About lab
Sarma2012 - Interaction topologies of MAPK cascade (M3_K1_PSEQ_short_duration_signal)
This Biosimulant lab wraps Sarma2012 - Interaction topologies of MAPK cascade (M3_K1_PSEQ_short_duration_signal) as a runnable signaling model with a companion visualization module.
Clean Biosimulant lab for MAPK/ERK receptor signaling. 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 Sarma2012 - Interaction topologies of MAPK cascade (M3 K1 PSEQ short duration signal) propagate receptor or RAS/ERK pathway activity? 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 MAPK kinase kinase, MAPK kinase kinase P, MAPK kinase, source-defined MKK_P state, MAPK kinase PP, and MAP kinase, and related outputs, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.
In this captured run, MAPK kinase kinase P moved from 0 to 1.634 across 1.0 simulation windows.
Output Visualizations
Summary table for Sarma2012 - Interaction topologies of MAPK cascade (M3_K1_PSEQ_short_duration_signal), reporting the scientific question, observed answer, dominant module, and caveat.
Trajectories of MAPK kinase kinase P, MAPK kinase kinase, MAPK kinase, source-defined MKK_P state, MAPK kinase PP, and MAP kinase across the 1.0 simulation. In this run MAPK kinase kinase P climbed from 0 to 1.634 and MAPK kinase kinase fell from 300.0 to 298.4 — the largest movements among the focused observables.
Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: MAP kinase = 1200.0, MAPK kinase = 1199.9, MAPK kinase kinase = 298.4, with 7 more observables below.
Model Context
- Core model:
models/core - Visualization model:
models/visualisation - Standard:
other - Upstream source:
biomodels_ebi:MODEL1204280015 - License:
CC0 - Visual scope: receptor-to-MAPK cascade signaling
- 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 MAPK kinase kinase | signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model.initial_mapk_kinase_kinase | Initial level of MAPK kinase kinase. Maps to SBML symbol species_1; exposed as a traceable initial-condition perturbation. |
Outputs
| Output | Maps To | Role |
|---|---|---|
mapk_kinase_kinase | signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model.mapk_kinase_kinase | MAPK kinase kinase. |
mapk_kinase_kinase_p | signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model.mapk_kinase_kinase_p | MAPK kinase kinase P. |
mapk_kinase | signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model.mapk_kinase | MAPK kinase. |
state | signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model.state | Available to the visualization model and downstream workflows. |
summary | signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model.summary | Available to the visualization model and downstream workflows. |
species_labels | signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_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 MAPK/ERK receptor signaling. Values are native SBML quantities; equations, parameters, and initial values remain in the bundled source file.
Runtime
Runs
Metadata
Manifest
{
"io": {
"inputs": [
{
"name": "initial_mapk_kinase_kinase",
"label": "Initial MAPK kinase kinase",
"maps_to": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model.initial_mapk_kinase_kinase",
"description": "Initial level of MAPK kinase kinase. Maps to SBML symbol `species_1`; exposed as a traceable initial-condition perturbation."
}
],
"outputs": [
{
"name": "mapk_kinase_kinase",
"label": "MAPK kinase kinase",
"maps_to": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model.mapk_kinase_kinase",
"description": "MAPK kinase kinase. Maps to SBML symbol `species_1` and is emitted in native SBML units."
},
{
"name": "mapk_kinase_kinase_p",
"label": "MAPK kinase kinase P",
"maps_to": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model.mapk_kinase_kinase_p",
"description": "MAPK kinase kinase P. Maps to SBML symbol `species_2` and is emitted in native SBML units."
},
{
"name": "mapk_kinase",
"label": "MAPK kinase",
"maps_to": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model.mapk_kinase",
"description": "MAPK kinase. Maps to SBML symbol `species_3` and is emitted in native SBML units."
},
{
"name": "state",
"label": "Observable state",
"maps_to": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model.state"
},
{
"name": "summary",
"label": "Simulation summary",
"maps_to": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model.summary"
},
{
"name": "species_labels",
"label": "Observable labels",
"maps_to": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model.species_labels"
}
]
},
"tags": [
"signaling",
"systems",
"systems-biology",
"sbml",
"faithful",
"biomodels_ebi",
"mapk"
],
"title": "Sarma2012 - Interaction topologies of MAPK cascade (M3_K1_PSEQ_short_duration_signal) Lab",
"models": [
{
"path": "owned/models/signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model",
"alias": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model",
"provenance": {
"owned_path": "owned/models/signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model"
}
},
{
"path": "owned/models/visualisation",
"alias": "visualisation",
"provenance": {
"owned_path": "owned/models/visualisation"
}
}
],
"wiring": [
{
"to": [
"visualisation.signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model_state"
],
"from": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model.state"
},
{
"to": [
"visualisation.signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model_summary"
],
"from": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model.summary"
},
{
"to": [
"visualisation.signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model_species_labels"
],
"from": "signaling_sbml_sarma2012_interaction_topologies_of_mapk_cascade_model1204280015_model.species_labels"
}
],
"runtime": {
"duration": 1,
"initial_inputs": {},
"communication_step": 0.1
},
"description": "Clean Biosimulant lab for MAPK/ERK receptor signaling. Values are native SBML quantities; equations, parameters, and initial values remain in the bundled source file.",
"schema_version": "2.0"
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