Forum:Need Advice On How To Become A Senior Bioinformatician
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8.4 years ago
calicruz206 ▴ 30

Hi im 21, young, smart and friendly. I am currently studying a biotechnology degree with the aim of becoming a senior bioinformatician. I would love to get advice from my friends here on biostars.org on how someone could become one. Please share your experiences and tell me what you would of done differently. If you are a lucky senior bioinformatician i would doubly prefer your wisdom :)

regards

Cali

bioinformatician bioinformatics Forum • 3.3k views
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Here is a free advice (from a not so senior bioinformatician): learn to ask well formed and precise questions. I'm actually very serious, by the way. My pleasure to help ;|

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Forgive me for confusing you, I am new to this website. Very wise indeed, Asking the right questions is the first step to solving a problem.

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You cannot be forgiven since there was no offence. Being new is no excuse for making incoherent questions. Meditate on the difference between these two questions: "How can I nourish myself" and "Where can I buy a barbecue chicken". The first one is so general as to be meaningless. The answer can be as simple as "eat" or as complex to fill a life of exploration. The second one, however, can actually be answered. Try to ask questions that are clear and can be answered. You will learn more and people will not be irritated by the naivety of what you ask.

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Welcome to Biostar! The question will be most certainly be closed because it is too generic. Nevertheless, please feel free to navigate the website and read the previous discussions. You can find some non-technical questions in the Forum section, which is probably a good starting point for you.

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Believe it or not this is not a bioinformatics question, but should have been assigned to the forum type.

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8.4 years ago

I agree with Eric Normandeau that your question is an example on how not to ask questions - even after changing the title. So much so that my first impression was that this might have been generated by a software and it is simply a Turing test.

Let me list the problems just in case this is not actually a robot posting, and if you can solve those you will be well on your way to your goal.

  • Title: "Help Please" is meaningless, it exudes weakness and lack of initiative. Make an effort to summarize the question in the title
  • Starting with listing your age, and that you are young and smart - these are all irrelevant to the question. In fact stating that you are smart is very off putting
  • "Lucky senior bioinformatician" - luck has got nothing to do with that - at most perhaps in that luck does indeed favor the prepared. But you are now actually insulting those that are successful in saying they must have been lucky.

The actual answer to your generic question is generic answer.

  • Be good at what you do, and do it for a long time. Voila! You are now senior and successful at your job.
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The last point is absolutely spot on. Getting 'senior' in your job title is simply a matter of sticking at one discipline long enough to achieve it. It's amazing what 'getting old' does for career progression!

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+1, you really made me laugh with your generic answer and its 'logical' conclusion :)

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8.4 years ago
Medhat 9.0k

I think you should look at this article "i am not senior at all" How Not to Be a Bioinformatician :)

and this is quoted from a blog

"The most important 'skill' to have is PATIENCE, just enough to avoid an early death due to bashing your head against the wall when trying to get convoluted R, C, C++, Python, Perl, etc packages to run. Half your life will be spent resolving dependencies only to find that when it all finally compiles it's useless anyway. Welcome to NGS! ;-)

But seriously, nix sysadmin skills are *essential. Usually some flavor of Linux, but you may have to mess around with Solaris if you're running Sun equipment. If you're moving serious quantities of data then you're going to need decent servers (we use 64-bit, 32 CPU, 130GB RAM, 4TB onboard systems with 32TB Sun Thumpers as NAS). Even having competent dedicated sysadmins on deck will not release you from having to have solid command-line skills. Get a VPN set up or get familiar with SSH and SSH tunneling (for secure VNC for example), both can work well together and allow you to work happily remotely. Consider DynDNS if you have a dynamic IP at a remote site.

A 'scripting' language is essential. It doesn't matter what, but the bioinformatics community seems to prefer being stuck in the early 1990's with Perl while the rest of the world is moving on. As painful as Perl is when compared to something like Python, it's hard to argue against the depth of modules available.

Interpreted languages are getting better and better but you'll still need a compiled language at some point. I prefer C++ (with Boost) because it's slightly less painful than C and almost as fast when compiled with -O3.

Database skills are also essential. MySQL is a good compromise between efficiency and ease of use and nobody can argue with the price. Be sure to configure it to make the most of your systems (use block rather than file storage and tweak my-huge.cnf).

For statistics, R is popular with the bioinformatics community <strike>despite the fact that it's one of the most awful hacked-together, inconsistent, illegible, slow, lumps of crap in existence. Leveraging other peoples' R packages can sometimes be a time-saver, but if you're really serious then pay the money and use Mathematica.</strike>

Finally, there's the important aspect of visualization that often gets forgotten until it's too late. A decent charting package is worth the money. A genome browser that slots in happily with your choice of server-side setup is also advantageous.

If you're in a team of bioinformaticists and can delegate specific roles then great. Otherwise, you're expected to be a Swiss army knife."

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1) I disagree that all bioinformaticians need sysadmin skills. If you're in a small lab and running your own cluster, sure. Many of us have sysadmin teams who handle that heavy lifting, though. standard unix tools? yes. Network switch config? no. 2) I disagree with your assessment of R 3) database skills may or may not be essential, depending on which subfield you're in.

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partially agree :) as i do not have sysadmin so you are for your own you may need this tools and knowledge. about R i think you will be dealing with statistics one way or another if you do not need R you will need other flavor

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To clarify, I think R is a good tool to know. The part I disagree with is the "lump of crap" statement. It has it's quirks and flaws, but is worth knowing.

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agree with you i hope that you can see that i stated that "and this is quoted from a blog" in the first of my comment, this is what other senior bioinformation said not me at all as i am not a senior

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8.4 years ago

Please ask some meaningful questions. Being young and smart are not qualifications for becoming a Bioinformatician. First answer the question, what is bioinformatics ? and you will automatically get the answer for your question(How to become a senior Bioinformatician).

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