Network simulations and inferring network connectivity, Simulation in MATLAB

The objective of this problem is to simulate reaction networks for different connectivity. Another objective is to guess the network connectivity from given experimental data. Matlab code has been provided to you (attached) for a large number of reaction networks. Your first task is to just run the matlab code for a variety of networks and examine the trends in the results. We have split the matlab code provided to you into two parts (i) function files that contain the differential equations describing a network e.g. "reactionsABCDE.m" and (ii) corresponding script files that run the function for a given set of parameters e.g. run_reactionsABCDE.m

Tasks to perform

(a) Simulation of Linear Reaction Networks:

Run the matlab code provided to you for the following linear reaction networks (A → B, A → B → C, A→ B → C → D, and A→ B → C → D → E). Comment on the trends for the time dependent profiles for the starting reactant in the network, the intermediates and the end-points in the network. Develop an intuition for the time dependent behavior of various components?

Can you guess the sequence of a linear reaction network if you are given the data for individual species just by looking at the trends? You will use the heuristic information on such trends to reduce the search space in the network connectivity inference problem (part c) on more complicated branched networks with inhibition and activation.

(b) Simulation of Branched Reaction Networks

Run the matalb code provided to you for the following branched reaction networks (i) ABC_AD which is linear ABC with a branching from A to D (ii) ABC_BD which is linear ABC with a branching from B to D. Examine the branched reaction network shown below for the species A through G. Write down the corresponding differential equations and create a function file.

Create script files with different parameter values and simulate the branched network below.

Provide the simulated results for the case where all ki have the value of 1.0

(c) Inferring Network Connectivity from Experimental Data. Our objective is to guess the network connectivity from available experimental data.

The following experimental data are provided to you (as plots and as tables). Based on experience from forward simulation of known networks, can you guess the connectivity of the network? There is a species in one network that is inhibiting another species in the second network. Assume all k values to be 1. Guess network connectivity, simulate the network and try to figure out which metabolite is inhibiting which reaction. Assume that the coefficient of inhibition follows the form: 1/(1+[C]^n) where [C] is the concentration of the inhibiting metabolite and 'n' is the Hill coefficient. The function xlsread can be used to input the data from the EXCEL file into matlab if desired.

Posted Date: 2/15/2013 4:40:13 AM | Location : United States

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