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Title: Designing and Developing a Visual Framework Integrating an RNA Mapping Algorithm and a Genome Rearrangement Algorithm in Bioinformatics

Speaker: Asma Rikli, MSc.

Software Engineering Department, CCIS, KSU, Riyadh, KSA.

Synopsis:

Biologists traditionally visually examine and analyze biological samples to understand the phenomena behind them and gain insight. This approach, if not automated, is prone to human error and unsuitable for quantitative comparison of several results. Visualization of biological data is one of the main challenges derived from its massive volume and complexity, hence the need for improving the usability, integration and standardization of bioinformatics visualization tools. Furthermore, two important bioinformatics processes that analyze Ribo Nucleic Acids (RNAs) are their alignment and rearrangement. However, majority of alignment and rearrangement algorithms are based on RNA sequence while its functionality depends on its structure. Fortunately, two innovative algorithms: The Component Based Pair-Wise RNA Secondary Structure Alignment Algorithm (CompPSA) and the Genome Rearrangement for RNA Secondary Structure Using Component Based Representation Algorithm (DCJ-RNA) have been recently proposed utilizing the new component-based representation of the RNA structure. In this thesis, we develop the RNA Alignment, Rearrangement, and Visualization framework (ARV), which integrates the implementations of the CompPSA and DCJ-RNA algorithms and visualizes their inputs and results while enabling users' maximum interaction with the RNA structures. Moreover, ARV is the first tool/framework to enable extensive user interaction with the inputs and outputs of an RNA alignment or RNA rearrangement algorithm, and among the only two tools/frameworks that visualize the inputs and results of RNA alignment or rearrangement. In this thesis, we also propose a process that integrates user-centered design with component based software engineering (UCD-CBSE) through utilizing advantages of user centered design (UCD) as well as component base software engineering (CBSE) in addition to addressing the cost and inconvenience of including real users in the development process. This process is applied in ARV's development and is later assessed in terms of its ability to build usable software through evaluating the usability of ARV, which is its case study. Furthermore, we propose a usability evaluation method (HueristicQQ) that generates both quantitative and qualitative results through adapting four heuristic sets and incorporating a thinking aloud protocol. This method is used in the comparative usability study of ARV and existing RNA secondary structure visualization tools, where our usability evaluation of RNA secondary structure visualization tools is the first up to our knowledge. Moreover, results of the usability evaluation of ARV were significantly positive both quantitatively and qualitatively.

 

Date/Time: Tuesday, May 17, 2016 at 12:00pm

Location: F52 in Building 6  - Broadcast to Studio 4Room 2087 in CCIS Building 3