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Model Intestinal Microflora In Computer Simulation: MIMIC S-J

Werring, R. (2003) Model Intestinal Microflora In Computer Simulation: MIMIC S-J. Master's Thesis / Essay, Computing Science.

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Abstract

The Centre for High Performance Computing of the University of Groningen has developed a project called MIMICS (Model Intestinal Micro-flora In Computer Simulation) [1]. The aim of this project is to develop simulation tools that can be used to examine the interaction between the host and its intestinal micro-flora. The main tool of MIMICS is a large scale cellular automation, initially designed to examine the interactions in the lumen of the intestine [2]. This program was written in the program language FORTRAN 90. It has been optimized for parallel computation and runs on the Cray SV I e supercomputer. Main quality that was envisaged in the development of the current tool was speed of computation whilst the ease of use or modifiability was considered to be less important. This means that with the current tool it is difficult to add new interactions. Therefore addition of a wall in the simulation (4] did already require considerable redesign of the tool. In order to make it easier to carry out new simulation tasks, a tool should be developed that provides more flexibility. A graphical user interface should be added for improvement of the ease of use. However, not too much speed should be sacrificed, especially when the model becomes more complex and computationally intensive. In this context a new project has been started up, which is subject of this report. First aim of this project is to explore which design strategy can provide a tool that has sufficient modifiability, ease of use and speed. For that purpose, the applicability of the existing software engineer methods [5, 6] will be investigated. On the basis of the chosen architecture, a new tool will be developed. Finally this tool will be implemented in order to demonstrate its functionality. Chapters 2 and 3 of this report are the result of a literature study into the current MIMICS project and evaluation tools of software architecture of programs. In chapter 4 the terms of reference for the new software tool are defined, including the evaluation method that will be chosen to assess notably its modifiability. In chapterS and 6 the development and implementation of the new software tool is described. Chapters 7 and 8 explain the user interface of the new tool, and how to create a simulation. Finally, chapter 9 gives an analysis of the new the tool.

Item Type: Thesis (Master's Thesis / Essay)
Degree programme: Computing Science
Thesis type: Master's Thesis / Essay
Language: English
Date Deposited: 15 Feb 2018 07:29
Last Modified: 15 Feb 2018 07:29
URI: http://fse.studenttheses.ub.rug.nl/id/eprint/8859

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