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Bioinformatics Assignment 1: Question 4a Screenshots

The document summarizes simulations of the stochastic simulation algorithm (SSA) using R. It includes 8 figures showing the results of SSA simulations with different initial conditions and substrate/enzyme copy numbers. The simulations demonstrate the effects of noise on the system as time increases and copy numbers decrease. Comparisons are made between SSA and stochastic BioNetGen model simulations, finding they produce almost identical graphs.

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Michael Gboneh
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38 views5 pages

Bioinformatics Assignment 1: Question 4a Screenshots

The document summarizes simulations of the stochastic simulation algorithm (SSA) using R. It includes 8 figures showing the results of SSA simulations with different initial conditions and substrate/enzyme copy numbers. The simulations demonstrate the effects of noise on the system as time increases and copy numbers decrease. Comparisons are made between SSA and stochastic BioNetGen model simulations, finding they produce almost identical graphs.

Uploaded by

Michael Gboneh
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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Bioinformatics Assignment 1

Michael Gboneh ([email protected])

March 9, 2016

Question 4a Screenshots

Figure 1: Screenshot of the Schlogl with initial condition X(0) = 0

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Figure 2: Screenshot of the Schlogl with initial condition X(0) = 250

Figure 3: Screenshot of the Schlogl with initial condition X(0) = 1000

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Question 3b Report
In this report, we consider a simulation of the stochastics simulation algorithm using R, below are the
findings illustrated through graphs and some interpretations.
The graph below represents the R implementation for the simulation with copy numbers for substrate
being 200 and enzyme 100.

100.png

Figure 4: SSA with S = 200 and E = 100

Observation:
The curve are not very smooth indication the level of noise within the system.
As time increases,the substrate numbers decrease to zero.
there is an initial decrease in the enzyme numbers,they then increases to form the final product.they
increases because they are used in the formation of the final product.

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copy number.png

Figure 5: SSA with S = 2000 and E = 1000

Observation:
From the curve, we see that the level of noise within the system has reduce.
The is an observed The copy numbers of the reactants and products slight increases and slightly sharp
decreases respectively.

Simulations Using the stochastic BioNetGen model.

Figure 6: stochastic BioNetGen model simulation

Observation:

From the observation, the two simulations (Stochastic BioNetGen model and The Stochastics Simulation
Algorithm) produce almost the same graphs.

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Figure 7: SSA

Figure 8: SSA

From observation of the graphs, the simulations are the same.

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