Last updated in March 2023
"keep it simple, stupid"
Hiruna Samarakoon
hiruna@unsw.edu.au
Uninversity of New South Wales, Sydeny 2032, Australia
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Contents:
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
Academic publications
- Samarakoon, H., Ferguson, J.M., Gamaarachchi, H. and Deveson, I.W., 2023. Accelerated nanopore basecalling with SLOW5 data format. bioRxiv, pp.2023-02.
- 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 .
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
Agricultural Biotechnology Center, University of
Peradeniya
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.
The project had three objectives.
- Designing a smartphone application
for analyzing nanopore DNA
sequencing data
- Aggregate the computing power of smartphones using a server-client setup for
real-time DNA analysis in parallel to DNA sequencing
- Algorithmic enhancement in DNA methylation profiling pipeline to limit data storage requirements and
introduce complete real-time DNA methylation profiling using smartphones.
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
Learning is a never-ending journey. I have taken some online courses in this pandemic situation.
I've started a new habit of writing to share knowledge with a wide audience.
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).