Software & Tools
A collection of open source software, published Rust crates, PyPI packages, bioinformatics algorithms, and developer utilities.
Signature Tools & Applications
Highlighted desktop, web, and CLI applications
Clipper
A versatile clipboard management and note-taking application designed specifically for developers. Runs natively on macOS and Linux, leveraging Tauri for a lightweight and secure footprint.
IceBreak
A shared group break timer to coordinate breaks seamlessly across time zones. Built as a full-stack Go and React production template deployed on AWS using Terraform.
Kmertools
A high-performance k-mer based feature extraction tool designed for metagenomics analysis, DNA vectorization, and fast genomic sequence mining. Available via Cargo, Bioconda, and PyPI.
Published Rust Crates (crates.io)
Open source crates published to the Rust community on crates.io
lambdamux
AWS Lambda HTTP routing library with attribute macros and API Gateway adapters. Enables declarative route mapping with zero runtime overhead on serverless Lambdas.
rs-avl
A generic, high-performance AVL tree implementation in Rust with range queries, floor/ceiling search, and traversal iterators. Also published to PyPI.
Python & Database Packages (PyPI)
Python libraries and database frameworks published to PyPI
avldb
A typed, embedded document database framework built on top of Rust-backed AVL indexes. Fast, extensible, and designed for in-memory and persistent document querying.
s3-avldb
Cloud-native Amazon S3 storage backend plugin for avldb, enabling serverless embedded database querying directly against S3 object storage.
cogent3-pykmertools
A Cogent3 integration plugin for pykmertools, enabling fast k-mer sequence extraction directly inside Cogent3 computational biology workflows.
Metagenomics & Plasmid Recovery
Algorithms and models developed during PhD research at the Australian National University
MetaBCC-LR
First long-read metagenomics binning tool introducing the k-mer coverage histogram concept. Uses t-SNE for dimension reduction and DBSCAN for clustering.
LRBinner
Unified composition and coverage binning using deep auto-encoders combined with an innovative clustering algorithm for long reads. Published in WABI 2021 and AMB.
OBLR
Read-overlap graph binning for long reads using UMAP cluster detection and GraphSAGE representation learning, accelerated with CUDA RAPIDS.
Sequence Vectorization & High-Performance Tools
Optimized parallel tools using memory-mapped I/O and GPU acceleration
Seq2Vec
Converts metagenomics long reads or contigs into oligo-nucleotide frequency vectors. Engineered for speed and robustness using memory-mapped output files to operate in parallel.
Seq2CovVec
Generates coverage vectors for long reads and contigs based on the k-mer coverage histogram methodology introduced in MetaBCC-LR.
Computer Vision, GPU, WASM & Embedded IoT
Developer utilities, serverless templates, WebAssembly modules, and embedded firmware
kmertools-wasm
WebAssembly (WASM) distribution of kmertools, enabling client-side in-browser DNA vectorization and biological sequence analysis.
CUDA K-Mer Counting & Algorithms
High-performance GPU implementations of k-mer counting, biological data analysis, and the Needleman-Wunsch sequence alignment algorithm.
Object Annotation Maker
Automated dataset bootstrapping tool for training object detectors by synthesizing target images across variable backgrounds.
Serverless Boilerplate
Production-ready AWS Lambda serverless boilerplate for rapid prototyping and cloud web service deployment (used in vinyl.lk).
M5StickC Plus 2 Smart Clock
Custom embedded IoT smart clock firmware engineered for the M5StickC Plus 2 (ESP32) development board.