Interests
- Bioinformatics
- Metagenomics
- Data Mining and Information Retrieval
- Machine Learning
- Data Structures and Algorithms
- Software Architecture
Projects
Phables: Phage bubbles resolve bacteriophage genomes in viral metagenomic samples
- Phables is a tool developed to resolve bacteriophage genomes using phage bubbles in viral metagenomic data.
- Phables models cyclic phage-like components in the viral metagenomic assembly as flow networks, models as a minimum flow decomposition problem and resolves genomic paths corresponding to flow paths determined.
- Technologies used: Python 3
- View project
MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs
- MetaCoAG is an NGS data-based metagenomic contig binning tool that makes use of the connectivity information found in assembly graphs, apart from the composition and coverage information.
- MetaCoAG makes use of single-copy marker genes along with a graph matching technique and a label propagation technique to bin contigs.
- Technologies used: Python 3
- View project
- View conference presentation
- View conference publication
- View extended journal publication
GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs
- GraphBin2 is an extension of GraphBin which refines the binning results obtained from existing tools and is able to assign contigs to multiple bins.
- GraphBin2 uses the connectivity and coverage information from assembly graphs to adjust existing binning results on contigs and to infer contigs shared by multiple species.
- Technologies used: Python 3
- View project
- View conference presentation
- View conference publication
- View extended journal publication
GraphBin: Refined Binning of Metagenomic Contigs using Assembly Graphs
- GraphBin is a metagenomic contig binning tool that makes use of the contig connectivity information from the assembly graph to bin contigs.
- It utilizes the binning result of an existing binning tool and a label propagation algorithm to correct mis-binned contigs and predict the labels of contigs that are discarded due to the short length.
- Technologies used: Python 3
- View project
- Seminar Talk
- View publication
Pipeline Monitor
- A scheduler to execute and run a pipeline of commands in a supercomputing facility.
- The program can schedule a graph-like execution sequence.
- View project
An Interactive Workflow Solution to Support Bioinformatics Analyses
- A generic software framework that can be used to construct bioinformatics workflows by both biologists and bioinformaticians with any level of programming expertise.
- This framework incorporates novel web application development technologies to support specific requirements of bioinformatics software for workflow creation.
- View project
- View publication
Change Detection in Distributed Digital Collections
- An efficient change detection and notification system to track changes occurring in web pages and notify interested users.
- Final Year Project carried out for the completion of the degree BSc. Engineering (Hons.) in Computer Science and Engineering.
- Technologies used include Java, H2O.ai, Jsoup, AngularJS, PHP, HTML, CSS, MySQL
View My Work
Vijini Mallawaarachchi 