February 11, 2013 is one of the days I won’t forget in my academic life. I was so excited, enthusiastic and more than ready to pursue my Master’s programme in Bioinformatics, which was designed to start with some intense course work to get everyone up to speed with the computing skills essential for research projects. But I was in for a rude awakening.
On day one of classes, I was introduced to the command-line interface (CLI) for the first time.
The first thing we were instructed to do was to make sure we were working in the home directory. As I stared at that prompt (“the dollar sign” as I called it), I had no idea what to type in there. Hearing the guy sitting next to me saying that he “checked the path and is sure he’s in the right directory,” a stream of questions rushed into my mind. What is a path? What is a home directory? How do I even get started with this terminal? And the big one – am I in the right class and did I choose my Master’s programme right?
Coming from a molecular biology background, the closest work related to bioinformatics I had done at that stage was to perform BLAST searches, playing with pdb files in PyMol and a number of multiple sequence alignments used to make phylogenetic trees, all of which were graphical user interface (GUI) applications. This little exposure had sparked an interest for me to start pursuing a career with a Bioinformatics component in it.
Little did I know that there was another way (the preferred way) of doing cool things in Bioinformatics – the CLI.
The CLI is very intimidating at first, but once you get the hang of it, it makes your life as a computational biologist easier. Also, like a riding a bike, once you get the concepts it’s not easy to forget.
Despite those first-day challenges, I was still convinced I had made the right study choice, so this helped to keep me going.
Fast forward a few years later – I received a graduate assistant scholarship for my PhD, and during this time I discovered I had a passion for knowledge sharing. As part of my scholarship requirements, I was tutoring a third-year genome analysis course, and realised that some of these folks were new to the command-line and in the same boat as I was on February 11, 2013.
I not only enjoyed helping these students get past the command line and through their third year, I also started helping my fellow PhD colleagues with getting started with their genomic data analysis. At one point during my thesis writing, my supervisor had to stop me from spending most of my time in helping. To me, it was refreshing, and provided some escape time from the pressure of PhD life.
The realisation of this passion made me to apply for a role with Genomics Aotearoa as a training coordinator, and these first few months have been nothing but exciting!
Genomics Aotearoa is a collaborative platform established to ensure that New Zealand is internationally participating and leading in the fields of genomics and bioinformatics.
One of Genomic Aotearoa’s projects which is critical to genomics research is bioinformatics capability, where bioinformatics tools and strategies needed to analyse information are provided.
The bioinformatics capability project aims to address the increasing local demand for data analysis methods as well as training. The concept is to develop material/pipelines that can be accessed by everyone, and to offer hands-on bioinformatics workshops. Post-doctoral researchers with strong bioinformatics background have been brought onboard to develop open-source and reusable data analysis material and pipelines to benefit the genomics research community.
My role as the training coordinator is to assist with the coordination and organisation of New Zealand-wide training workshops, and to interact with Genomics Aotearoa researchers and other relevant individuals to determine training needs and priorities.
At this stage, the development of introductory, intermediate and advanced bioinformatics training material for genomics researchers is underway. Together with our partner, NeSI, coordination and delivery of data science and bioinformatics training workshops has already begun around the country.
Better bioinformatics capability underpins our ability to analyse genomic sequence data, which is essential to deliver the true benefits of genomics to New Zealand.
It is exciting to me that I’ll be able to use my skills to help people take their skills further, and that they will in turn pass that knowledge and processes on to their colleagues. That means we can overall make a difference and have influence over our own future health, the conservation of New Zealand’s precious environment and our economic wellbeing.
It’s a great place to be, and makes knowing CLI very cool indeed.
Ngoni Faya, Training Coordinator, Genomics Aotearoa