Hasindu Gamaarachchi
Senior Lecturer at UNSW
Sydney, New South Wales, Australia
Summary
👤
Senior🎓
Top SchoolHasindu Gamaarachchi is a Senior Lecturer and genomics computing engineer with a decade of experience building domain-specific computer systems for ultra-efficient, real-time genomic data processing. Based in Sydney, he combines academic research (PhD candidate at UNSW) with hands-on systems engineering at the Garvan Institute to translate high-performance algorithms into production-ready tools. His open-source contributions include performance and resource-fix improvements to nanopolish and maintenance of Bioconda recipes, showing attention to file-handling robustness and reproducible scientific packaging. He focuses on optimizing low-level parallelism and build automation to enable faster, more reliable nanopore data analysis for clinical and research workflows.
10 years of coding experience
4 years of employment as a software developer
Bachelor of the Science of Engineering (BScEng), Bachelor of the Science of Engineering (BScEng) at University of PeradeniyaKingswood CollegeUNSW Sydney
Sinhalese, English
Github Skills (17)
gnu-make10
c-language10
package-management10
bash10
conda10
makefile10
cplus10
build-automation10
file-handling10
bioinformatics10
cpp10
cprogramming-language10
openmp9
yaml8
genome-assembly8
Programming languages (10)
Github contributions (5)
jts/nanopolish
Feb 2018 - May 2022
Signal-level algorithms for MinION data
Role in this project:
Back-end Developer
Back-end DeveloperContributions:4 reviews, 20 commits, 10 PRs in 4 years 4 months
Contributions summary:Hasindu primarily focused on improving the `nanopolish` codebase. They addressed a critical issue by closing open files to prevent resource exhaustion. Further contributions included optimizing performance by changing the OpenMP scheduling in the BAM processor and enhancing the call-methylation module by incorporating a batch size parameter and modifying its default value, impacting both performance and usability. Additional work involved the merging of the fast5_rewrite branch and updating slow5 polya functionality, demonstrating expertise in file handling and integration.
signalpythonsciencegenome-assemblyc-plus-plus
bioconda/bioconda-recipes
Aug 2020 - Jul 2022
Conda recipes for the bioconda channel.
Role in this project:Automation Engineer / Build & Release Engineer
Automation Engineer / Build & Release EngineerContributions:1 review, 8 commits, 16 PRs in 1 year 11 months
Contributions summary:Hasindu primarily contributed to the automation and build processes within the bioconda-recipes repository. Their commits focused on updating build scripts (`build.sh` files), modifying configuration files, and integrating dependencies. The user regularly updated recipes for various bioinformatics tools, including f5c and slow5tools, reflecting a focus on maintaining and enhancing the build process for scientific software packages. This included adding and adjusting compiler flags and managing build dependencies.
recipescondabiocondabioinformaticspackage-management
Find and Hire Top DevelopersWe’ve analyzed the programming source code of over 60 million software developers on GitHub and scored them by 50,000 skills. Sign-up on Prog,AI to search for software developers.