MRes Bioinformatics: Systems Biology Coursework

Issue date: 29/02/2008
Due date: 14/03/2008, 4pm.

(1) Create an SBML model for the artificial signalling cascade (for outline form see below) [6 marks]

(2) Modify your model to include negative feedback [2 marks]

(2) Produce time-plot simulations for the behaviours of (1) and (2). Try to to produce oscillations for the negative feedback model. [4 marks]

(3) Give a representation of the pathway with negative feedback and explicitly including the phosphotases as a graph, using set notation. [4 marks]

(4) Give a representation of the pathway with negative feedback and explicitly including the phosphotases as an adjacency matrix [4 marks]

Notes: Your submission should comprise
(i) a hard-copy submission including the

This hard-copy should be submitted to Mrs Margaret Jackson in the Bioinformatics Research Centre, Joseph Black building, B3.09.

(ii) An email submission of your SBML model and any accompanying simulation files. PENALTY FOR NO ELECTRONIC SUBMISSION = -6 marks
to gux@dcs.gla.ac.uk using as the subject line the following:
MRes systems biology coursework submission from YOURNAME

cascade.png

Rate constants and initial concentrations required for the modelling and simulation of the pathway are:

k1=100, k2=4, k3=1
k1'=k1, k2'=k2 etc
kk1=k1, kk2=k2 etc.
Inhibition ki1=1000000, ki2=0.4

Take initial concentrations of the unphosphoyrlated proteins as 100 units, the kinases as 1 unit, the phosphotases as 1 unit, and everything else as zero.