Last updated in March 2023

"keep it simple, stupid"

Hiruna Samarakoon

Contents:

• Education
• Academic publications
• Awards and recognition
• Work experience
• Final year research project
• Projects
• Other Interests and Activities

Education

School of Computer Science and Engineering, University of New South Wales - Sydney, Australia : May 2021 - Present

Garvan Institute of Medical Research - Sydney, Australia : May 2021 - Present

• PhD Candidate in Computer Science and Engineering
• Field of Research - Medical biotechnology diagnostics and Energy-efficient computing

Faculty of Engineering, University of Peradeniya - Peradeniya, Sri Lanka : Nov 2015 - Aug 2020

• B. Sc. (Eng) in Computer Engineering: GPA: 3.95/4.00

Trinity College - Kandy, Sri Lanka : 2006 - 2014

• I was ranked 64th in Sri Lanka in the GCE Advanced Level examination 2014 in Physical Science stream with 4 Distinction passes

Academic publications

1. Samarakoon, H., Ferguson, J.M., Gamaarachchi, H. and Deveson, I.W., 2023. Accelerated nanopore basecalling with SLOW5 data format. bioRxiv, pp.2023-02.


2. Samarakoon, H., Ferguson, J.M., Jenner, S.P., Amos, T.G., Parameswaran, S., Gamaarachchi, H. and Deveson, I.W., 2022. Flexible and efficient handling of nanopore sequencing signal data with slow5tools. bioRxiv, pp.2022-06 .


3. Gamaarachchi, H., Samarakoon, H., Jenner, S.P., Ferguson, J.M., Amos, T.G., Hammond, J.M., Saadat, H., Smith, M.A., Parameswaran, S. and Deveson, I.W., 2022. Fast nanopore sequencing data analysis with SLOW5. Nature biotechnology, pp.1-4.


4. Nilanthi, R.M.R., Samarakoon, H., Jayawardana, N., Hathurusinghe, B., Wijesundara, S. and Bandaranayake, P.C.G., 2022. Strobilanthes glandulata (Acanthaceae), a new species from Sri Lanka based on morphological and molecular evidence. Phytotaxa, 573(1), pp.1-14.


5. Nilanthi, R.M.R., Samarakoon, H., Jayawardana, N., Wijesundara, S. and Bandaranayake, P.C.G., 2021. Strobilanthes medahinnensis (Acanthaceae) a new species, based on morphological and molecular data, from the Peak Wilderness Nature Reserve, Sri Lanka. Phytotaxa, 514(1), pp.26-38.


6. Samarakoon, H., Punchihewa, S., Senanayake, A., Hammond, J.M., Stevanovski, I., Ferguson, J.M., Ragel, R., Gamaarachchi, H. and Deveson, I.W., 2020. Genopo: a nanopore sequencing analysis toolkit for portable Android devices. Communications biology, 3(1), pp.1-5.


7. Gamaarachchi, H., Lam, C.W., Jayatilaka, G., Samarakoon, H., Simpson, J.T., Smith, M.A. and Parameswaran, S., 2020. GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis. BMC bioinformatics, 21(1), pp.1-13.

Awards and Recognition

• 2022 - Presented work listed under publications (2) at Australasian Genomic Technologies Association (AGTA) 2022


• 2020: Presented the work listed under publications (6) as one of the top three spotlight speakers at Nanopore Community Meeting (NCM) 2020 - a conference dedicated to scientific research using nanopore DNA/RNA sequencing.


• 2020: 2nd runners up at Data Storm v1.0, a machine learning and data science competition, organized by the Rotaract clubs of the University of Moratuwa and University of Colombo.


• 2019: 2nd runners up at Brainstorm 2019, Sri Lanka's Premier Biomedical Engineering Design Competition, organized by the IEEE EMBS Student Branch Chapter at the University of Moratuwa.


• 2018: 1st runners up at iHack 4.0, a 24-hour inter-university software development hackathon, organized by University of Colombo School of Computing ISACA Student Group


• 2017: 2nd runners up at ACES Hackathon 2017 a software development hackathon, organized by the Association of Computer Engineering Students (ACES), Faculty of Engineering, University of Peradeniya.


• 2016 and 2017: successful participation at ACES Coders, an algorithmic programming competition organized by ACES.

Work experience

Agricultural Biotechnology Center, University of Peradeniya

• Research assistant
  August 2020 - March 2021

  Working on plant genomics

20face Enschede, the Netherlands - a company providing privacy proof biometrics

• Industrial training internship
  February 2019 - August 2019

  The company has its facial recognition algorithm based on deep learning. I joined the development team to extend this proof of concept to a commercially viable software development kit (SDK). I engaged in designing interfaces to wrap SDK for different programming languages. My work included evaluating the algorithms, setting up proof of concepts, solving database management issues, testing/debugging SDK, and dealing with continuous integration/delivery.

Undergraduate final year research project

The project had three objectives.

1. Designing a smartphone application for analyzing nanopore DNA sequencing data
2. Aggregate the computing power of smartphones using a server-client setup for real-time DNA analysis in parallel to DNA sequencing
3. Algorithmic enhancement in DNA methylation profiling pipeline to limit data storage requirements and introduce complete real-time DNA methylation profiling using smartphones.

Projects

The following are some of the projects I have worked on during my undergraduate studies. Please visit https://github.com/hiruna72 for more information.

• An IoT of autonomous fishing boats
  

  An IoT network with a set of autonomous bots that can harvest fish, working individually, and communicating with a local relay node, which is overseen by a central server was built. A client can set up relay nodes in different locations, deploy the fishing bots, and use the central server to get live updates.

• Peripheral Interface Controller as a USB interface
  Documentation 2019

  Built a general-purpose input/output interface using PIC18F4550 that is compatible with USB 2.0, 3.0 protocol. The interface can be further extended using multiplexers along with an external power supply.

• Packet Forwarding Simulator
  

  Open-source software was designed to examine the associated delays and traffic in a predefined network topology. Adding new packets and modifying the topology are supported at runtime through a GUI

Other Interests and Activities

Learning is a never-ending journey. I have taken some online courses in this pandemic situation.

• R programming
• Statistics for Genomic Data Science
• FPGA computing systems: Background knowledge and introductory materials

I've started a new habit of writing to share knowledge with a wide audience.

• HMM for Gene Annotation
• Compiling HDF5 on Android with multi-threading support

I find myself as an enthusiastic sportsman. I play football regularly. I have won university colors for Hockey in three consecutive years - 2016/17/18. I was lucky enough to be the vice-captain of the college Hockey team (2006-2010).