Introduction to BioModels Database and tutorial about modelling signalling pathways (10th October 2010)

Materials

1) BioModels talk:
	
	biomdtalk_10Oct2010.pdf 

2) Course Tutorial Handouts:
	tutorial_10Oct2010.pdf

3) Encoding and Simulation model:

    Bistability (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 files	: bistability.xml (saved model when encoded 
                          using SBMLeditor) and BIOMD0000000258.xml 
			  (These two files could be imported to 
			  COPASI for simulation)

    MAPK cascade:

    ii.	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)

   iii. 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 file	: 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)

   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) 

   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)