Date of Award


Document Type

Master Thesis

Degree Name

Masters of Science (Research)


Computer Science

First Advisor

Dr Paul Walsh

Second Advisor

Dr Roy Sleator

Third Advisor

Dr Paul Rothwell



Vioinformatics is the application of computer science and related disciplines to the field of molecular biology. There are currently many web and desktop tools available for biologists to perform bioinformatic tasks. These tools often require users to manually and repeatedly co-ordinate multiple applications to produce a result, which is time consuming and error prone for the user. As a result, workflow tools have been developed to automate these tasks. Many of these tools require expert knowledge of the techniques and supporting databases within the area of bioinformatics. Biologists learning to use these workflow tools can find it difficult as they lack the knowledge needed to build workflows and the lack of usability in some workflow tools made the tools difficult to use. This thesis is therefore concerned with developing a prototype bioinformatics workflow tool that allows biologists with scant knowledge of bioinformatics and no computer programming knowledge to rapidly and effortlessly annotate large amounts of DNA and protein sequences.

A user-centred development approach was used to develop the prototype, where users were involved in the development from the very beginning when requirements were being gathered. Several requirements gathering techniques were used to gather information from biologists about the bioinformatic tools they use and also what features they would need in a bioinformatics workflow tool. Information was also gathered by looking at existing bioinformatic workflow tools and how these tools do not meet the needs of biologists. The information gathered was used in the development of the prototype tool.

The user-centred approach continued throughout the development. Cognitive walkthroughs with biologists were used to evaluate the prototype GUI and the findings were used to drive the development of the tool by improving and adding features. User testing on the tool was carried out to determine if the tool met user's needs. Users were able to create workflows and browse results with no help or documentation present. Usability inspection methods were also used to discover usability problems with the software. Findings from the result of this study may guide future development of software tools for biologists.

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