About lab
Leber2016 Tfh Tfr Differentiation Lab
Expanded Tfh/Tfr differentiation model for Helicobacter pylori infection executed directly from bundled SBML.
Scientific question: Does the simulated network favor Tfh or Tfr differentiation?
This lab keeps the bundled SBML file as the scientific source of truth. The core model runs through TelluriumSBMLBioModule; friendly outputs map back to raw SBML symbols in models/core/model.yaml.
Controls
The public controls below map to SBML boundary signals or named drug parameters and do not alter the bundled equations.
interleukin_2_signal(IL-2 signal): Sets the constant IL-2 upstream signal in the Tfh/Tfr differentiation network. Maps to SBML symbolIL2.stat5_signal(STAT5 signal): Sets the constant STAT5 upstream signal in the Tfh/Tfr differentiation network. Maps to SBML symbolSTAT5.
What You'll See
This captured run uses the default configuration for Leber2016 Follicular T Cell Differentiation Lab, simulating 10 model-time units with results reported every 1. Public controls include IL-2 signal, STAT5 signal; this capture uses the lab defaults from runtime.initial_inputs. The visible outputs include Naive CD4 T cells, Natural regulatory T cells, Follicular helper T cells, Follicular regulatory T cells, Bcl6, and 5 more. The core wrapper uses an internal integration step of 0.1.
Output Visualizations
The run interpretation table summarizes the completed default run and the main activity changes across the configured outputs.
The developmental state trajectory plots the selected observables over the simulated time course so their dynamics can be compared directly.
The largest activity ranges chart ranks the outputs by how much they varied during the run.
The Follicular helper T cells vs Follicular regulatory T cells scatter plot compares the two highlighted outputs to show how their simulated trajectories relate to each other.
Expanded Tfh/Tfr differentiation model for Helicobacter pylori infection executed directly from bundled SBML.
Runtime
Runs
Metadata
Manifest
{
"io": {
"inputs": [
{
"name": "interleukin_2_signal",
"label": "IL-2 signal",
"units": "native SBML value",
"default": 0.0001,
"maps_to": "leber2016_follicular_t_cell_differentiation.interleukin_2_signal",
"description": "Sets the constant IL-2 upstream signal in the Tfh/Tfr differentiation network. Maps to SBML symbol `IL2`."
},
{
"name": "stat5_signal",
"label": "STAT5 signal",
"units": "native SBML value",
"default": 0,
"maps_to": "leber2016_follicular_t_cell_differentiation.stat5_signal",
"description": "Sets the constant STAT5 upstream signal in the Tfh/Tfr differentiation network. Maps to SBML symbol `STAT5`."
}
],
"outputs": [
{
"name": "naive_cluster_of_differentiation_four_t_cells",
"label": "Naive CD4 T cells",
"maps_to": "leber2016_follicular_t_cell_differentiation.naive_cluster_of_differentiation_four_t_cells",
"description": "Naive CD4 T cells. Maps to SBML symbol `NaiveCD4`."
},
{
"name": "natural_regulatory_t_cells",
"label": "Natural regulatory T cells",
"maps_to": "leber2016_follicular_t_cell_differentiation.natural_regulatory_t_cells",
"description": "Natural regulatory T cells. Maps to SBML symbol `nTreg`."
},
{
"name": "follicular_helper_t_cells",
"label": "Follicular helper T cells",
"maps_to": "leber2016_follicular_t_cell_differentiation.follicular_helper_t_cells",
"description": "Follicular helper T cells. Maps to SBML symbol `Tfh`."
},
{
"name": "follicular_regulatory_t_cells",
"label": "Follicular regulatory T cells",
"maps_to": "leber2016_follicular_t_cell_differentiation.follicular_regulatory_t_cells",
"description": "Follicular regulatory T cells. Maps to SBML symbol `Tfr`."
},
{
"name": "b_cell_lymphoma_six",
"label": "Bcl6",
"maps_to": "leber2016_follicular_t_cell_differentiation.b_cell_lymphoma_six",
"description": "Bcl6. Maps to SBML symbol `Bcl6`."
},
{
"name": "b_lymphocyte_induced_maturation_protein_one",
"label": "Blimp1",
"maps_to": "leber2016_follicular_t_cell_differentiation.b_lymphocyte_induced_maturation_protein_one",
"description": "Blimp1. Maps to SBML symbol `Blimp1`."
},
{
"name": "forkhead_box_p3",
"label": "FOXP3",
"maps_to": "leber2016_follicular_t_cell_differentiation.forkhead_box_p3",
"description": "FOXP3. Maps to SBML symbol `FoxP3`."
},
{
"name": "signal_transducer_and_activator_of_transcription_3",
"label": "STAT3",
"maps_to": "leber2016_follicular_t_cell_differentiation.signal_transducer_and_activator_of_transcription_3",
"description": "STAT3. Maps to SBML symbol `STAT3`."
},
{
"name": "interleukin_6",
"label": "IL-6",
"maps_to": "leber2016_follicular_t_cell_differentiation.interleukin_6",
"description": "IL-6. Maps to SBML symbol `IL6`."
},
{
"name": "interleukin_21",
"label": "IL-21",
"maps_to": "leber2016_follicular_t_cell_differentiation.interleukin_21",
"description": "IL-21. Maps to SBML symbol `IL21`."
},
{
"name": "state",
"maps_to": "leber2016_follicular_t_cell_differentiation.state",
"description": "Full friendly observable record."
},
{
"name": "summary",
"maps_to": "leber2016_follicular_t_cell_differentiation.summary",
"description": "Core model run summary."
},
{
"name": "species_labels",
"maps_to": "leber2016_follicular_t_cell_differentiation.species_labels",
"description": "Friendly observable display labels."
}
]
},
"title": "Leber2016 Follicular T Cell Differentiation Lab",
"models": [
{
"path": "owned/models/leber2016_follicular_t_cell_differentiation",
"alias": "leber2016_follicular_t_cell_differentiation",
"parameters": {
"model_path": "data/BIOMD0000000625.xml",
"integration_step": 0.1
},
"provenance": {
"owned_path": "owned/models/leber2016_follicular_t_cell_differentiation"
}
},
{
"path": "owned/models/visualisation",
"alias": "visualisation",
"provenance": {
"owned_path": "owned/models/visualisation"
}
}
],
"wiring": [
{
"to": [
"visualisation.core_state"
],
"from": "leber2016_follicular_t_cell_differentiation.state"
},
{
"to": [
"visualisation.core_summary"
],
"from": "leber2016_follicular_t_cell_differentiation.summary"
},
{
"to": [
"visualisation.core_species_labels"
],
"from": "leber2016_follicular_t_cell_differentiation.species_labels"
}
],
"runtime": {
"duration": 10,
"initial_inputs": {},
"communication_step": 1
},
"description": "Expanded Tfh/Tfr differentiation model for Helicobacter pylori infection executed directly from bundled SBML.",
"schema_version": "2.0"
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