Tutorial on modelling signalling pathways

Quick overview of the supporting files

1) Introduction to models that are used in this tutorial:
	tutorial introduction (PDF)

2) Course Tutorial Handouts:
	Exercise: model building & simulation (PDF)

3) Bistability (MAPK double phosphorylation):

   i.  Ortega F, Garcés JL, Mas F, Kholodenko BN, Cascante M. Bistability from double phosphorylation in signal transduction. Kinetic and structural requirements. FEBS J 2006 Sep;273(17):3915-26. 
        [BIOMD0000000258] 
	
	Reference	: Ortega2006.pdf
	SBML file	: BIOMD0000000258.xml (to be imported to COPASI for simulation)
	COPASI file	: ortega_parameterscan_sss.cps (open in COPASI and run parameter scan simulation to get the plot) 
	                  ortega_parameterscan_bistable.cps (open in COPASI and run parameter scan simulation to get the plot) 

4) MAPK cascade:

   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)

	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)

5) p53/MDM2 circuit:

        Proctor CJ, Gray DA. Explaining oscillations and variability in the p53-Mdm2 system. BMC Syst Biol. 2008 Aug 18;2:75.
        Reference       : Proctor2008.pdf

   i.   p53 stabilization by ARF - BIOMD0000000189

        SBML file       : BIOMD0000000189.xml (to be imported to COPASI for simulation)
        COPASI file     : proctorARF_timecourse.cps (open in COPASI and run Time-course simulation to get the plot)

   ii.  p53 stabilization by ATM - BIOMD0000000188

        SBML file       : BIOMD0000000188.xml (to be imported to COPASI for simulation)
	COPASI file     : proctorATM_timecourse.cps (open in COPASI and run Time-course simulation to get the plot)

6) Repressilator:

        Elowitz MB, Leibler S. A synthetic oscillatory network of transcriptional regulators.
        Nature 2000 Jan;403(6767):335-8. -(BIOMD0000000012)

        Reference       : Elowitz2000.pdf
        SBML file       : BIOMD0000000012.xml (to be imported to COPASI for simulation)
        COPASI file     : elowitz_timecourse.cps (open in COPASI and run Time-course simulation to get the plot)