GSTDMB 2012: DYNAMICAL MODELLING FOR BIOLOGY AND MEDICINE

Introducory quiz

Lecture Notes

lect1_intro.pdf: Mathematical modelling and Systems Biology

lect2_ModellingWithDifferentialEquations.pdf: Introduction to modelling with differential equations

lect3_MultiVariableModels.pdf: Multi-variable models

lect4_parameters.pdf: Parameter estimation and sensitivity analysis

Practical 1 files

Single-variable models (using CellDesigner). The worksheet can be found here: GSTDMB2012_CellDesignerPractical-SingleVariable.pdf.

SBML files (see also the BioModels Database):
PositiveFeedback.xml | toggle_mro_new.xml | repressilator_mro.xml | BIOMD0000000005.xml | BIOMD0000000079.xml | BIOMD0000000209_Chickarmane.xml | MAPK.xml

Practical 2 files

Multi-variable models (using CellDesigner). This practical considers a toggle switch model and a multicomponent negative feedback loop which oscillates when feedback is regulated by a dimer of transcription factors. The worksheet can be found here: GSTDBM2012_CellDesignerPractical-MultiVariable.pdf.

SBML files: Toggle switch | Negative feedback | Negative feedback regulated by dimerisation | Simplified Repressilator | Full Repressilator model

Practical 3 files

GSTDMB2012_prac-copasi.pdf
This practical uses COPASI to fit the parameters of a simple positive feedback model.
COPASI files - one model file and four data files: positivefeedback.cps | positivefeedback_timecourse_ic1_i05.txt | positivefeedback_timecourse_ic2_i05.txt | positivefeedback_timecourse_ic1_i20.txt | positivefeedback_timecourse_ic2_i20.txt

The worksheet together with Copasi file and data files can be found in this archive: GSTDMB2012_prac-parameters.zip


Last update: 10 July 2012 | Maintained by Markus Owen | © Markus Owen 2012