Software Applications
[2018] Human-computing game to solve Multiple Sequence Alignment (MSA) of biological sequences
The alignment of multiple sequences of DNA requires higher computing capabilities. This project addresses MSA by developing a human-computing game through crowdsourcing. The application allows players to align multiple sequences of biological data (given in the form of patterns) such that a maximum alignment score is obtained.
Main contributor: Amila Senadheera
Source/ Application: Genenigma
Publication DOI: https://doi.org/10.1145/3314367.3314374
[2018] Bioinformatics data format converter
Various formats are used in bioninformatics and the results are produced by different algorithms in several types (XML, TEXT, etc). This mainly affects programs that involve biological worklflows, where step by step processing of results is performed.
Main contributor: Damitha Lenadora
Source/ Application: MorfiConvert
Publication: To be published in MerCon 2019
[2018] Web-based visual simulator for bioinformatics alignment algorithms
In the domain of bioinformatics alignment algorithms, currently, there is a lack of web-based visual simulators for pairwise sequence alignment algorithms to visualize the dynamic programming steps along with the dynamic matrix. There exists Java applications and some tools that address few algorithms, and do not consider the intermediate dynamic steps. Thus, having a web-based, interactive visual simulator is a requirement for the learning process of the theories behind several algorithms, effectively.
This project addresses a web-based visual simulator for pairwise sequence alignment algorithms such as Neddleman-Wunsch, Smith-Waterman to interactively visualize the dynamic programming steps along with the dynamic programming matrix. The user can input two sequences simultaneously to check the best alignment and values for the given matches, mismatches and penalties for the gaps. The system is developed using Angular JS and provides the best alignment of two sequences step by step on a grid. In addition, there are components to visualize the aligned sequences using TCoffee and Dialign algorithms. The user needs to input a file which contains the aligned sequences in FASTA format for the multiple sequence alignment visualizers.
Main contributor: Anuradha Karunarathna
Application: PerfectAligner
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[2019] Visualizer for Microarray data/Gene expression data
In genomics and computational biology there is a separation between the data generators and analysers, with respect to the required knowledge on the theories behind those tasks. In recent years the publicly available genomic datasets have increased dramatically, and there is a requirement of efficient and effective tools to analyse and visualize those data.
Visualizer for microarray data/gene expression data is a web-based tool, which produces dynamic, informative and interactive genomic data visualization for the gene expression data sets entered by the user. This provides an intuitive user interfaces and direct access to large public domain data sets. The GUI facilitates users to load private or directly access large public domain data sets.
Although, the existing R language provides libraries to visualize microarray data, they are not available online and with the existing settings, the bioinformaticians need a knowledge on computer programming to visualize them. GeneLab application provides an easy to use, web-based tool for the users with less knowledge in programming and computational biology. This tool produces dynamic, informative and interactive genomic data visualization with a user-friendly GUI, and enhances the performance and delivers scalable analytics through the platform
Main contributor: Jithmi Shashirangana
Source/ Application: GeneLab
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[2019 - 2020] ADHD Web application
Main contributors: Senuri De Silva, Sanuwani Dayarathne, Gangani Ariyarathne