CPIB SUMMER SCHOOL 2011: INTRODUCTION TO BIOLOGICAL MODELLING

Day 1: Data, Networks and Models

Lecture 1.2: Introduction to modelling with differential equations (Owen) + associated quiz

Practical 1: CellDesigner / Analysis of single-variable models
Here is the SBML for the initial model PositiveFeedback.xml.
Additional example SBML files (see also the BioModels Database):
BIOMD0000000005.xml | BIOMD0000000079.xml | BIOMD0000000209_Chickarmane.xml | MAPK.xml

Day 2: Multi-variable models

Lecture 2.1: Building multi-variable models (Monk/Owen)

Lecture 2.2: Analysing multi-variable differential equation models (Monk/Owen)

Practical 2: Building and simulating multivariable models
This practical uses CellDesigner to build and simulating some multi-variable models, including the toggle switch, and a multicomponent negative feedback loop which oscillates when feedback is regulated by a dimer of transcription factors.
SBML files: Toggle switch | Negative feedback | Negative feedback regulated by dimerisation | Simplified Repressilator | Full Repressilator model

Day 3: Parameter estimation and sensitivity; Stochastic models

Lecture 3.1: Parameter estimation and sensitivity analysis (Owen)

Practical 3.1: Parameter estimation and sensitivity analysis
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

Lecture 3.2: Stochastic models (Monk)

Practical 3.2: Stochastic models
This practical uses COPASI to compare stochastic and deterministic simulations.
COPASI files - two model files: constitutive.cps | autoactivating.cps

Day 4: Multicellular modelling

Lecture 4.1: Spatial models - signalling, transport and growth (Monk)

Practical 4: Spatial models
MATLAB files - six model files: expode.m | simple_solver.m | notch_ring.m | notch_square.m | diffusion_grad.m | gierer_meinhardt.m

Lecture 4.2: Multiscale models and applications (Owen)