Tutorial about modelling signalling pathways and lecture on BioModels Database (27th April 2012)

Materials

1) Introduction to models that are used in this tutorial:
	tutorial_presentation.pdf

2) Course Tutorial Handouts:
	tutorial_handout.pdf

3) Mathematical Models of MAPK cascade:

	Reference	: Vayttaden2004.pdf (Evolution of MAPK models)

   i.	Huang CY, Ferrell JE Jr. Ultrasensitivity in the mitogen-activated protein kinase
	cascade. Proc Natl Acad Sci U S A. 1996 Sep 17;93(19):10078-83.
	[BIOMD0000000009]

	Reference	: Huang1996.pdf
	SBML file	: BIOMD0000000009.xml (to be imported to COPASI for simulation)
	COPASI file	: huang_timecourse.cps (open in COPASI and run Time-course simulation to get the plot) 
			  huang_parameterscan.cps (open in COPASI and run paramter scan to get the plot)

   ii.	Kholodenko BN. Negative feedback and ultrasensitivity can bring about oscillations 
	in the mitogen-activated protein kinase cascades. Eur J Biochem. 2000 Mar;267(6):1583-8. -
	[BIOMD0000000010]
	
	Reference	: Kholodenko2000.pdf
	Simulation without negative feedback:
	COPASI files	: kholodenko.cps (COPASI base file: without negative feedback)
			  kholodenko_timecourse.cps (open in COPASI and run Time-course simulation to get the plot)
			  kholodenko_parameterscan.cps (open in COPASI and run parameter scan to get the plot)

	Simulation with Negative feedback:
	SBML file	: BIOMD0000000010.xml
	COPASI file	: kholodenko_nf.cps (COPASI file with negative feedback)
			  kholodenko_nf_timecourse.cps (open in COPASI and run Time-course simulation to get the plots (timecourse and phaseplot)
			  kholodenko_nf_parameterscan.cps (open in COPASI and run parameter scan to get the plots (timecourse and phaseplot)

  iii.	Markevich NI, Hoek JB, Kholodenko BN. Signaling switches and bistability arising from multisite
        phosphorylation in protein kinase cascades. J Cell Biol 2004 Feb 2;164(3):353-9. 
        [BIOMD0000000027] 
	
	Reference	: Markevich2004.pdf
	SBML file	: BIOMD0000000027.xml (to be imported to COPASI for simulation)
	COPASI file	: markevich_parameterscan1.cps (open in COPASI and run parameter scan simulation to get the plot) 
	                  markevich_parameterscan1.cps (open in COPASI and run parameter scan simulation to get the plot)