Nelson2000- HIV-1 general model 1

  public model
Model Identifier
BIOMD0000000875
Short description

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.

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To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
Format
SBML (L2V4)
Related Publication
  • A model of HIV-1 pathogenesis that includes an intracellular delay.
  • Nelson PW, Murray JD, Perelson AS
  • Mathematical biosciences , 2/ 2000 , Volume 163 , pages: 201-215 , PubMed ID: 10701304
  • Department of Mathematics, Duke University, Durham, NC 27708, USA.
  • 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.
Contributors
Submitter of the first revision: Lukas Endler
Submitter of this revision: Mohammad Umer Sharif Shohan
Modellers: Lukas Endler, Mohammad Umer Sharif Shohan

Metadata information

is (2 statements)
BioModels Database MODEL8268650277
BioModels Database MODEL8268650277

isDescribedBy (1 statement)
PubMed 10701304

hasTaxon (1 statement)
Taxonomy Homo sapiens

isVersionOf (2 statements)
hasProperty (1 statement)
Mathematical Modelling Ontology Ordinary differential equation model

Curation status
Curated
Tags

Connected external resources

SBGN view in Newt Editor

Name Description Size Actions

Model files
Nelson2000.xml SBML L2V4 representation of Nelson2000 HIV-1_general_model 26.71 KB Preview | Download

Additional files
MODEL8268650277-biopax2.owl Auto-generated BioPAX (Level 2) 7.25 KB Preview | Download
MODEL8268650277-biopax3.owl Auto-generated BioPAX (Level 3) 12.77 KB Preview | Download
MODEL8268650277.m Auto-generated Octave file 3.60 KB Preview | Download
MODEL8268650277.pdf Auto-generated PDF file 162.37 KB Preview | Download
MODEL8268650277.png Auto-generated Reaction graph (PNG) 30.94 KB Preview | Download
MODEL8268650277.sci Auto-generated Scilab file 226.00 Bytes Preview | Download
MODEL8268650277.svg Auto-generated Reaction graph (SVG) 15.39 KB Preview | Download
MODEL8268650277.vcml Auto-generated VCML file 19.40 KB Preview | Download
MODEL8268650277.xpp Auto-generated XPP file 2.42 KB Preview | Download
MODEL8268650277_url.xml old xml file 13.24 KB Preview | Download
MODEL8268650277_urn.xml Auto-generated SBML file with URNs 14.13 KB Preview | Download
Nelson2000.cps COPASI version 4.24 (Build 197) representation of Nelson2000 HIV-1_general_model 59.34 KB Preview | Download
Nelson2000.sedml SEDML L1V2 representation of Nelson2000 HIV-1_general_model 3.70 KB Preview | Download

  • Model originally submitted by : Lukas Endler
  • Submitted: Jul 22, 2009 3:17:34 PM
  • Last Modified: Nov 26, 2019 1:39:42 PM
Revisions
  • Version: 5 public model Download this version
    • Submitted on: Nov 26, 2019 1:39:42 PM
    • Submitted by: Mohammad Umer Sharif Shohan
    • With comment: Automatically added model identifier BIOMD0000000875
  • Version: 2 public model Download this version
    • Submitted on: Sep 23, 2009 4:52:15 PM
    • Submitted by: Lukas Endler
    • With comment: Current version of Nelson2000_HIV-1_general_model
  • Version: 1 public model Download this version
    • Submitted on: Jul 22, 2009 3:17:34 PM
    • Submitted by: Lukas Endler
    • With comment: Original import of Nelson 2000 HIV-1 general model

(*) You might be seeing discontinuous revisions as only public revisions are displayed here. Any private revisions unpublished model revision of this model will only be shown to the submitter and their collaborators.

Legends
: Variable used inside SBML models


Species
Species Initial Concentration/Amount
V I

C14283 		134000.0 item
T

uninfected 		180000.0 item
V NI 0.0 item
T i

infected cell 		1675.0 item
Reactions
Reactions Rate Parameters
V_I => plasma*c*V_I c = 3.0 1/ms
T => T_i; V_I plasma*k*V_I*T k = 3.43E-8 l/(s*#)
=> V_NI; T_i plasma*np*N*delta*T_i np = 0.5 1; N = 480.0 1; delta = 0.5 1/ms
=> V_I; T_i plasma*(1-np)*N*delta*T_i np = 0.5 1; N = 480.0 1; delta = 0.5 1/ms
T => plasma*delta1*T delta1 = 0.03 1/ms
=> T plasma*lambda lambda = 10.0 #/(l*s)
T_i => plasma*delta*T_i delta = 0.5 1/ms
V_NI => plasma*c*V_NI c = 3.0 1/ms
Curator's comment:
(added: 26 Nov 2019, 13:38:47, updated: 26 Nov 2019, 13:38:47)
The model has been encoded in COPASI 4.24 (Build 197) and the Figure 2 of the publication has been generated. The value of np was 0.05 for the right and 0.08 for the left one. The figures are very much similar to the publication although the left one is a bit high at the end in the publication but our simulated model did not show that.