About lab
Chen2011/2 - bone marrow invasion relative model
This Biosimulant lab wraps Chen2011/2 - bone marrow invasion relative model as a runnable oncology model with a companion visualization module.
The paper describes a model of tumor invasion to bone marrow. It can be used to explore treatment-response dynamics and compare scenario outcomes across configurations.
What You'll See
The lab asks: What oncology-relevant state dominates the bundled SBML simulation over the baseline run? It runs for 10.0 time units with a communication step of 1.0. The run uses the model defaults declared by the curated SBML wrapper. The generated visualizations focus on H, and T, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.
In this captured run, H peaked at 0.8737 and H moved by 0.3737 native units across 10.0 simulation windows.
Output Visualizations
Summary table for Chen2011/2 - bone marrow invasion relative model, reporting the scientific question, observed answer (largest change: H at 0.3737 native units), evidence (peak observable: H), dominant module, and caveat.
Trajectories of H, and T across the 10.0 simulation. In this run H climbed from 0.5000 to 0.8737 — the largest movements among the focused observables.
Endpoint ranking of the focused observables. Top 2 by final value: H = 0.8737, T = 0.00012.
Model Context
- Core model:
models/core - Visualization model:
models/visualisation - Standard:
other - Upstream source:
biomodels_ebi:BIOMD0000000795 - License:
CC0 - Visual scope: Tumor-system state trajectories and dominant observable changes
- Caveat: Values are native SBML quantities; the cleanup does not reinterpret source equations.
Inputs
| Input | Maps To | Default | Notes |
|---|
Outputs
| Output | Maps To | Role |
|---|---|---|
model_state_1 | oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model.model_state_1 | H observable. |
model_state_2 | oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model.model_state_2 | T observable. |
state | oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model.state | Full raw SBML observable record for reproducibility and downstream visualisation. |
summary | oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model.summary | Change and peak summary across the simulated SBML observables. |
species_labels | oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model.species_labels | Mapping from selected raw SBML observable symbols to display labels. |
Runtime
- Duration:
10.0 - Communication step:
1.0
Running Locally
biosimulant labs serve .
The paper describes a model of tumor invasion to bone marrow. Created by COPASI 4.26 (Build 213) This model is described in the article: Modeling invasion of metastasizing cancer cells to bone marrow.
Runtime
Runs
Metadata
Manifest
{
"io": {
"inputs": [
{
"name": "initial_healthy_bone_marrow",
"label": "Healthy Bone Marrow",
"units": "native SBML value",
"default": 0.5,
"maps_to": "oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model.initial_healthy_bone_marrow",
"description": "Initial Healthy Bone Marrow. Sets the initial value of bundled SBML symbol `H`."
},
{
"name": "initial_tumor_burden",
"label": "Tumor Burden",
"units": "native SBML value",
"default": 0.0001,
"maps_to": "oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model.initial_tumor_burden",
"description": "Initial Tumor Burden. Sets the initial value of bundled SBML symbol `T`."
}
],
"outputs": [
{
"name": "healthy_bone_marrow",
"maps_to": "oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model.healthy_bone_marrow",
"description": "Healthy Bone Marrow observable. Maps to SBML symbol `H`."
},
{
"name": "tumor_burden",
"maps_to": "oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model.tumor_burden",
"description": "Tumor Burden observable. Maps to SBML symbol `T`."
},
{
"name": "state",
"maps_to": "oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model.state",
"description": "Full raw SBML observable record for reproducibility and downstream visualisation."
},
{
"name": "summary",
"maps_to": "oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model.summary",
"description": "Change and peak summary across the simulated SBML observables."
},
{
"name": "species_labels",
"maps_to": "oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model.species_labels",
"description": "Mapping from selected raw SBML observable symbols to display labels."
}
]
},
"tags": [
"biomodels_ebi",
"curated",
"faithful",
"oncology",
"physiology",
"sbml",
"systemsbiology",
"tumor-growth"
],
"title": "Chen2011/2 - bone marrow invasion relative model Lab",
"models": [
{
"path": "owned/models/oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model",
"alias": "oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model",
"provenance": {
"owned_path": "owned/models/oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model"
}
},
{
"path": "owned/models/visualisation",
"alias": "visualisation",
"provenance": {
"owned_path": "owned/models/visualisation"
}
}
],
"wiring": [
{
"to": [
"visualisation.oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model_state"
],
"from": "oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model.state"
},
{
"to": [
"visualisation.oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model_summary"
],
"from": "oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model.summary"
},
{
"to": [
"visualisation.oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model_species_labels"
],
"from": "oncology_sbml_chen2011_2_bone_marrow_invasion_relative_model_biomd0000000795_model.species_labels"
}
],
"runtime": {
"duration": 10,
"initial_inputs": {},
"communication_step": 1
},
"description": "The paper describes a model of tumor invasion to bone marrow. Created by COPASI 4.26 (Build 213) This model is described in the article: Modeling invasion of metastasizing cancer cells to bone marrow.",
"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.