Forum:What made you interested in Bioinformatics?
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3.7 years ago
Hussain Ather ▴ 960

Why bioinformatics? An open-ended for-fun question.

What made you interested in the field and how did you ended up sticking through it?

career bioinformatics Forum • 2.5k views
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I have no idea if editing it is possible, but this would be excellent as a forum rather than a question. You can select forum from the dropdown menu when you're creating the post. Just for future reference if you have other open-ended ideas like this.

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Just changed it. thanks!

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3.7 years ago

Here is an interesting, recent paper on the evolving role of bioinformaticians

Computational biologists: moving to the driver's seat, Genome Biology 201718:223

Incidentally, the word BioStar is meant to capture this exact sentiment and has recognized this direction eight years ago ;-)

In the information-driven life sciences the bioinformatician it the true star of the show.

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Hi Istvan, if I can kindly ask, when did you first begin to see the separation (conceptually) of bioinformatics from computer science (I think that you have a bground in comp science)? I remember looking through my comp. science lecture notes ~15 years ago and there was only minor mention of things like BLAST and Clustal. When I later studied biology, there were small sections on bioinformatics, againly maInly surrounding BLAST but also phylogenetic analyses based on microsatellite markers.

I only recall thinking about the importance of bioinformatics ~7 years ago, around when Biostars was founded.

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I would say once I had to analyze real bioinformatics data I realized how far "theory" is from "practice". And how much creativity and the ability to chart your own course is required in this field. Unlike other science, nobody knows what they are supposed to be doing. It's awesome!

It was then when I understood that biology is unlike other sciences (I have a Physics PhD). The Higgs boson was found by experiments deviating at infinitesimal levels - everything else falls into the Standard Model at five digits accuracy etc. Good luck with that in Biology. On the other hand you need to put in many-many years into quantum chromodynamics or gravitation to be able to contribute to society - yet you can be a great asset to the world after a semester of bioinformatics if you put your mind to it.

Same with algorithms - they are ok, but with all mathematical concepts, life does not follow them strictly. Each organism tries to outwit the other and survive at all costs, they couldn't care less about parsimony and other concepts that we routinely use to make sense of the data we obtain.

Which suits one well, but you have to become a wizard and not a magician.

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Thanks Istvan! Sometimes I wish that biology would follow the rules but it never does.

And what a great resource is Biostars!

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3.7 years ago

I became interested by necessity, as I expect is the case with many scientists over the last ten years. My lab needed someone to take the reigns from a post-doc that was leaving and since I was a bright-eyed first year graduate student with zero computational background, I was apparently the perfect fit. I blundered through the first six months or so, picked up Python, bash, and a bit of R knowledge along the way and managed to cobble together functional pipelines to handle lots of ChIP-seq, mRNA microarray, and RNA-seq data. Turns out trying to learn bioinformatics with little guidance or formal training is a bit of a pain, who would have thought?

I like to think I've come a long way in the last few years, but I still learn new things daily. Reading my code from a few years ago makes me shudder, and doing analyses now only takes a few days rather than the weeks it would have taken me back then. I think part of what allowed me to get through the really frustrating roadblocks was that I could always do bench work for a few hours or days and get my mind off things. Though that can be a challenge in its own right, as jumping back and forth between the two multiple times a day can be jarring.

Overall, bioinformatics is just a great challenge. It requires analytic skills and critical thinking coupled with biological knowledge and the ability to extrapolate what the results of your analyses might mean in reality. It's fun, and the parts that aren't fun (common data munging, file format conversions, etc) can mostly be automated. Which is kind of fun in itself.

I hope I can find a position that allows me to utilize those skill sets even if bioinformatics isn't my main responsibility.

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+1 for doing it because you have to!

For me, I've always been a computer nerd and wanted to learn to program, but you need a problem to solve, its very difficult to just 'sit down and code something' (beyond Hello world). My own lab work requires this (not to mention it's nice to have computational data to fall back on when all the lab work inevitably fails!). Bioinfx projects were the problem/kickstart I needed.

I did a specifically interdisciplinary Masters and PhD, so I was made to learn to program for some of my exams. I just kept it going, and now it's also a hobby! Plus, I've always been annoyed that life scientists are looked down upon because of the usual phobia we/they have of more quantitative fields like maths/physics/chemistry, so I wanted to buck the trend.

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Oh, and I never, ever, ever want to see a graph made in Excel ever again now that I know how to use ggplot, matplotlib, plotly et al.

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3.7 years ago
JC 12k

I was hooked by the possibility to understand the biology behind the data and to use HPC for this.