Tutorial about modelling signalling pathways and lecture on BioModels Database (27th June 2013)

Date:
27th June 2013
Event:
Joint EMBL-EBI-Wellcome Trust Course: In silico Systems Biology
Topic:
Tutorial about modelling signalling pathways and lecture on BioModels Database

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:

   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)

  iii.  Ortega F, Garc├ęs 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) 


BioModels Database course materials