metaid_0000028
kinetic law: 001436
modifier: 001424
product: 001412
fast: false
reversible: false
name: release of non infectious virions on lysis
type: Reaction

001472
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

001207
exponent: 1.0
scale: 0
multipler: 86400.0
kind: SECOND
type: SBMLUnit

001448
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

metaid_0000003
constant: true
size: 1.0
spatial dimensions: 3.0
name: plasma
type: Compartment

metaid_0000013
unit: 001231
name: per day
type: SBMLUnitsDef

001243
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000032
constant: false
units: dimensionless
value: NaN
name: HIV
type: Parameter

001376
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

001496
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

001267
exponent: -1.0
scale: -3
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000023
kinetic law: 001364
modifier: 001352
modifier: 001340
product: 001328
fast: false
reversible: false
name: T-cell infection
type: Reaction

metaid_0000007
notes: uninfected T-cells
constant: false
boundary condition: true
has only substance units: false
initial concentration: 180000.0
initial amount: NaN
in compartment: metaid_0000003
name: T
type: Species

metaid_0000027
notes: proetease inhibitor efficacy
constant: true
units: dimensionless
value: 0.1
name: np
type: Parameter

metaid_0000017
unit: 001304
unit: 001291
unit: 001279
name: ml per (item*day)
type: SBMLUnitsDef

001231
exponent: -1.0
scale: 0
multipler: 86400.0
kind: SECOND
type: SBMLUnit

metaid_0000008
notes: infected T-cells
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000003
name: T*
type: Species

001316
exponent: 1.0
scale: 0
multipler: 1.0
kind: DIMENSIONLESS
type: SBMLUnit

metaid_0000024
constant: true
units: metaid_0000013
value: 0.0
name: m
type: Parameter

metaid_0000010
notes: non-infectious virus (VNI )
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000003
name: V_NI
type: Species

001328
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

metaid_0000016
unit: 001267
unit: 001255
name: items per ml
type: SBMLUnitsDef

metaid_0000020
notes: virions released per cell upon lysis
constant: true
units: metaid_0000021
value: 480.0
name: N
type: Parameter

metaid_0000030
kinetic law: 001484
reactant: 001472
fast: false
reversible: false
name: non-infect. virion clearance
type: Reaction

001412
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

metaid_0000005
unit: 001207
name: day
type: SBMLUnitsDef

001279
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000011
notes: delay between T-cell infection and lysis
constant: true
units: metaid_0000005
value: 1.0
name: tau
type: Parameter

001219
exponent: 1.0
scale: 0
multipler: 1.0
kind: ITEM
type: SBMLUnit

MODEL8102792069
reaction: metaid_0000029
volume units: metaid_0000015
species: metaid_0000010
curated: false
units def: metaid_0000006
parameter: metaid_0000012
reaction: metaid_0000026
parameter: metaid_0000032
reaction: metaid_0000030
parameter: metaid_0000027
species: metaid_0000007
length unit: length
units def: metaid_0000005
units def: metaid_0000021
parameter: metaid_0000020
units def: metaid_0000013
area units: area
substance units: metaid_0000006
species: metaid_0000009
is described by: http://identifiers.org/pubmed/10701304
parameter: metaid_0000011
parameter: metaid_0000019
parameter: metaid_0000024
units def: metaid_0000016
rule: metaid_0000033
compartment: metaid_0000003
units def: metaid_0000015
parameter: metaid_0000022
reaction: metaid_0000023
name: Nelson2000_HIV-1_intracellular_delay
type: SBMLModel
notes: described in: A model of HIV-1 pathogenesis that includes an intracellular delay. Nelson PW, Murray JD, Perelson AS; Math Biosci. 2000 Feb;163(2):201-15. PMID: 10701304 ; doi: 10.1016/S0025-5564(99)00055-3 Abstract: Mathematical modeling combined with experimental measurements have yielded important insights into HIV-1 pathogenesis. For example, data from experiments in which HIV-infected patients are given potent antiretroviral drugs that perturb the infection process have been used to estimate kinetic parameters underlying HIV infection. Many of the models used to analyze data have assumed drug treatments to be completely efficacious and that upon infection a cell instantly begins producing virus. We consider a model that allows for less then perfect drug effects and which includes a delay in the initiation of virus production. We present detailed analysis of this delay differential equation model and compare the results to a model without delay. Our analysis shows that when drug efficacy is less than 100%, as may be the case in vivo, the predicted rate of decline in plasma virus concentration depends on three factors: the death rate of virus producing cells, the efficacy of therapy, and the length of the delay. Thus, previous estimates of infected cell loss rates can be improved upon by considering more realistic models of viral infection. Author Keywords: HIV; Delay; Viral life cycle; T-cells As the initial conditions for the intergrations where not known, approximate inital conditions for the steady state at k=3.47*10 -8 where chosen ( T * =1675 ). The model does not reprodue the results given in the article quantitatively, but the time courses are quite similar. For running the model, the initial conditions for t < 0 should be the same as the steady state ones. This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related…
reaction: metaid_0000031
units def: metaid_0000017
reaction: metaid_0000028
time units: metaid_0000005
species: metaid_0000008

metaid_0000009
notes: infectious virius (VI )
constant: false
boundary condition: false
has only substance units: false
initial concentration: 134000.0
initial amount: NaN
in compartment: metaid_0000003
name: V_I
type: Species

001255
exponent: 1.0
scale: 0
multipler: 1.0
kind: ITEM
type: SBMLUnit

metaid_0000029
kinetic law: 001460
reactant: 001448
fast: false
reversible: true
name: clearance of infectious virions
type: Reaction

001291
exponent: -1.0
scale: 0
multipler: 86400.0
kind: SECOND
type: SBMLUnit

metaid_0000019
constant: true
units: metaid_0000013
value: 0.5
name: delta
type: Parameter

metaid_0000021
unit: 001316
name: virions_per_cell
type: SBMLUnitsDef

metaid_0000015
unit: 001243
name: ml
type: SBMLUnitsDef

metaid_0000031
kinetic law: 001508
reactant: 001496
fast: false
reversible: false
name: infected Tcell lysis
type: Reaction

metaid_0000022
constant: true
units: metaid_0000013
value: 3.0
name: c
type: Parameter

metaid_0000006
unit: 001219
name: items
type: SBMLUnitsDef

metaid_0000012
constant: true
units: metaid_0000017
value: 3.43E-8
name: k
type: Parameter

001304
exponent: -1.0
scale: 0
multipler: 1.0
kind: ITEM
type: SBMLUnit

metaid_0000026
kinetic law: 001400
modifier: 001388
product: 001376
fast: false
reversible: false
name: release of infectious virions on lysis
type: Reaction