On blogging

When I was an honours student (in Australia an honours degree is a one year [in practice, it’s about ten months] undergraduate research program you can take after your Bachelor’s and has nothing to do with the traditional meaning of the word “honours”), I literally jumped into the deep end of bioinformatics. I recall joining…

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On learning

Sometime in the past this blog was called “Musings from a PhD candidate”, despite hardly writing any blog posts that were of the contemplative sort. It later evolved to “Musings from an unlikely candidate” because I had received my PhD, which I thought was quite an unlikely event given my background. However, this carried a…

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Add Docker to your toolkit

Docker has been around for 8 years and it has become a very popular platform for developing software. In the 2020 Stack Overflow Developer Survey, 39.2% of professional developers (total of 44,705) reported that they have done development work using Docker. Docker is only behind Linux and Windows! For the full list check out Stack…

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Creating reproducible documentation

When I was first learning about SAMtools, I kept my notes in a Wiki. I would type the SAMtools commands in the terminal and copy and paste the output into my Wiki. It was a tedious task but it was a useful resource that I would refer back to frequently. The latest version of my…

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Running RStudio Server with Docker

I highly recommend using RStudio if you use R because it makes working with R so much easier. I primarily use RStudio for writing up my analyses in R Markdown. Some RStudio features I couldn’t live without include: Vim keybindings, code completion, and code highlighting (rainbow parentheses are awesome!). Other nice features I like to…

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SQL group by statement on the command line

The GROUP BY statement allows you to perform operations in a group wise manner. I first learned of the Useful FILe and stream Operations (filo) repository a long long time ago and keep coming back to it over and over again. The filo toolkit comes with three tools: groupBy, stats, and shuffle. The groupBy tool…

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Monte Carlo integration

I recently came across this question: “You have a function called random that randomly generates a number between 0 to 1. Use this to calculate pi.” Worded differently, the question is asking you to estimate pi using random numbers. As you can read in the script for Life of Pi (one of my favourite movies):…

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Ten years

As of today, it has been a decade since my first post on this blog. It started aimlessly during my PhD as a place to post analysis notes for myself and ten years later it still remains so. However, over the years I have started to focus more on better project management practices and on…

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Sequence analysis of SARS-CoV-2 part 3

This post is a continuation of a series of posts on the sequence analysis of SARS-CoV-2; see part 1 and part 2 if you haven’t already. Since my first post, I found out that you can blast sequences against a Betacoronavirus database on NCBI BLAST. The database, as of 2020/03/10, has a total of 7,844…

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Sequence analysis of SARS-CoV-2 part 2

I ended my previous post on the sequence analysis of SARS-CoV-2 with the amino acid alignment of the spike protein from SARS-CoV-2 (MN908947) and Bat coronavirus RaTG13 (MN996532). The spike protein is of specific interest as it is due to its binding with the angiotensin converting enzyme 2 (ACE2) receptor that it is able to…

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