Waugh2006 - Diabetic Wound Healing - TGF-B Dynamics

  public model
Model Identifier
BIOMD0000000680
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 MODEL1006230011
BioModels Database BIOMD0000000680

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
BIOMD0000000680_url.xml SBML L2V4 representation of Waugh2006 - Diabetic Wound Healing - TGF-B Dynamics 33.42 KB Preview | Download

Additional files
BIOMD0000000680-biopax2.owl Auto-generated BioPAX (Level 2) 5.78 KB Preview | Download
BIOMD0000000680-biopax3.owl Auto-generated BioPAX (Level 3) 6.25 KB Preview | Download
BIOMD0000000680.m Auto-generated Octave file 3.75 KB Preview | Download
BIOMD0000000680.pdf Auto-generated PDF file 148.36 KB Preview | Download
BIOMD0000000680.png Auto-generated Reaction graph (PNG) 4.27 KB Preview | Download
BIOMD0000000680.sci Auto-generated Scilab file 210.00 Bytes Preview | Download
BIOMD0000000680.svg Auto-generated Reaction graph (SVG) 845.00 Bytes Preview | Download
BIOMD0000000680.vcml Auto-generated VCML file 900.00 Bytes Preview | Download
BIOMD0000000680.xpp Auto-generated XPP file 1.91 KB Preview | Download
BIOMD0000000680_urn.xml Auto-generated SBML file with URNs 33.40 KB Preview | Download
Waugh2006_2.cps Curated and annotated copasi file. 45.76 KB Preview | Download
Waugh2006_2.sedml SED-ML file to produce figure 2 (bottom row) of the reference publication. A parameter scan with one interval will change the value of alpha from 0.5 (normal) to 0.8 (diabetic). 3.13 KB Preview | Download

  • Model originally submitted by : Camille Laibe
  • Submitted: Jun 23, 2010 10:11:54 AM
  • Last Modified: Mar 1, 2018 1:02:54 PM
Revisions
  • Version: 3 public model Download this version
    • Submitted on: Mar 1, 2018 1:02:54 PM
    • Submitted by: administrator
    • With comment: Curated and annotated XML file
  • Version: 2 public model Download this version
    • Submitted on: Jun 25, 2010 1:10:18 PM
    • Submitted by: Camille Laibe
    • With comment: Current version of Waugh2006_WoundHealingMacrophageDynamics_Diabetic_ModelC
  • Version: 1 public model Download this version
    • Submitted on: Jun 23, 2010 10:11:54 AM
    • Submitted by: Camille Laibe
    • With comment: Original import of Waugh2006_WoundHealingMacrophageDynamics_Diabetic_ModelC

(*) 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
T

TGF-beta 		6.0 mol
phi R

macrophage ; Wound Repair 		200.0 mol
phi I

inflammatory macrophage ; macrophage 		200.0 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)
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)
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
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
Curator's comment:
(added: 01 Mar 2018, 15:03:27, updated: 01 Mar 2018, 15:03:27)
Figure 2 (bottom row) of the reference publication illustrating TGF-B dynamics has been curated. The time scale used in the curated, diabetic wound simulation (bottom) is twice as long as in the reference publication. A parameter scan with one interval can change the value of alpha from 0.5 (normal) to 0.8 (diabetic). The simulations were performed in COPASI 4.22 (Build 170) and the figures were generated in MATLAB R2014b.