About lab
Geißert2020 - Yersinia enterocolitica co-infection in mice Lab
Curated immunology lab using the bundled source model as the scientific source of truth.
What You'll See
This captured run documents the default Geißert2020 - Yersinia enterocolitica co-infection in mice configuration for 10.0 time units with a 1.0 communication step. Default inputs include Initial Wild Type Yersinia Enterocolitica In Mucosa and Initial Wild Type Yersinia Enterocolitica In Lumen. Reported outputs include commensal_bacteria_in_mucosa, commensal_bacteria_in_lumen, wild_type_yersinia_enterocolitica_in_mucosa, and mutant_yersinia_enterocolitica_in_mucosa. The screenshots below pair the run-interpretation table with Pathogen and immune response and Largest state excursions so the README shows both trajectories and the strongest state changes from the same dark-mode run.
Output Visualizations
The run-interpretation table summarizes the configured Geißert2020 - Yersinia enterocolitica co-infection in mice simulation and its final-state diagnostics.
The Pathogen and immune response time series follows the selected immune, pathogen, tumor, or signaling quantities across the simulated horizon.
The largest state excursions chart ranks the state variables that moved furthest during the run.
This model simulates the colonization of the mouse gut with different strains of Yersinia enterocolitica. Thereby it takes the host-immune repsone into account.
Runtime
Runs
Metadata
Manifest
{
"io": {
"inputs": [
{
"name": "initial_wild_type_yersinia_enterocolitica_in_mucosa",
"label": "Initial Wild Type Yersinia Enterocolitica In Mucosa",
"units": "item",
"default": 10,
"maps_to": "immunology_sbml_gei_ert2020_yersinia_enterocolitica_co_infection_model2002070001_model.initial_wild_type_yersinia_enterocolitica_in_mucosa",
"description": "Initial Wild Type Yersinia Enterocolitica In Mucosa. Sets the initial value of bundled SBML species `x2`."
},
{
"name": "initial_wild_type_yersinia_enterocolitica_in_lumen",
"label": "Initial Wild Type Yersinia Enterocolitica In Lumen",
"units": "item",
"default": 1000,
"maps_to": "immunology_sbml_gei_ert2020_yersinia_enterocolitica_co_infection_model2002070001_model.initial_wild_type_yersinia_enterocolitica_in_lumen",
"description": "Initial Wild Type Yersinia Enterocolitica In Lumen. Sets the initial value of bundled SBML species `x5`."
}
],
"outputs": [
{
"name": "commensal_bacteria_in_mucosa",
"maps_to": "immunology_sbml_gei_ert2020_yersinia_enterocolitica_co_infection_model2002070001_model.commensal_bacteria_in_mucosa"
},
{
"name": "commensal_bacteria_in_lumen",
"maps_to": "immunology_sbml_gei_ert2020_yersinia_enterocolitica_co_infection_model2002070001_model.commensal_bacteria_in_lumen"
},
{
"name": "wild_type_yersinia_enterocolitica_in_mucosa",
"maps_to": "immunology_sbml_gei_ert2020_yersinia_enterocolitica_co_infection_model2002070001_model.wild_type_yersinia_enterocolitica_in_mucosa"
},
{
"name": "mutant_yersinia_enterocolitica_in_mucosa",
"maps_to": "immunology_sbml_gei_ert2020_yersinia_enterocolitica_co_infection_model2002070001_model.mutant_yersinia_enterocolitica_in_mucosa"
},
{
"name": "wild_type_yersinia_enterocolitica_in_lumen",
"maps_to": "immunology_sbml_gei_ert2020_yersinia_enterocolitica_co_infection_model2002070001_model.wild_type_yersinia_enterocolitica_in_lumen"
},
{
"name": "state",
"maps_to": "immunology_sbml_gei_ert2020_yersinia_enterocolitica_co_infection_model2002070001_model.state"
},
{
"name": "summary",
"maps_to": "immunology_sbml_gei_ert2020_yersinia_enterocolitica_co_infection_model2002070001_model.summary"
},
{
"name": "species_labels",
"maps_to": "immunology_sbml_gei_ert2020_yersinia_enterocolitica_co_infection_model2002070001_model.species_labels"
}
]
},
"title": "Geißert2020 - Yersinia enterocolitica co-infection in mice Lab",
"models": [
{
"path": "owned/models/immunology_sbml_gei_ert2020_yersinia_enterocolitica_co_infection_model2002070001_model",
"alias": "immunology_sbml_gei_ert2020_yersinia_enterocolitica_co_infection_model2002070001_model",
"provenance": {
"owned_path": "owned/models/immunology_sbml_gei_ert2020_yersinia_enterocolitica_co_infection_model2002070001_model"
}
},
{
"path": "owned/models/visualisation",
"alias": "visualisation",
"provenance": {
"owned_path": "owned/models/visualisation"
}
}
],
"wiring": [
{
"to": [
"visualisation.immunology_sbml_gei_ert2020_yersinia_enterocolitica_co_infection_model2002070001_model_state"
],
"from": "immunology_sbml_gei_ert2020_yersinia_enterocolitica_co_infection_model2002070001_model.state"
},
{
"to": [
"visualisation.immunology_sbml_gei_ert2020_yersinia_enterocolitica_co_infection_model2002070001_model_summary"
],
"from": "immunology_sbml_gei_ert2020_yersinia_enterocolitica_co_infection_model2002070001_model.summary"
},
{
"to": [
"visualisation.immunology_sbml_gei_ert2020_yersinia_enterocolitica_co_infection_model2002070001_model_species_labels"
],
"from": "immunology_sbml_gei_ert2020_yersinia_enterocolitica_co_infection_model2002070001_model.species_labels"
}
],
"runtime": {
"duration": 10,
"initial_inputs": {},
"communication_step": 1
},
"description": "This model simulates the colonization of the mouse gut with different strains of Yersinia enterocolitica. Thereby it takes the host-immune repsone into account.",
"schema_version": "2.0"
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