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Source-faithful physiology lab for Nelson, Murray, Perelson, 2000. Public controls and outputs are mapped to real source symbols for source-model physiology.
Manifest
{
"io": {
"inputs": [
{
"name": "initial_infectious_virus_vi",
"label": "Initial Infectious Virus Vi",
"maps_to": "physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model.initial_infectious_virus_vi",
"description": "Initial value for Infectious Virus Vi. Maps to source symbol `VI`. Units: virons_per_ml. Naming evidence: source symbol, component, or units provide a direct public name.",
"accepted_units": [
"virons_per_ml"
]
},
{
"name": "initial_vni",
"label": "Initial Vni",
"maps_to": "physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model.initial_vni",
"description": "Initial value for Vni. Maps to source symbol `VNI`. Units: virons_per_ml. Naming evidence: source symbol, component, or units provide a direct public name.",
"accepted_units": [
"virons_per_ml"
]
}
],
"outputs": [
{
"name": "state",
"label": "Selected Source State",
"maps_to": "physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model.state"
},
{
"name": "summary",
"label": "Simulation Summary",
"maps_to": "physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model.summary"
},
{
"name": "trajectory",
"label": "Source Trajectory",
"maps_to": "physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model.trajectory"
},
{
"name": "variable_labels",
"label": "Observable Labels",
"maps_to": "physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model.variable_labels"
},
{
"name": "infectious_virus_vi",
"label": "Infectious Virus Vi",
"maps_to": "physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model.infectious_virus_vi",
"description": "Infectious Virus Vi. Maps to source symbol `VI`. Units: virons_per_ml. Naming evidence: source symbol, component, or units provide a direct public name."
},
{
"name": "vni",
"label": "Vni",
"maps_to": "physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model.vni",
"description": "Vni. Maps to source symbol `VNI`. Units: virons_per_ml. Naming evidence: source symbol, component, or units provide a direct public name."
},
{
"name": "log_vi",
"label": "Log Vi",
"maps_to": "physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model.log_vi",
"description": "Log Vi. Maps to source symbol `log_VI`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
},
{
"name": "log_virus_total",
"label": "Log Virus Total",
"maps_to": "physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model.log_virus_total",
"description": "Log Virus Total. Maps to source symbol `log_virus_total`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
},
{
"name": "virus_total",
"label": "Virus Total",
"maps_to": "physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model.virus_total",
"description": "Virus Total. Maps to source symbol `virus_total`. Units: virons_per_ml. Naming evidence: source symbol, component, or units provide a direct public name."
},
{
"name": "t_star",
"label": "T Star",
"maps_to": "physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model.t_star",
"description": "T Star. Maps to source symbol `T_star`. Units: cells_per_ml. Naming evidence: source symbol, component, or units provide a direct public name."
}
]
},
"title": "Nelson2000 - Hiv 1 Pathogenesis That Includes Intracellular Delay Delay Lab",
"models": [
{
"path": "models/core",
"alias": "physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model",
"parameters": {
"model_path": "data/nelson_murray_perelson_2000_delay.cellml",
"integration_step": 0.01
}
},
{
"path": "models/visualisation",
"alias": "visualisation"
}
],
"wiring": [
{
"to": [
"visualisation.physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model_state"
],
"from": "physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model.state"
},
{
"to": [
"visualisation.physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model_summary"
],
"from": "physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model.summary"
},
{
"to": [
"visualisation.physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model_trajectory"
],
"from": "physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model.trajectory"
},
{
"to": [
"visualisation.physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model_variable_labels"
],
"from": "physiology_cellml_nelson_murray_perelson_2000_nelsonmurrayperelson2000_model.variable_labels"
}
],
"package": "nelson2000-hiv-1-pathogenesis-that-includes-intracellul-35d329db",
"runtime": {
"duration": 0.01,
"settle_steps": 1,
"initial_inputs": {},
"communication_step": 0.01
},
"version": "1.0.0",
"description": "Source-faithful physiology lab for Nelson, Murray, Perelson, 2000. Public controls and outputs are mapped to real source symbols for source-model physiology.",
"schema_version": "2.0"
}Runtime
Duration0.01
Comms Step0.01
Settle Steps1
Runs
Total0
Completed0
Failed0
Metadata
Packagenelson2000-hiv-1-pathogenesis-that-includes-intracellul-35d329db
Created2026-05-23
Updated2026-06-13
physiologycellmlphysiomefaithfulvisualisationother