About lab
Brummel-Ziedins2012 - Contribution of the PC pathway to thrombin generation
This Biosimulant lab wraps Brummel-Ziedins2012 - Contribution of the PC pathway to thrombin generation as a runnable signaling model with a companion visualization module.
Clean Biosimulant lab for systems signaling model: Brummel-Ziedins2012 - Contribution of the PC pathway to thrombin generation. 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 Brummel-Ziedins2012 - Contribution of the PC pathway to thrombin generation shift hormone-linked signaling readouts? 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 TF state, TF VII, source-defined VII state, TF Viia, source-defined VIIA state, and source-defined XA state, and related outputs, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.
In this captured run, TF:VII moved from 0 to 1.42e-13 across 1.0 simulation windows.
Output Visualizations
Summary table for Brummel-Ziedins2012 - Contribution of the PC pathway to thrombin generation, reporting the scientific question, observed answer, dominant module, and caveat.
Trajectories of TF:VII, TF, VII, TF:VIIa, VIIa, and Xa across the 1.0 simulation. In this run TF:VII climbed from 0 to 1.42e-13 and TF fell from 5e-12 to 4.86e-12 — the largest movements among the focused observables.
Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: ATIII = 3.6e-06, II = 1.4e-06, X = 1.6e-07, with 7 more observables below.
Model Context
- Core model:
models/core - Visualization model:
models/visualisation - Standard:
other - Upstream source:
biomodels_ebi:MODEL1807180002 - License:
CC0 - Visual scope: metabolic and hormone 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 source-defined TF state | signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model.initial_source_defined_tf_state | Initial level of source-defined TF state. Maps to SBML symbol TF; exposed as a traceable initial-condition perturbation. |
Outputs
| Output | Maps To | Role |
|---|---|---|
viii_ica1 | signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model.viii_ica1 | VIII Ica1. |
source_defined_lca1_state | signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model.source_defined_lca1_state | source-defined LCA1 state. |
apc_lca1 | signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model.apc_lca1 | APC LCA1. |
state | signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model.state | Available to the visualization model and downstream workflows. |
summary | signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model.summary | Available to the visualization model and downstream workflows. |
species_labels | signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_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: Brummel-Ziedins2012 - Contribution of the PC pathway to thrombin generation. Values are native SBML quantities; equations, parameters, and initial values remain in the bundled source file.
Runtime
Runs
Metadata
Manifest
{
"io": {
"inputs": [
{
"name": "initial_source_defined_tf_state",
"label": "Initial source-defined TF state",
"maps_to": "signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model.initial_source_defined_tf_state",
"description": "Initial level of source-defined TF state. Maps to SBML symbol `TF`; exposed as a traceable initial-condition perturbation."
}
],
"outputs": [
{
"name": "viii_ica1",
"label": "VIII Ica1",
"maps_to": "signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model.viii_ica1",
"description": "VIII Ica1. Maps to SBML symbol `VIII_Ica1` and is emitted in native SBML units."
},
{
"name": "source_defined_lca1_state",
"label": "source-defined LCA1 state",
"maps_to": "signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model.source_defined_lca1_state",
"description": "source-defined LCA1 state. Maps to SBML symbol `LCA1` and is emitted in native SBML units."
},
{
"name": "apc_lca1",
"label": "APC LCA1",
"maps_to": "signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model.apc_lca1",
"description": "APC LCA1. Maps to SBML symbol `APC_LCA1` and is emitted in native SBML units."
},
{
"name": "state",
"label": "Observable state",
"maps_to": "signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model.state"
},
{
"name": "summary",
"label": "Simulation summary",
"maps_to": "signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model.summary"
},
{
"name": "species_labels",
"label": "Observable labels",
"maps_to": "signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model.species_labels"
}
]
},
"tags": [
"signaling",
"systems",
"systems-biology",
"sbml",
"faithful",
"biomodels_ebi",
"coagulation",
"physiology"
],
"title": "Brummel-Ziedins2012 - Contribution of the PC pathway to thrombin generation Lab",
"models": [
{
"path": "owned/models/signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model",
"alias": "signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model",
"provenance": {
"owned_path": "owned/models/signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model"
}
},
{
"path": "owned/models/visualisation",
"alias": "visualisation",
"provenance": {
"owned_path": "owned/models/visualisation"
}
}
],
"wiring": [
{
"to": [
"visualisation.signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model_state"
],
"from": "signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model.state"
},
{
"to": [
"visualisation.signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model_summary"
],
"from": "signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model.summary"
},
{
"to": [
"visualisation.signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model_species_labels"
],
"from": "signaling_sbml_brummel_ziedins2012_contribution_of_the_pc_pathw_model1807180002_model.species_labels"
}
],
"runtime": {
"duration": 1,
"initial_inputs": {},
"communication_step": 0.1
},
"description": "Clean Biosimulant lab for systems signaling model: Brummel-Ziedins2012 - Contribution of the PC pathway to thrombin generation. Values are native SBML quantities; equations, parameters, and initial values remain in the bundled source file.",
"schema_version": "2.0"
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