Bioinformatic freestyling in York

CACHE researcher, David Vendrami – Blog #1 2016 – recalls his science visit to York:

“2016 is (and hopefully is also going to be) a really exciting and interesting year: many things have already happened and many others are expected to take place! I increased my oyster sample collections with specimens from Japan and British Columbia (which are the locations from which the pacific oyster Crassostrea gigas was introduced into Europe). Another student showed interest in my (our) research and asked to take an internship with me. I am writing my second paper and we found a very good potential candidate to join the CACHE project as an Early Stage Researcher (ESR) here in Bielefeld, Germany.

However, today I’d like to talk to you about something else: the two weeks that I spent with my colleague Martin in York during March. We went to the UK to learn some more ‘bioinformatics’ from Dr Kanchon Dasmahapatra, who is based with the University of York, and I can tell you that it was extremely useful! Kanchon proved to be a great teacher and our skills in bioinformatics increased a lot in just two weeks! I now feel way more comfortable in this field and I’m really looking forward to applying what I learnt to my data and to share this new knowledge with my CACHE colleagues, who are planning to analyse some NGS data!

Blog #1 York DSCN0359

From left to right: Dr Kanchon, Martin and me.

I have to admit that each day in York involved a lot of intense thinking, but we also had the opportunity to visit the city (York is a really lovely city), meet awesome people and to chill out. Kanchon also invited us and his research group for lunch at his place, where we had delicious food and spent the afternoon chatting and getting to know each other outside of the working environment.

Unfortunately, among all of this cool stuff, something bad happened too: my favorite soccer team was defeated on a very very important match… But who cares? Now I am a bioinformatics freestyler and I want to become even better!”


What is bioinformatics? Is a set of informatics tools to analyse biological data. Specifically NGS data. The reason is that the amount of data produced by this hi-tech machine is so huge that you can not even think about analysing it by hand or with standard programs or software. You need to use bioinformatics tools.

What is NGS data? NGS data (next generation sequencing data) is data produced using hi-tech machines. This hi-tech machine basically read the DNA and produce an output which consists of the sequences of the DNA which was read. You will obtain a enormous amount of data.



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