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This is a kinetic model of the monomeric photosystem II (PSII). The model is partially based on the earlier model used for simulation of the flash-induced period-four damped oscillation of oxygen evol.
Manifest
{
"io": {
"inputs": [
{
"name": "initial_model_state_pq",
"label": "Initial Model State Pq",
"maps_to": "systemsbiology_sbml_model3631586579_url_xml_model3631586579_model.initial_model_state_pq",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `PQ`."
},
{
"name": "initial_y_dox",
"label": "Initial Y Dox",
"maps_to": "systemsbiology_sbml_model3631586579_url_xml_model3631586579_model.initial_y_dox",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `YDox`."
},
{
"name": "initial_s1_yphab",
"label": "Initial S1 Yphab",
"maps_to": "systemsbiology_sbml_model3631586579_url_xml_model3631586579_model.initial_s1_yphab",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `S1YPHAB`."
},
{
"name": "initial_s1_ypha_bm",
"label": "Initial S1 Ypha Bm",
"maps_to": "systemsbiology_sbml_model3631586579_url_xml_model3631586579_model.initial_s1_ypha_bm",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `S1YPHABm`."
},
{
"name": "initial_model_state_yd",
"label": "Initial Model State Yd",
"maps_to": "systemsbiology_sbml_model3631586579_url_xml_model3631586579_model.initial_model_state_yd",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `YD`."
},
{
"name": "initial_s3_yp_pp_hm_am_bmm",
"label": "Initial S3 Yp Pp Hm Am Bmm",
"maps_to": "systemsbiology_sbml_model3631586579_url_xml_model3631586579_model.initial_s3_yp_pp_hm_am_bmm",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `S3YpPpHmAmBmm`."
}
],
"outputs": [
{
"name": "state",
"maps_to": "systemsbiology_sbml_model3631586579_url_xml_model3631586579_model.state"
},
{
"name": "summary",
"maps_to": "systemsbiology_sbml_model3631586579_url_xml_model3631586579_model.summary"
},
{
"name": "species_labels",
"maps_to": "systemsbiology_sbml_model3631586579_url_xml_model3631586579_model.species_labels"
},
{
"name": "model_state_pq",
"maps_to": "systemsbiology_sbml_model3631586579_url_xml_model3631586579_model.model_state_pq"
},
{
"name": "y_dox",
"maps_to": "systemsbiology_sbml_model3631586579_url_xml_model3631586579_model.y_dox"
},
{
"name": "s1_yphab",
"maps_to": "systemsbiology_sbml_model3631586579_url_xml_model3631586579_model.s1_yphab"
},
{
"name": "s1_ypha_bm",
"maps_to": "systemsbiology_sbml_model3631586579_url_xml_model3631586579_model.s1_ypha_bm"
},
{
"name": "model_state_yd",
"maps_to": "systemsbiology_sbml_model3631586579_url_xml_model3631586579_model.model_state_yd"
},
{
"name": "s3_yp_pp_hm_am_bmm",
"maps_to": "systemsbiology_sbml_model3631586579_url_xml_model3631586579_model.s3_yp_pp_hm_am_bmm"
}
]
},
"tags": [
"systemsbiology",
"sbml",
"biomodels_ebi",
"faithful",
"curated"
],
"title": "Url Xml Lab",
"models": [
{
"path": "models/core",
"alias": "systemsbiology_sbml_model3631586579_url_xml_model3631586579_model"
},
{
"path": "models/visualisation",
"alias": "visualisation"
}
],
"wiring": [
{
"to": [
"visualisation.systemsbiology_sbml_model3631586579_url_xml_model3631586579_model_state"
],
"from": "systemsbiology_sbml_model3631586579_url_xml_model3631586579_model.state"
},
{
"to": [
"visualisation.systemsbiology_sbml_model3631586579_url_xml_model3631586579_model_summary"
],
"from": "systemsbiology_sbml_model3631586579_url_xml_model3631586579_model.summary"
},
{
"to": [
"visualisation.systemsbiology_sbml_model3631586579_url_xml_model3631586579_model_species_labels"
],
"from": "systemsbiology_sbml_model3631586579_url_xml_model3631586579_model.species_labels"
}
],
"package": "url-xml",
"runtime": {
"duration": 1,
"initial_inputs": {},
"communication_step": 0.1
},
"version": "1.0.0",
"description": "This is a kinetic model of the monomeric photosystem II (PSII). The model is partially based on the earlier model used for simulation of the flash-induced period-four damped oscillation of oxygen evol.",
"schema_version": "2.0"
}Runtime
Duration1
Comms Step0.1
Runs
Total0
Completed0
Failed0
Metadata
Packageurl-xml
Created2026-05-17
Updated2026-06-13
systemsbiologysbmlbiomodels_ebifaithfulcuratedvisualisationother