metaid_0000029
kinetic law: 041463
reactant: 041451
fast: false
reversible: true
name: clearance of infectious virions
type: Reaction

metaid_0000021
unit: 041209
name: virions_per_cell
type: SBMLUnitsDef

041209
exponent: 1.0
scale: 0
multipler: 1.0
kind: DIMENSIONLESS
type: SBMLUnit

041124
exponent: -1.0
scale: 0
multipler: 86400.0
kind: SECOND
type: SBMLUnit

041475
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

041173
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000038
kinetic law: 041294
reactant: 041282
fast: false
reversible: false
name: loss of uninfected T-cell
type: Reaction

041148
exponent: 1.0
scale: 0
multipler: 1.0
kind: ITEM
type: SBMLUnit

metaid_0000008
notes: infected T-cells
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1675.0
initial amount: NaN
in compartment: metaid_0000003
name: T*
type: Species

041318
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

041258
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

041197
exponent: -1.0
scale: 0
multipler: 1.0
kind: ITEM
type: SBMLUnit

metaid_0000034
kinetic law: 041270
product: 041258
fast: false
reversible: false
name: creation of T-cells
type: Reaction

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

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

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

041234
exponent: -1.0
scale: -3
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000026
kinetic law: 041403
modifier: 041391
product: 041378
fast: false
reversible: false
name: release of infectious virions on lysis
type: Reaction

metaid_0000017
unit: 041197
unit: 041185
unit: 041173
name: ml per (item*day)
type: SBMLUnitsDef

041100
exponent: 1.0
scale: 0
multipler: 86400.0
kind: SECOND
type: SBMLUnit

metaid_0000037
constant: true
units: metaid_0000013
value: 0.03
type: Parameter

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

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

metaid_0000013
unit: 041124
name: per day
type: SBMLUnitsDef

metaid_0000031
kinetic law: 041366
reactant: 041354
fast: false
reversible: false
name: infected T-cell lysis
type: Reaction

041161
exponent: -1.0
scale: -3
multipler: 1.0
kind: LITRE
type: SBMLUnit

041282
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

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

041136
exponent: 1.0
scale: -3
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000023
kinetic law: 041342
modifier: 041330
product: 041318
reactant: 041306
fast: false
reversible: false
name: T-cell infection
type: Reaction

041378
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

041306
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

041221
exponent: 1.0
scale: 0
multipler: 1.0
kind: ITEM
type: SBMLUnit

041185
exponent: -1.0
scale: 0
multipler: 86400.0
kind: SECOND
type: SBMLUnit

metaid_0000036
unit: 041246
unit: 041234
unit: 041221
name: items per (ml*day)
type: SBMLUnitsDef

metaid_0000016
unit: 041161
unit: 041148
name: items per ml
type: SBMLUnitsDef

metaid_0000032
notes: number of both infectious and non-infectous virions per ml
constant: false
units: metaid_0000016
value: NaN
name: HIV
type: Parameter

041354
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

metaid_0000006
unit: 041112
name: items
type: SBMLUnitsDef

041246
exponent: -1.0
scale: 0
multipler: 86400.0
kind: SECOND
type: SBMLUnit

metaid_0000030
kinetic law: 041487
reactant: 041475
fast: false
reversible: false
name: non-infect. virion clearance
type: Reaction

metaid_0000028
kinetic law: 041439
modifier: 041427
product: 041415
fast: false
reversible: false
name: release of non infectious virions on lysis
type: Reaction

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

MODEL8268650277
parameter: metaid_0000027
units def: metaid_0000006
reaction: metaid_0000023
units def: metaid_0000015
reaction: metaid_0000026
units def: metaid_0000016
parameter: metaid_0000020
parameter: metaid_0000022
time units: metaid_0000005
parameter: metaid_0000037
is described by: http://identifiers.org/pubmed/10701304
curated: false
length unit: length
type: SBMLModel
units def: metaid_0000005
reaction: metaid_0000029
reaction: metaid_0000034
reaction: metaid_0000028
compartment: metaid_0000003
parameter: metaid_0000012
species: metaid_0000010
units def: metaid_0000013
reaction: metaid_0000031
species: metaid_0000007
rule: metaid_0000033
area units: area
units def: metaid_0000017
name: Nelson2000_HIV-1_general_model
parameter: metaid_0000019
units def: metaid_0000021
notes: This is the general model without delay described by the equation system (1) 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 there are no results given for this model in the article it cannot be checked for MIRIAM compliance. The SBML file should be equivalent to the described ODE file though. 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 or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedica…
substance units: metaid_0000006
parameter: metaid_0000035
units def: metaid_0000036
parameter: metaid_0000032
volume units: metaid_0000015
reaction: metaid_0000030
species: metaid_0000008
reaction: metaid_0000038
species: metaid_0000009

metaid_0000035
constant: true
units: metaid_0000036
value: 10.0
type: Parameter

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

metaid_0000015
unit: 041136
name: ml
type: SBMLUnitsDef

metaid_0000005
unit: 041100
name: day
type: SBMLUnitsDef

041415
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

041112
exponent: 1.0
scale: 0
multipler: 1.0
kind: ITEM
type: SBMLUnit

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

041451
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference