Anuradha Wickramarachchi, PhD

Anuradha

Engineer · Scientist · Researcher

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Anuradha Wickramarachchi, PhD

Anuradha

Engineer · Scientist · Researcher

Adelaide, Australia

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Copyright © 2026 Anuradha

Software Engineer · Scientist · Researcher

Anuradha Wickramarachchi, PhD

Adelaide, Australia
•
hello@anuradhawick.com

I am a Software Engineer at AML3D developing algorithms for advanced manufacturing applications (Wire Arc Additive Manufacturing – WAAM). With a PhD in Computer Science from the Australian National University (ANU) and background as a Solutions Architect at CSIRO, I bridge software engineering, computational science, and research across advanced manufacturing, distributed cloud systems, and machine learning.

Previously at Commonwealth Scientific and Industrial Research Organisation (CSIRO), I designed and built solutions for population-scale health and biosecurity problems that scale to real-world population sizes.

I am passionate about high-performance computing, distributed cloud systems, data engineering, bioinformatics, and computational geometry.

Work Experience

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Software Engineer

AML3D

2024 - Present • Australia

Developing core algorithms and software pipelines for advanced industrial manufacturing applications (Wire Arc Additive Manufacturing – WAAM).

  • Design and implement computational geometry and algorithmic control pipelines for robotic metal 3D printing (WAAM).
  • Develop high-performance toolpath generation, slicing, and kinematic planning algorithms.
  • Bridge advanced computational engineering, software development, and industrial manufacturing automation.

Solutions Architect

Commonwealth Scientific and Industrial Research Organisation (CSIRO)

2022 - 2024 • Canberra, Australia

Designed and built solutions for population-scale health and biosecurity problems with the Transformational Bioinformatics Group.

  • Architected and built cloud-native distributed platforms and pipelines handling population-scale genomics and infectious disease biosecurity data.
  • Designed scalable genomic search and data exchange protocols including GA4GH Beacon standards (sBeacon, AskBeacon).
  • Led DevOps, Infrastructure as Code (Terraform), and cloud infrastructure architecture across distributed teams.
  • Awarded CSIRO Entrepreneurship Award 2024 (Indonesia biosecurity platform) and CSIRO Science & Engineering Award 2022 (SARS-CoV-2 monitoring capability).

Education

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Doctor of Philosophy in Computer Science

School of Computing, Australian National University

August 2018 - December 2022 • Canberra, Australia

Models and algorithms for analysing genomic data from microbial communities. I used machine learning models (ANNs and GNNs) and algorithms (for feature generation and clustering) to analyse metagenomic data for understanding microbial communities.

  • ANU Merit Fee Remission and PhD Scholarships recipient
  • Developed novel graph-based and deep-learning metagenomic binners (GraphBin, LRBinner, MetaBCC-LR, PlasLR)

BSc (Hons) Computer Science and Engineering

Department of Computer Science and Engineering, University of Moratuwa

February 2014 - December 2017 • Moratuwa, Sri Lanka

Graduated with First Class Honours. Final year project on "Personal cloud device with peer to peer remote file sharing". GPA of 4.06/4.2.

  • First class honours with Dean's list recognition for all 8 semesters
  • Mahapola Sri Lankan undergraduate merit-based scholarship recipient
  • GCE Advanced Level Island Rank 68 (District Rank 4)

Publications

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46 Papers 477 Citations Synced:
Google Scholar
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Skills

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Dev Ops & Cloud

  • Terraform & Infrastructure as Code (IaC)
  • Population-scale genomic data platform development
  • CI/CD Pipelines (GitHub Actions, GitLab CI)
  • High scale systems architecture & AWS Serverless (Lambda, API Gateway, DynamoDB, S3, CloudFront)

Programming Languages

  • Rust
  • Go
  • Python
  • C / C++
  • Java
  • JavaScript / TypeScript
  • Node.js

Command line and web development of research software in Rust, Go and Python. Industrial experience in ReactJS, MongoDB, AWS Serverless and AWS developer console. Research experience in Python, C and C++.

