The Genome generator

Abstract

The aim of the project is to create an extended Java based version of the GenomeGenerator software, originally created in the year 2000 by Robert W. McGrail, RebeccaThomas and Michael Tibbets. The Genome Generator is used to simulate and displayinformation on the development of junk DNA. In order to achieve that aim the GenomeGenerator displays various information on genomic build up derived from given user-inputrequirements.This document addresses the motivation for the work done, describes the work andaddresses related work which has been reviewed during the process.This document describes the ideas behind the software, the underlying algorithms and theprocess of development. This document will describe the software developed, it's intendedusage and capabilities.The implementation of the software is discussed and various design issues that had to betaken into account during the development process are discussed.Evaluation of the software is discussed and future testing and development ideas aredescribed.The Java version of the Genome Generator has been in development since early October2003. The first months of the project were spent analyzing and evaluating the existingsoftware, which is written in Scheme, and the research surrounding the creation of thatgenerator. The design of the algorithm and user interface started in October 2003 and inJanuary 2004 the first version of the user interface was ready. The first version of afunctioning generator was ready in late February 2004. Upon reviewing the algorithm usedsome glitches were discovered and a complete reconstruction of the software provednecessary. These issues will be further discussed in the chapters on design andimplementation.Due to various factors the implementation of a graphical display of the statistical outputwas somewhat hindered. Several graphical packages available over the Internet were tested and evaluated, but none of them proved adequate. The idea was to use as much offreely available software as possible, to be able to keep all aspects of this software freeand therefor keep the software itself freely available to those that might benefit from it.However some of the software originally considered, proved to be not as freely availableas seemed at first. These issues will be further discussed under the section onimplementation.