Introduction to BioModels Database and tutorial about modelling signalling pathways using COPASI (13th April 2010)

Materials

I) BioModels Talk:
	biomdtalk_13April2010.ppt

II) Introduction to models that will be used in the tutorial:
        tutorial_present13April2010.pdf

III) Course Tutorial Handouts:
        tutorial_13April2010.pdf
        tutorial_13April2010.pdf

1) MAPK cascade:

        Reference               : Vayttaden2004.pdf (Evolution of modeling with 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)

2) 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) 

3) 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)