About lab
Vernoux2011_AuxinSignaling_AuxinSingleStepInput
This Biosimulant lab wraps Vernoux2011_AuxinSignaling_AuxinSingleStepInput as a runnable signaling model with a companion visualization module.
Clean Biosimulant lab for systems signaling model: Vernoux2011_AuxinSignaling_AuxinSingleStepInput. 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 Vernoux2011 AuxinSignaling AuxinSingleStepInput respond through its source-defined plant signaling states? 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 Aux indole-3-acetic acid, auxin response factor, Aux indole-3-acetic acid Aux indole-3-acetic acid, Aux indole-3-acetic acid auxin response factor, source-defined MRNA state, and Auxin, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.
In this captured run, source-defined MRNA state moved from 1.000 to 1.835 across 1.0 simulation windows.
Output Visualizations
Summary table for Vernoux2011_AuxinSignaling_AuxinSingleStepInput, reporting the scientific question, observed answer, dominant module, and caveat.
Trajectories of source-defined MRNA state, Aux indole-3-acetic acid auxin response factor, auxin response factor, Aux indole-3-acetic acid Aux indole-3-acetic acid, Aux indole-3-acetic acid, and Auxin across the 1.0 simulation. In this run source-defined MRNA state climbed from 1.000 to 1.835 — the largest movements among the focused observables.
Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: Aux indole-3-acetic acid auxin response factor = 10.475, auxin response factor = 10.370, Aux indole-3-acetic acid Aux indole-3-acetic acid = 10.277, with 3 more observables below.
Model Context
- Core model:
models/core - Visualization model:
models/visualisation - Standard:
other - Upstream source:
biomodels_ebi:BIOMD0000000351 - License:
CC0 - Visual scope: plant signaling response
- 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 Auxin | signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model.initial_auxin | Initial level of Auxin. Maps to SBML symbol aux; exposed as a traceable initial-condition perturbation. |
Outputs
| Output | Maps To | Role |
|---|---|---|
aux_indole_3_acetic_acid | signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model.aux_indole_3_acetic_acid | Aux indole-3-acetic acid. |
auxin_response_factor | signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model.auxin_response_factor | auxin response factor. |
aux_indole_3_acetic_acid_aux_indole_3_acetic_acid | signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model.aux_indole_3_acetic_acid_aux_indole_3_acetic_acid | Aux indole-3-acetic acid Aux indole-3-acetic acid. |
state | signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model.state | Available to the visualization model and downstream workflows. |
summary | signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model.summary | Available to the visualization model and downstream workflows. |
species_labels | signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_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: Vernoux2011_AuxinSignaling_AuxinSingleStepInput. Values are native SBML quantities; equations, parameters, and initial values remain in the bundled source file.
Runtime
Runs
Metadata
Manifest
{
"io": {
"inputs": [
{
"name": "initial_auxin",
"label": "Initial Auxin",
"maps_to": "signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model.initial_auxin",
"description": "Initial level of Auxin. Maps to SBML symbol `aux`; exposed as a traceable initial-condition perturbation."
}
],
"outputs": [
{
"name": "aux_indole_3_acetic_acid",
"label": "Aux indole-3-acetic acid",
"maps_to": "signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model.aux_indole_3_acetic_acid",
"description": "Aux indole-3-acetic acid. Maps to SBML symbol `I` and is emitted in native SBML units."
},
{
"name": "auxin_response_factor",
"label": "auxin response factor",
"maps_to": "signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model.auxin_response_factor",
"description": "auxin response factor. Maps to SBML symbol `A` and is emitted in native SBML units."
},
{
"name": "aux_indole_3_acetic_acid_aux_indole_3_acetic_acid",
"label": "Aux indole-3-acetic acid Aux indole-3-acetic acid",
"maps_to": "signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model.aux_indole_3_acetic_acid_aux_indole_3_acetic_acid",
"description": "Aux indole-3-acetic acid Aux indole-3-acetic acid. Maps to SBML symbol `D_II` and is emitted in native SBML units."
},
{
"name": "state",
"label": "Observable state",
"maps_to": "signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model.state"
},
{
"name": "summary",
"label": "Simulation summary",
"maps_to": "signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model.summary"
},
{
"name": "species_labels",
"label": "Observable labels",
"maps_to": "signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model.species_labels"
}
]
},
"tags": [
"signaling",
"systems",
"systems-biology",
"sbml",
"faithful",
"biomodels_ebi",
"plant-signaling"
],
"title": "Vernoux2011_AuxinSignaling_AuxinSingleStepInput Lab",
"models": [
{
"path": "owned/models/signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model",
"alias": "signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model",
"provenance": {
"owned_path": "owned/models/signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model"
}
},
{
"path": "owned/models/visualisation",
"alias": "visualisation",
"provenance": {
"owned_path": "owned/models/visualisation"
}
}
],
"wiring": [
{
"to": [
"visualisation.signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model_state"
],
"from": "signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model.state"
},
{
"to": [
"visualisation.signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model_summary"
],
"from": "signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model.summary"
},
{
"to": [
"visualisation.signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model_species_labels"
],
"from": "signaling_sbml_vernoux2011_auxinsignaling_auxinsinglestepinput_biomd0000000351_model.species_labels"
}
],
"runtime": {
"duration": 1,
"initial_inputs": {},
"communication_step": 0.1
},
"description": "Clean Biosimulant lab for systems signaling model: Vernoux2011_AuxinSignaling_AuxinSingleStepInput. Values are native SBML quantities; equations, parameters, and initial values remain in the bundled source file.",
"schema_version": "2.0"
}Sign in to start your own run. Public-lab history stays visible here.
Select a run from History to view its results.