic redox signalling model with negative feedback regulation (Model 2) Lab
About lab
Martinez-Guimera2017 - Generic redox signalling model with negative feedback regulation (Model 2)
This Biosimulant lab wraps Martinez-Guimera2017 - Generic redox signalling model with negative feedback regulation (Model 2) as a runnable signaling model with a companion visualization module.
Clean Biosimulant lab for systems signaling model: Martinez-Guimera2017 - Generic redox signalling model with negative feedback regulation (Model 2). It can be used to explore second-messenger and pathway-signaling dynamics and compare scenario outcomes across configurations.
What You'll See
The lab asks: How does Martinez-Guimera2017 - Generic redox signalling model with negative feedback regulation (Model 2) express its source-modeled signaling motif over the baseline run? 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 Oxidant, source-defined AOX state, Activator, Sensor, Sensor OX, and Function, and related outputs, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.
In this captured run, Oxidant moved from 0 to 0.0910 across 1.0 simulation windows.
Output Visualizations
Summary table for Martinez-Guimera2017 - Generic redox signalling model with negative feedback regulation (Model 2), reporting the scientific question, observed answer, dominant module, and caveat.
Trajectories of Oxidant, Sensor, Activator, Reductant, Intermediate, and Function across the 1.0 simulation. In this run Oxidant climbed from 0 to 0.0910 and Sensor fell from 10.000 to 9.927 — the largest movements among the focused observables.
Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: source-defined AOX state = 100.0, Reductant = 99.936, Relay = 10.000, with 7 more observables below.
Model Context
- Core model:
models/core - Visualization model:
models/visualisation - Standard:
other - Upstream source:
biomodels_ebi:MODEL2001080001 - License:
CC0 - Visual scope: phosphorylation and regulatory motif dynamics
- Caveat: Values are native SBML quantities; equations, parameters, units, and initial values remain in the bundled source file.
Inputs
| Input | Maps To | Default | Notes |
|---|---|---|---|
| Initial Inhibitor | signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model.initial_inhibitor | Initial level of Inhibitor. Maps to SBML symbol Inhibitor; exposed as a traceable initial-condition perturbation. |
Outputs
| Output | Maps To | Role |
|---|---|---|
inactive | signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model.inactive | Inactive. |
oxidant | signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model.oxidant | Oxidant. |
source_defined_aox_state | signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model.source_defined_aox_state | source-defined AOX state. |
state | signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model.state | Available to the visualization model and downstream workflows. |
summary | signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model.summary | Available to the visualization model and downstream workflows. |
species_labels | signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model.species_labels | Available to the visualization model and downstream workflows. |
Runtime
- Duration:
1.0 - Communication step:
0.1
Running Locally
biosimulant labs serve .
Clean Biosimulant lab for systems signaling model: Martinez-Guimera2017 - Generic redox signalling model with negative feedback regulation (Model 2). Values are native SBML quantities; equations, parameters, and initial values remain in the bundled source file.
Runtime
Runs
Metadata
Manifest
{
"io": {
"inputs": [
{
"name": "initial_inhibitor",
"label": "Initial Inhibitor",
"maps_to": "signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model.initial_inhibitor",
"description": "Initial level of Inhibitor. Maps to SBML symbol `Inhibitor`; exposed as a traceable initial-condition perturbation."
}
],
"outputs": [
{
"name": "inactive",
"label": "Inactive",
"maps_to": "signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model.inactive",
"description": "Inactive. Maps to SBML symbol `Inactive` and is emitted in native SBML units."
},
{
"name": "oxidant",
"label": "Oxidant",
"maps_to": "signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model.oxidant",
"description": "Oxidant. Maps to SBML symbol `Oxidant` and is emitted in native SBML units."
},
{
"name": "source_defined_aox_state",
"label": "source-defined AOX state",
"maps_to": "signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model.source_defined_aox_state",
"description": "source-defined AOX state. Maps to SBML symbol `AOX` and is emitted in native SBML units."
},
{
"name": "state",
"label": "Observable state",
"maps_to": "signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model.state"
},
{
"name": "summary",
"label": "Simulation summary",
"maps_to": "signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model.summary"
},
{
"name": "species_labels",
"label": "Observable labels",
"maps_to": "signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model.species_labels"
}
]
},
"tags": [
"signaling",
"systems",
"systems-biology",
"sbml",
"faithful",
"biomodels_ebi",
"stress-response"
],
"title": "MODEL2001080001 - Martinez-Guimera2017 - Generic redox signalling model with negative feedback regulation (Model 2) Lab",
"models": [
{
"path": "owned/models/signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model",
"alias": "signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model",
"provenance": {
"owned_path": "owned/models/signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model"
}
},
{
"path": "owned/models/visualisation",
"alias": "visualisation",
"provenance": {
"owned_path": "owned/models/visualisation"
}
}
],
"wiring": [
{
"to": [
"visualisation.signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model_state"
],
"from": "signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model.state"
},
{
"to": [
"visualisation.signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model_summary"
],
"from": "signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model.summary"
},
{
"to": [
"visualisation.signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model_species_labels"
],
"from": "signaling_sbml_martinez_guimera2017_generic_redox_signalling_mo_model2001080001_model.species_labels"
}
],
"runtime": {
"duration": 1,
"initial_inputs": {},
"communication_step": 0.1
},
"description": "Clean Biosimulant lab for systems signaling model: Martinez-Guimera2017 - Generic redox signalling model with negative feedback regulation (Model 2). Values are native SBML quantities; equations, parameters, and initial values remain in the bundled source file.",
"schema_version": "2.0"
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