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
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
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
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