Team:Newcastle/Modeling/Population

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Contents 1 Population modelling 2 Visualisation 3 Distributed Computing 4 References

Population modelling

One of the models which we are producing is one concerning the population numbers of our bacteria. It looks at how our additions to the DNA may affect the growth of the bacterial population.

This model is currently being implemented in the Java programming language, and connects to other models which we have written in CellML. Due to the design of the program, the team has enlisted the help of some very powerful computers. The next iteration of the program is to use distributed computing and the "Amazon Cloud" to extend the size of the bacterial population.

Visualisation

Below is a basic visualisation of one of the early versions of our simulation:

Distributed Computing

Distributed Computing (also known as Cloud or Grid computing) is the use of multiple computing processors, which can be spread around the world to accomplish a single given task. The processes on the machines may also communicate with each other, instead of simply acting independently.

Due to early versions of our bacterial population simulation program using a lot of CPU time and RAM, we attempted to think of ways to be able to speed up the processing times and expand the simulation. These early simulations were fairly small scale, but as each bacterial cell runs as an independent Thread, every system that we ran it on began to slow down dramatically.

Keith Flanagan, a Researcher at Newcastle University, along with others from the School of Computing Science, had been working on a software system for grid computing applications in the scientific field, called Microbase. Microbase has been used in Microbial Genome Comparison and Analysis. Flanagan suggested that Microbase could aid us in the development of a distributed version of our bacterial population simulation.

Using Microbase we are running our simulation on the Amazon Elastic Compute Cloud, a service provided by the e-commerce company Amazon.com, which gives users access to a resizeable large number of powerful machines. Prior to running our simulations using Amazon's computers, we tested our program using some of the machines in some of the University's computer clusters.

References

• [http://aws.amazon.com/ec2/ Amazon Elastic Compute Cloud]