Tutorial on modelling chemical kinetics with COPASI

Presentation: "The many faces of modelling in biology"

Presentation: "Introduction to chemical kinetics"

Tutorial handout: "Building and Simulating Models using COPASI"

Material needed for the course:

MAPK model from Huang and Ferrell 1996 in SBML: Huang1996.xml

MAPK model from Kholodenko 2000, without feedback: Kholodenko2000-noFeedback.cps

MAPK model from Kholodenko 2000, with feedback: Kholodenko2000-Feedback.cps

Model of gene switch without feedback: Switch-noFeedback.cps

Model of gene switch without feedback: Switch-Feedback.cps

Model for parameter estimation: Autophagy.cps

Dataset for parameter estimation: ATG13.csv