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PhD Student 🇱🇰 at ANU 🇦🇺 | Computational Genomics 👩🏻‍🔬🧬 | Data Science 👩🏻‍💻 | Music 🎵 | Astronomy 🔭 | Travel 🎒 | vijinimallawaarachchi.com

10 lessons I have learned throughout my PhD so far

Two years have passed since I started my PhD, and recently I have been reflecting at what I have learned. It has been a roller coaster ride with many ups and downs. There were many sleepless nights, frustrating moments and of course, many learning experiences.

In this article, I would like to share with you 10 lessons I have learned throughout the past 2 years while being a research student in a field related to data science. If you are planning to start an academic career or you have already started, I hope you find these 10 lessons useful. …


Hands-on Tutorials

Strategies and tools for evaluating metagenomic binning results

Natural environments such as lake water, soil and niches of the human body (gut, skin, etc.) are home to trillions of microbes. These microscopic communities are complex and diverse, and we can learn a lot about their effects by studying their composition and interactions. If you have come across my article on Software Tools for Reference-free Binning of Metagenomes, you may know that there are different approaches developed throughout the past few decades to perform metagenomic binning where you place sequences into bins corresponding to different taxonomic groups (species, genera, etc.).

How can we evaluate the results produced by metagenomic…


Poetry Prompt: Greeting Cards

Collage of handmade cards by the author

As I make greeting cards
For my love of cardmaking and creativity
I collect random leftover stuff

When I saw the notification on Medium that Rochelle Silva has tagged me in her poem Impossible to Throw Away, I felt so happy to be reminded of how I have been making greeting cards since I was a kid. I have been sending handmade Christmas cards (yes, handmade by me!) to all my teachers who have taught me from kindergarten to high school. I also send handmade birthday and Christmas cards to my family and friends.

I collect random stuff (it can…


A simple introduction to matching in bipartite graphs with Python code examples

Graph matching can be applied to solve different problems including scheduling, designing flow networks and modelling bonds in chemistry. In this article, I will give a basic introduction to bipartite graphs and graph matching, along with code examples using the python library NetworkX.

Image by Author

Before moving to the nitty-gritty details of graph matching, let’s see what are bipartite graphs.

Bipartite Graphs

According to Wikipedia,

A bipartite graph is a graph whose vertices can be divided into two disjoint and independent sets U and V such that every edge connects a vertex in U to one in V.

In a bipartite graph, we have…


What you must know about antibiotic resistance

Antibiotic resistance occurs when bacteria develop resistance towards the medicines that are designed to destroy them. The bacteria will not respond to medicine and continue to grow, leading to severe complications and even death. This has led to serious implications, especially in people with chronic illnesses as we become unable to treat infections and affect global health. In this article, let’s see what is antibiotic resistance, how it occurred in the first place, its impact and what steps can be taken to prevent and control its impact.

Image by Arek Socha from Pixabay

Antibiotics

Bacteria are single-cell organisms that can be found everywhere. Your body houses trillions…


5 things I learned while writing my first article for a top journal

If you are into research like I am, you may know that getting your work published in a top journal is a huge achievement and you can gain more reach to your work. I was able to publish my first piece of work in my PhD in a top journal. In this article, I will share with you 5 things I learned while writing my first journal article.

Image by StartupStockPhotos from Pixabay

1. Select the Right Journal

Selecting the right journal is crucial to getting your work published. The scope of the journal should be relevant to your field. …


A sight from under the sea

Image by 俊 何 from Pixabay

Blue as the sky
Filled with might
As waters sigh
In currents of fight

Bubbles and speckles
Splashing on waves
Nubbles and freckles
Crashing on caves

Home for the world
Of the aquatic living
All being whirled
In the wail of reliving

The beauty in blue
She covers the world
As they all drew
In a wonder-world

I found this poem as a draft in my thoughts blog Thoughts by Viji. This poem was inspired by the song Under the Sea from “The Little Mermaid” cartoon. …


Punctuation in music

Image by Steve Buissinne from Pixabay

Similar to languages, music also has its own punctuation marks to help the listeners understand and enjoy what is played. If it weren’t for music’s punctuation marks, it would have been monotonous and boring to listen. Don’t worry, I won’t be going into technical details of music. This article is a short poem highlighting the different punctuation marks in music. Enjoy!

Music is a language
With its own punctuation
Everyone can enjoy
During all life moments

Slurs mark phrases of music as
Commas and semi-colons do in a sentence
Double bar lines mark the end of a piece as
Full-stops do…


What are marker genes, their usage and how to predict them?

When we think of the word marker, the first thing that comes to our minds is something that is used to indicate a place. For example, it can be your current location on Google Maps or it can be the place where you planted some seeds in your garden. Similarly, in genomics studies, we can find marker genes in bacterial genomes. In this article, I will introduce you to marker genes used in metagenomics analysis, how they are used and walk you through an example of a commonly used gene prediction tool.

Image by Mahmoud Ahmed from Pixabay

What are Marker Genes/Genetic Markers?

According to Wikipedia,

A genetic marker is a…

Vijini Mallawaarachchi

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