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Xenophagy, also known as antibacterial autophagy, is a process of capturing and eliminating cytosolic pathogens, like Salmonella. Salmonella is the best-studied model organism for xenophagy.
Manifest
{
"io": {
"inputs": [
{
"name": "initial_m_torc1inactive",
"label": "Initial M Torc1inactive",
"maps_to": "systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model.initial_m_torc1inactive",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `P382`."
},
{
"name": "initial_m_torc1_ulk1comp",
"label": "Initial M Torc1 Ulk1comp",
"maps_to": "systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model.initial_m_torc1_ulk1comp",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `P384`."
},
{
"name": "initial_m_torc1_ulk1comp_scv",
"label": "Initial M Torc1 Ulk1comp Scv",
"maps_to": "systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model.initial_m_torc1_ulk1comp_scv",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `P415`."
},
{
"name": "initial_signal_sc_vdamage",
"label": "Initial Signal Sc Vdamage",
"maps_to": "systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model.initial_signal_sc_vdamage",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `P400`."
},
{
"name": "initial_signal_autophagy_induction",
"label": "Initial Signal Autophagy Induction",
"maps_to": "systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model.initial_signal_autophagy_induction",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `P408`."
},
{
"name": "initial_p62_i",
"label": "Initial P62 I",
"maps_to": "systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model.initial_p62_i",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `P352`."
}
],
"outputs": [
{
"name": "state",
"maps_to": "systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model.state"
},
{
"name": "summary",
"maps_to": "systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model.summary"
},
{
"name": "species_labels",
"maps_to": "systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model.species_labels"
},
{
"name": "m_torc1inactive",
"maps_to": "systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model.m_torc1inactive"
},
{
"name": "m_torc1_ulk1comp",
"maps_to": "systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model.m_torc1_ulk1comp"
},
{
"name": "m_torc1_ulk1comp_scv",
"maps_to": "systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model.m_torc1_ulk1comp_scv"
},
{
"name": "signal_sc_vdamage",
"maps_to": "systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model.signal_sc_vdamage"
},
{
"name": "signal_autophagy_induction",
"maps_to": "systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model.signal_autophagy_induction"
},
{
"name": "p62_i",
"maps_to": "systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model.p62_i"
}
]
},
"tags": [
"microbiology",
"systemsbiology",
"sbml",
"biomodels_ebi",
"faithful",
"curated"
],
"title": "Scheidel2016 In Silico Knockout Studies Of Xenophagy Capturing Of Salmo Lab",
"models": [
{
"path": "models/core",
"alias": "systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model"
},
{
"path": "models/visualisation",
"alias": "visualisation"
}
],
"wiring": [
{
"to": [
"visualisation.systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model_state"
],
"from": "systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model.state"
},
{
"to": [
"visualisation.systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model_summary"
],
"from": "systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model.summary"
},
{
"to": [
"visualisation.systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model_species_labels"
],
"from": "systemsbiology_sbml_scheidel2016_in_silico_knockout_studies_of_xenop_model1904150001_model.species_labels"
}
],
"package": "scheidel2016-in-silico-knockout-studies-of-xenophagy-ca-0b99267c",
"runtime": {
"duration": 1,
"initial_inputs": {},
"communication_step": 0.1
},
"version": "1.0.0",
"description": "Xenophagy, also known as antibacterial autophagy, is a process of capturing and eliminating cytosolic pathogens, like Salmonella. Salmonella is the best-studied model organism for xenophagy.",
"schema_version": "2.0"
}Runtime
Duration1
Comms Step0.1
Runs
Total0
Completed0
Failed0
Metadata
Packagescheidel2016-in-silico-knockout-studies-of-xenophagy-ca-0b99267c
Created2026-05-17
Updated2026-06-13
microbiologysystemsbiologysbmlbiomodels_ebifaithfulcuratedvisualisationother