Bioinformatics Tools & Libraries

  • Aligners: minimap2, BLAST+, Edlib
  • Libraries: libminimap2, GATK, Biopython, Edlib
  • Boost C++ Libraries

Machine Learning & Data Science

  • PyTorch
  • TensorFlow
  • XGBoost
  • Dask
  • RAPIDS
  • scikit-learn
  • Graph Neural Networks (GNNs)

Software and Tools

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Research Software (7)

RSBio-Seq

Fast lightweight genomic sequence reader/writer in Rust

github.com/anuradhawick/rsbio-seq

KmerTools

High performance k-mer generation tool

github.com/anuradhawick/kmertools

OBLR

PacBio/ONT graph based binner for metagenomics

github.com/anuradhawick/oblr

LRBinner

PacBio/ONT reads binning tool using deep learning and assembly graphs

github.com/anuradhawick/LRBinner

MetaBCC-LR

PacBio/ONT reads binning tool by coverage and composition

github.com/anuradhawick/MetaBCC-LR

PlasLR

Plasmid classification extension for PacBio/ONT reads

github.com/anuradhawick/PlasLR

GraphPlas

Graph based plasmid classification extension tool

github.com/anuradhawick/GraphPlas

General & Web Applications (5)

Clipper

Clipboard manager with productivity features

github.com/anuradhawick/clipper

TypeFaster

AWS Serverless website to practice touch typing

typefaster.anuradhawick.com

IceBreak

AWS Serverless website for group interval-breaks

icebreak.anuradhawick.com

Vinyl.LK

AWS Serverless/Atlas Mongo hosted catalog for Sri Lankan vinyl records

vinyl.lk

YOLO Object Annotation Maker

Custom desktop tool for rapid YOLO annotation generation

github.com/anuradhawick/Object-Annotation-Maker

Posters and Presentations

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  • ABACBS+SBEI 2025

    Talk on AskBeacon (AI driven data exchange at scale), Poster on TRECA (trusted research environments and clinical applications), and Panelist at SBEI 2025

    2025

  • GA4GH Connect 2024

    Proposals for Using the OR Boolean Operator in GA4GH Beacon Protocol

    2024

  • ICG 2023

    sBeacon – ontology aware querying of genomic data at scale

    2023

  • Microbiology Society Meeting 2022

    Metagenomics binning by coverage and composition for long reads

    2022

  • RECOMB-CG 2022

    Metagenomics binning of long reads using read-overlap graphs

    2022

  • WABI 2021

    LRBinner: binning long reads in metagenomics datasets

    2021

  • GLBIO 2021

    PlasLR Enables Adaptation of Plasmid Prediction for Error-Prone Long Reads

    2021

  • ISMB 2020

    MetaBCC-LR: metagenomics binning by coverage and composition for long reads

    2020

Awards and Achievements

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Academic

  • ANU Merit Fee Remission and PhD Scholarships (Australian National University)
  • Dean's List recognition for all 8 semesters during BSc (Hons), University of Moratuwa
  • Mahapola Sri Lankan Undergraduate Merit Scholarship
  • GCE Advanced Level Island Rank 68 (District Rank 4 in Sri Lanka)

CSIRO Awards

  • Entrepreneurship Award 2024 – For providing bioinformatics and data exchange capability for Indonesia
  • Science and Engineering Award 2022 – For increasing Indo-Pacific SARS-CoV-2 monitoring capability

Industry & National Awards

  • Merit Award – National Best Quality ICT Awards (NBQSA) Oct 2017 (Sri Lanka) for Final Year Honours Project
  • Merit Award – National Best Quality ICT Awards (NBQSA) Oct 2016 (Sri Lanka) for Taxi Master Project

Hackathons & Competitions

  • First Place: IDEA Challenge 2017
  • 1st Runners Up: Google I/O 2016 (May 2016)
  • First Place: IDEA Challenge 2016

Training and Certifications

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  • Certified Carpentries Instructor

    The Carpentries

    2024

  • Introduction to SaMD, IEC 62304 and IEC 82304-1

    Software as a Medical Device Standard Training

    2023

  • Deep Learning Specialization

    DeepLearning.AI

    2021

  • Getting Started with AI on JETSON NANO

    NVIDIA Deep Learning Institute

    2021

  • PyTorch for Deep Learning with Python Bootcamp

    Udemy

    2021

  • Machine Learning

    Stanford Online

    2020

Additional Information

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Beyond day-to-day engineering and research, I love tinkering on single-board computers (SBCs), travelling, cooking, taking care of my tiny garden, and gaming (PC/Xbox/PlayStation).

Websites