About lab
Padala2017- ERK, PI3K/Akt and Wnt signalling network (bRaf mutated)
This Biosimulant lab wraps Padala2017- ERK, PI3K/Akt and Wnt signalling network (bRaf mutated) 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 Padala2017- ERK, PI3K/Akt and Wnt signalling network (bRaf mutated) 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 source-defined APC state, APC Axin, APC Axin Gsk3b, APC B Catenin, AKT, and source-defined AXIN state, and related outputs, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.
In this captured run, free EGFR moved from 300.0 to 385.8 across 1.0 simulation windows.
Output Visualizations
Summary table for Padala2017- ERK, PI3K/Akt and Wnt signalling network (bRaf mutated), reporting the scientific question, observed answer, dominant module, and caveat.
Trajectories of free EGFR, EGF, bound EGFR, P RKIP, source-defined RKIP state, and source-defined NULL state across the 1.0 simulation. In this run free EGFR climbed from 300.0 to 385.8 and EGF fell from 600.0 to 596.2 — 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 PIP2 state = 700.0, MEK = 680.0, EGF = 596.2, with 7 more observables below.
Model Context
- Core model:
models/core - Visualization model:
models/visualisation - Standard:
other - Upstream source:
biomodels_ebi:BIOMD0000000653 - 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 P EGFR | signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model.initial_p_egfr | Initial level of P EGFR. Maps to SBML symbol pEGFR; exposed as a traceable initial-condition perturbation. | |
| Initial bound EGFR | signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model.initial_bound_egfr | Initial level of bound EGFR. Maps to SBML symbol bEGFR; exposed as a traceable initial-condition perturbation. | |
| Initial EGF | signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model.initial_egf | Initial level of EGF. Maps to SBML symbol EGF; exposed as a traceable initial-condition perturbation. |
Outputs
| Output | Maps To | Role |
|---|---|---|
apc_axin | signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model.apc_axin | APC Axin. |
apc_axin_gsk3b | signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model.apc_axin_gsk3b | APC Axin Gsk3b. |
apc_b_catenin | signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model.apc_b_catenin | APC B Catenin. |
state | signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model.state | Available to the visualization model and downstream workflows. |
summary | signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model.summary | Available to the visualization model and downstream workflows. |
species_labels | signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_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_p_egfr",
"label": "Initial P EGFR",
"maps_to": "signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model.initial_p_egfr",
"description": "Initial level of P EGFR. Maps to SBML symbol `pEGFR`; exposed as a traceable initial-condition perturbation."
},
{
"name": "initial_bound_egfr",
"label": "Initial bound EGFR",
"maps_to": "signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model.initial_bound_egfr",
"description": "Initial level of bound EGFR. Maps to SBML symbol `bEGFR`; exposed as a traceable initial-condition perturbation."
},
{
"name": "initial_egf",
"label": "Initial EGF",
"maps_to": "signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model.initial_egf",
"description": "Initial level of EGF. Maps to SBML symbol `EGF`; exposed as a traceable initial-condition perturbation."
}
],
"outputs": [
{
"name": "apc_axin",
"label": "APC Axin",
"maps_to": "signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model.apc_axin",
"description": "APC Axin. Maps to SBML symbol `APCAxin` and is emitted in native SBML units."
},
{
"name": "apc_axin_gsk3b",
"label": "APC Axin Gsk3b",
"maps_to": "signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model.apc_axin_gsk3b",
"description": "APC Axin Gsk3b. Maps to SBML symbol `APCAxinGSK3B` and is emitted in native SBML units."
},
{
"name": "apc_b_catenin",
"label": "APC B Catenin",
"maps_to": "signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model.apc_b_catenin",
"description": "APC B Catenin. Maps to SBML symbol `APCBCatenin` and is emitted in native SBML units."
},
{
"name": "state",
"label": "Observable state",
"maps_to": "signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model.state"
},
{
"name": "summary",
"label": "Simulation summary",
"maps_to": "signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model.summary"
},
{
"name": "species_labels",
"label": "Observable labels",
"maps_to": "signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model.species_labels"
}
]
},
"tags": [
"signaling",
"systems",
"systems-biology",
"sbml",
"faithful",
"biomodels_ebi",
"mapk",
"ras-erk",
"pi3k-akt",
"wnt",
"oncology"
],
"title": "Padala2017- ERK, PI3K/Akt and Wnt signalling network (bRaf mutated) Lab",
"models": [
{
"path": "owned/models/signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model",
"alias": "signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model",
"provenance": {
"owned_path": "owned/models/signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model"
}
},
{
"path": "owned/models/visualisation",
"alias": "visualisation",
"provenance": {
"owned_path": "owned/models/visualisation"
}
}
],
"wiring": [
{
"to": [
"visualisation.signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model_state"
],
"from": "signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model.state"
},
{
"to": [
"visualisation.signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model_summary"
],
"from": "signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model.summary"
},
{
"to": [
"visualisation.signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_model_species_labels"
],
"from": "signaling_sbml_padala2017_erk_pi3k_akt_and_wnt_signalling_netwo_biomd0000000653_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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