Waugh2006 - Diabetic Wound Healing - Treated and Untreated Macrophage Dynamics

  public model
Model Identifier
BIOMD0000000681
Short description

This a model from the article:
Macrophage dynamics in diabetic wound dealing.
Waugh HV, Sherratt JA. Bull Math Biol 2006 Jan;68(1):197-207 16794927 ,
Abstract:
Wound healing in diabetes is a complex process, characterised by a chronic inflammation phase. The exact mechanism by which this occurs is not fully understood, and whilst several treatments for healing diabetic wounds exist, very little research has been conducted towards the causes of the extended inflammation phase. We describe a mathematical model which offers a possible explanation for diabetic wound healing in terms of the distribution of macrophage phenotypes being altered in the diabetic patient compared to normal wound repair. As a consequence of this, we put forward a suggestion for treatment based on rectifying the macrophage phenotype imbalance.

This model was taken from the CellML repository and automatically converted to SBML.
The original model was: Waugh HV, Sherratt JA. (2006) - version=1.0
The original CellML model was created by:
Catherine Lloyd
c.lloyd@auckland.ac.nz
The University of Auckland

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). 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 Dedication for more information.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not..

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
  • Macrophage dynamics in diabetic wound dealing.
  • Waugh HV, Sherratt JA
  • Bulletin of mathematical biology , 1/ 2006 , Volume 68 , Issue 1 , pages: 197-207 , PubMed ID: 16794927
  • School of Mathematics and Computing, Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS, UK. hwaugh@ma.hw.ac.uk
  • Wound healing in diabetes is a complex process, characterised by a chronic inflammation phase. The exact mechanism by which this occurs is not fully understood, and whilst several treatments for healing diabetic wounds exist, very little research has been conducted towards the causes of the extended inflammation phase. We describe a mathematical model which offers a possible explanation for diabetic wound healing in terms of the distribution of macrophage phenotypes being altered in the diabetic patient compared to normal wound repair. As a consequence of this, we put forward a suggestion for treatment based on rectifying the macrophage phenotype imbalance.
Contributors
Submitter of the first revision: Camille Laibe
Submitter of this revision: administrator
Modellers: administrator, Camille Laibe

Metadata information

is (2 statements)
BioModels Database MODEL1006230098
BioModels Database BIOMD0000000681

isDescribedBy (2 statements)
PubMed 16794927
PubMed 16794927

hasTaxon (1 statement)
Taxonomy Homo sapiens

isVersionOf (1 statement)
hasProperty (1 statement)
Experimental Factor Ontology diabetes mellitus


Curation status
Curated

Tags

Connected external resources

SBGN view in Newt Editor

Name Description Size Actions

Model files

BIOMD0000000681_url.xml SBML L2V4 representation of Waugh2006 - Diabetic Wound Healing - Treated and Untreated Macrophage Dynamics 36.76 KB Preview | Download

Additional files

BIOMD0000000681-biopax2.owl Auto-generated BioPAX (Level 2) 5.83 KB Preview | Download
BIOMD0000000681-biopax3.owl Auto-generated BioPAX (Level 3) 6.30 KB Preview | Download
BIOMD0000000681.m Auto-generated Octave file 4.10 KB Preview | Download
BIOMD0000000681.pdf Auto-generated PDF file 150.18 KB Preview | Download
BIOMD0000000681.png Auto-generated Reaction graph (PNG) 4.27 KB Preview | Download
BIOMD0000000681.sci Auto-generated Scilab file 67.00 Bytes Preview | Download
BIOMD0000000681.svg Auto-generated Reaction graph (SVG) 845.00 Bytes Preview | Download
BIOMD0000000681.vcml Auto-generated VCML file 900.00 Bytes Preview | Download
BIOMD0000000681.xpp Auto-generated XPP file 2.26 KB Preview | Download
BIOMD0000000681_urn.xml Auto-generated SBML file with URNs 36.74 KB Preview | Download
Waugh2006_3.cps Curated and annotated copasi file. 50.22 KB Preview | Download
Waugh2006_3.sedml SED-ML file to produce figure 2 (top and middle rows) of the reference publication. A parameter scan with one interval will change the value of the dummy_variable from zero to one, which will then either keep alpha constant or change alpha to 0.2. 3.27 KB Preview | Download

  • Model originally submitted by : Camille Laibe
  • Submitted: Jun 23, 2010 10:12:38 AM
  • Last Modified: Mar 1, 2018 1:12:42 PM
Revisions
  • Version: 3 public model Download this version
    • Submitted on: Mar 1, 2018 1:12:42 PM
    • Submitted by: administrator
    • With comment: Curated and annotated XML file
  • Version: 2 public model Download this version
    • Submitted on: Jun 25, 2010 2:48:24 PM
    • Submitted by: Camille Laibe
    • With comment: Current version of Waugh2006_WoundHealingMacrophageDynamics_Diabetic_ModelA
  • Version: 1 public model Download this version
    • Submitted on: Jun 23, 2010 10:12:38 AM
    • Submitted by: Camille Laibe
    • With comment: Original import of Waugh2006_WoundHealingMacrophageDynamics_Diabetic_ModelA

(*) 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
K T

monocyte ; monocyte migration into blood stream ; monocyte
296.53 mol
phi I

macrophage ; inflammatory macrophage
200.0 mol
phi R

macrophage ; Wound Repair
200.0 mol
T

TGF-beta
6.0 mol
Reactions
Reactions Rate Parameters
K_T = tau1*T^3+tau2*T^2+tau3*T+tau4 [] tau4 = 1.75 1/(0.0115741*m³*s); tau2 = 21.94 0.0864*mm³/(g²*s); tau1 = -2.47 8.64e-11*m^6/(g³*s); tau3 = 6.41 1/(11.5741*Mg*s)
phi_I = (alpha*K_T+k1*k2*phi_I*(1-k3*(phi_I+phi_R)))-d1*phi_I (alpha*K_T+k1*k2*phi_I*(1-k3*(phi_I+phi_R)))-d1*phi_I k3 = 0.002 0.001*m³; d1 = 0.2 1/(0.0115741*ms); k2 = 0.693 1/(0.0115741*ms); alpha = 0.8 1; k1 = 0.05 1
phi_R = ((1-alpha)*K_T+k1*k2*phi_R*(1-k3*(phi_I+phi_R)))-d1*phi_R ((1-alpha)*K_T+k1*k2*phi_R*(1-k3*(phi_I+phi_R)))-d1*phi_R k3 = 0.002 0.001*m³; d1 = 0.2 1/(0.0115741*ms); k2 = 0.693 1/(0.0115741*ms); alpha = 0.8 1; k1 = 0.05 1
T = k4*phi_I-d2*T k4*phi_I-d2*T k4 = 0.07 0.0864*µg/s; d2 = 9.1 1/(0.0115741*ms)
Curator's comment:
(added: 01 Mar 2018, 13:13:53, updated: 01 Mar 2018, 13:13:53)
A similar figure of figure 4 of the reference publication illustrating total macrophage density dynamics has been produced. The time scale used in the curated simulation is twice as long as in the reference publication and the value of alpha was changed at t=22 instead of t=10. A parameter scan with one interval can change the value of the dummy_variable from zero to one, which will then either keep alpha constant (untreated, black curve) or change alpha to 0.2 (treated, red curve). The simulations were performed in COPASI 4.22 (Build 170) and the figures were generated in MATLAB R2014b.