1) Introduction to models that are used in this tutorial: tutorial_presentation.pdf 2) Course Tutorial Handout: 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 : Huang1996.xml (to be imported to COPASI for simulation) COPASI file : Huang1996_time_course.cps (open in COPASI and run Time-course simulation to get the plot) Huang1996_parameter_scan.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 : Kholodenko2000_noFeedback.cps (COPASI base file: without negative feedback) Kholodenko2000_noFeedback_time_course.cps (open in COPASI and run Time-course simulation to get the plot) Simulation with Negative feedback: SBML file : Kholodenko2000_negFeedback.xml COPASI file : Kholodenko2000_negFeedback.cps (COPASI file with negative feedback) Kholodenko2000_negFeedback_time_course.cps (open in COPASI and run Time-course simulation to get the plot)
iii. Markevich NI, Hoek JB, Kholodenko BN. Signalling 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 : Markevich2004_parameterscan1.cps (open in COPASI and run parameter scan to get the plot) Markevich2004_parameterscan2.cps (open in COPASI and run parameter scan to get the plot)