Research week 1: Python for biologists, how to work smarter not harder.

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Hi everyone! I have decided to write a weekly blogpost of my research experience this summer 😊

Starting off, I didn’t know what to expect. I had come up with the idea to study the prevalence of a resistant allele in worldwide amphibian species to the disease known as chytridiomycosis, something which may be of use in conservation management to preserve amphibian biodiversity. Since this is my first taste of actual scientific research, I had little idea how to go about researching this topic. I have just finished the second year of a Biomedical sciences degree and hope to specialise in a genetics moderatorship, so I have limited knowledge of what resources were available to me to put my idea into practice.

On Monday I started by looking through papers trying to find all the info I could on the known resistant MHC class II beta allele which would serve as the basis of my research and sampled roughly twenty papers trying to get a feel of how many gene sequences are out there for different amphibian species which I will be using week two to compare to the resistant allele and infer their resistance level to the disease. My hope is, if we know the resistant species, it could be helpful to reintroduction strategies where amphibian populations are declining. Adding resistant individuals back into the wild will offer protection from chytridiomycosis and reduce population decline.

I met with my supervisor for our first meeting on Tuesday afternoon and she was amazing help at giving direction to my plan. I thought I was going to have to go through all these sequences by hand, but her advice was to start learning to code so I can automate all the tedious aspects of my project. Honestly, I was not expecting to start my first week of what I’ve been describing to everyone as “frog research” by following along to Python tutorials on pythonforbiologists.org (which is an amazing resource for learning how to code if you are studying genetics!) but after spending 9-5 learning what the command prompt of my computer actually does and watching my code actually succeed was pretty satisfying.

To keep this post as succinct as possible (TLDR), my first week of research was not spent on my actual research but learning how to code, so when I finally get my hands on those delightful little frog sequences I won’t be wasting my time trawling through the literature. I worried about how I wasn’t spending my time diving straight into my work, but reflecting on it now, knowing how to code is a great skill to have as a geneticist. Starting off my python skills now will make my analysis more efficient and I’m looking forward to week two!

Jessica Mahon

Biological and Biomedical Sciences undergraduate student , Trinity College Dublin

Hi, I'm Jessica Mahon, and I am interested in genetics, both from a conservation and a human standpoint. I'm in 3rd year of Human Genetics at Trinity College Dublin. I'm from Ireland and speak both English and Irish. I spend my spare time taking part in yoga, meditating and enjoying the outdoors. 

My Laidlaw research project is based on the genetic susceptibility of amphibians to chytridiomycosis disease to find a new conservation method for susceptible amphibian species. I'd love to chat with others who are interested in genetics and science!