EpidermalERKMAPK Files

This folder contains various scripts to generate an SBML model describing
	activation (phosphorylation) of ERK-MAPK components across the 
	depth of human epidermis. The model was initially created in 
	MATLAB by Dr Jerry Gao (jerry.gao@unimelb.edu.au) and subsequently
	implemented in SBML for submission at BMC Systems Biology.

The associated manuscript should be referred to for further details:
	Cursons, J., Gao, J., Hurley, D.G., Print, C.G., Dunbar, 
		P.R, Jacobs, M.D. & Crampin, E.J. (2015).
		Regulation of ERK-MAPK Signalling in Human Epidermis.
		BMC Systems Biology, 9:41 (25 July 2015).
		DOI: 10.1186/s12918-015-0187-6
		PMID: 26209520


The modelling framework used here is a 'normalized-Hill differential 
	equation' approach, as described within:
	Kraeutler, Matthew J., Soltis, Anthony R., & Saucerman, Jeffrey J.
	(2010). Modeling cardiac ß-adrenergic signaling with normalized
	-Hill differential equations: comparison with a biochemical model.
	BMC Systems Biology. Nov, 18;4: pp. 157
	DOI: 10.1186/1752-0509-4-157
	PMID: 21087478

The resulting SBML model was deposited in BioModels Database [Li C et 
	al. BioModels Database: An enhanced, curated and annotated 
	resource for published quantitative kinetic models. BMC Systems
	Biology 2010, 4:92] and assigned the identifier MODEL1503270000.
	SED-ML scripts to execute this model at various spatial
	positions, are available together with various MATLAB scripts, 
	from:
		http://sourceforge.net/projects/epidermalerkmapk/


For further details, please contact:
	Joe Cursons: joseph.cursons@unimelb.edu.au 
	Edmund Crampin: edmund.crampin@unimelb.edu.au

Last updated 03/08/15


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General information (by file type):

py files: Two python scripts are included with this project:
	1) the SBML creation script, which uses libSBML to specify the model functions and components
	2) a general python script which takes the SEDML time course .csv file and plots the steady-state output
		to recapitulate Fig. 4 from the paper

XML files: this folder contains several XML files, which correspond to:
	1) the SBML model (SBML_...xml) describing the normalized-Hill differential equations
	2) SED-ML scripts (SEDML_...xml) which execute the SBML model under different conditions and produce 
		outputs presented within the above paper


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Information on specific files (alphabetical order):

createEpiMAPKSBMLModel.py - a python script which uses libSBML to create the Cursons2015_EpidermalERKMAPK SBML
	model.
	Note that this script is fairly well commented and contains some documentation on model
	 derivation/creation.

Fig4_fromSEDMLResults.png - the output figure generated by 'plotSEDMLOutput.py', showing SED-ML generated 
	results which recapitulate Fig. 4.

plotSEDMLOutput.py - a python script which takes the .csv output from the SED-ML simulations and produces
	a scatter plot to display the data for reproducing Fig. 4.

README.txt - this documentation file

SBML_Cursons2015_EpidermalERKMAPK.xml - an SBML model describing the normalized-Hill differential equations which
	are influenced by spatially-dependent Ca^2+ and CaM signals. For further details, please refer to the
	comments within the 'createEpiMAPKSBMLModel.py' script or the associated manuscript.

SEDML_EpidermalMAPK_varySpatPos_execTimeCourse.xml - a SED-ML script which takes the EpidermalERKMAPK model and
	evaluates it at different spatial positions across the epidermis, running the model for a small time
	period and allowing the steady-state to be reached. Outputs from this script at the time of release
	to sourceforge include:
	- SEDML_EpidermalMAPK_varySpatPos_execTimeCourse-output.emf - an export of the time course evaluation plots
	- SEDML_EpidermalMAPK_varySpatPos_execTimeCourse-output.csv - an export of the time course evaluation data
	- SEDML_EpidermalMAPK_varySpatPos_execTimeCourse-output_ScatPlot.png - a scatter plot of the final
		time-point within the above csv, created using 'plotSEDMLOutput.py'


SEDML_EpidermalMAPK_varySpatPos_execTimeCourse_noCamRafInhib.xml - a SED-ML script which takes the EpidermalERKMAPK 
	model with no CaM-mediated inhibition of Raf, and evaluates it at different spatial positions across the epidermis, 
	running the model for a small time period and allowing the steady-state to be reached. Outputs from this script at
	the time of releaseto sourceforge include:
	- SEDML_EpidermalMAPK_varySpatPos_execTimeCourse_noCamRafInhib-output.emf - an export of the time course
		evaluation plots, for the model where CaM inhibition of Raf has been removed
	- SEDML_EpidermalMAPK_varySpatPos_execTimeCourse_noCamRafInhib-output.csv - an export of the time course evaluation
		data, for the model where CaM inhibition of Raf has been removed
	- SEDML_EpidermalMAPK_varySpatPos_execTimeCourse_noCamRafInhib-output_ScatPlot.png - a scatter plot of the final
		time-point within the above csv, created using 'plotSEDMLOutput.py'