MODEL8268650277
type: SBMLModel
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
area units: area
parameter: metaid_0000037
is described by: http://identifiers.org/pubmed/10701304
curated: false
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
units def: metaid_0000017
name: Nelson2000_HIV-1_general_model
parameter: metaid_0000019
units def: metaid_0000021
length unit: length
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_0000027
type: Parameter
notes: protease inhibitor efficacy
constant: true
units: dimensionless
value: 0.1
name: np

metaid_0000006
type: SBMLUnitsDef
unit: 041112
name: items

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

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

metaid_0000009
type: Species
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

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

041318
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

metaid_0000008
type: Species
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*

041306
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

metaid_0000007
type: Species
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

metaid_0000015
type: SBMLUnitsDef
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name: ml

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scale: -3
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kind: LITRE

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

041378
type: SpeciesReference
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species: metaid_0000009

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

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

metaid_0000021
type: SBMLUnitsDef
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name: virions_per_cell

041209
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constant: true
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value: 3.0
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metaid_0000013
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name: per day

041124
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metaid_0000037
type: Parameter
constant: true
units: metaid_0000013
value: 0.03

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

041451
type: SpeciesReference
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species: metaid_0000009

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

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species: metaid_0000007

metaid_0000028
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kinetic law: 041439
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fast: false
reversible: false
name: release of non infectious virions on lysis

041415
type: SpeciesReference
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species: metaid_0000010

metaid_0000010
type: Species
notes: non-infectious virus (VNI )
constant: false
boundary condition: false
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constant: true
units: metaid_0000017
value: 3.43E-8
name: k

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

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

041354
type: SpeciesReference
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species: metaid_0000008

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

metaid_0000035
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constant: true
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value: 10.0

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name: items per (ml*day)

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kind: LITRE

041221
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kind: ITEM

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

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

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type: SpeciesReference
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species: metaid_0000010

metaid_0000038
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reversible: false
name: loss of uninfected T-cell

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