I’m a bioinformatician

Navel-gazingthis opinion piece, called “Who qualifies to be a bioinformatician?” seems to have prompted rather a lot of it. I’m breaking my extended silence to add my two-pennyworth on what being a bioinformatician means to me

  • Being a bioinformatician means being a biologist, programmer, sysadmin, statistician and grief counsellor, rolled into one
  • Being a bioinformatician means writing thousands of lines of glue code in [scripting language of choice]
  • Being a bioinformatician means teaching experienced scientists something new, and getting to see the dawning realization that it might just be useful
  • Being a bioinformatician means jumping through a 112 hoops to compile the latest and greatest tool, just to find it segfaults on anything other than the test data
  • Being a bioinformatician means embarking on what seems like a simple job, only to find six weeks later you’ve written yet another short-read aligner
  • Being a bioinformatician means crafting an exquisite pipeline that has to be subtly changed with each run because every dataset is a special little flower that needs bespoke treatment
  • Being a bioinformatician means writing yet another hacky data munging script that will break on the 32,356th line of the poorly defined, exception riddled, lumpen slurry of an input file you’re having to deal with this time
  • Being a bioinformatician means learning that Excel is an acceptable interoperability format, whether you like it or not (I don’t)
  • Being a bioinformatician means knowing enough biology, computing and statistics to be looked down on by purists in all three disciplines
  • Being a bioinformatician means playing a key role in an unparalleled range of exciting, cutting edge research
  • Being a bioinformatician means being part of an open, collaborative worldwide community who are genuinely supportive and helpful

Now, this list may be a little flippant in places — but it is intended to make a point. There are no hard and fast rules about what a bioinformatician is and isn’t, the label will mean different things to different people. But what it does involve is an unusually wide skill set, usually hard-won over many years, and the knowledge of when and where to apply those skills. It definitively doesn’t involve looking down on hardworking partitioners in the field purely because they don’t fit your elitist mould — the only thing this is likely to do is exclude those interested in the field, but who don’t fit your preconceived ideals.

If you want to let me know what being a bioinformatician means to you, feel free to comment below.

7 comments

  1. Hi Simon, as a fellow bioinformatician (how I wish it wasn’t such a mouthful!) since the turn of the century, I was amused to read your spot-on navel-gazing musings, especially the bit about “grief counselling”. I would add “customer relationship officer” to your already long list of role-descriptions, and perhaps they should make “bedside manner” a mandatory course for us folks, especially at institutions where dreaded cost-recovery is an uncomfortable elephant in the room — how do we even begin going about charging for the autopsy of an experiment that’s died a horrible death before even stepping into the sequencer. Ah, well, coroner duties aside, it is exciting work, and deeply satisfying, no matter how little (or long-in-coming) the reward 😉 Best wishes, Aaron aka Igor

  2. Let’s start with KW Project, a nonprofit iniatitive to share knowledge about this. The bioinformatician should know represent knowledge to increase the applications intelligence. We will find that neuroscience gives us the solution. No need to know low-level programming. There are many tools that can make any representation of reality. The problem lies in the generosity and integrity of the person.

    Bioinformatics is the final frontier.

  3. I would define it quite simplly – if you work in biology but spend most/all of your time analysing data on a computer rather than at the bench then you’re a bioinformatician. Whether you’re applying algorithms/software that others have written, or developing algorithms/software yourself it’s just part of the same thing. The key thing is that you work in biology, so if you are a sys admin for an HPC then you aren’t really a bioinformatician because biology isn’t at the core of what you do, making computers work is. Trying to draw a line between people who develop algorithms and people who apply them is just a bit ridiculous really because most people do a bit of both, although there are specialists at each end of the spectrum. ‘Bioinformatics’ itself is a skillset, and it should be very welcome that bench biologists take an interest in what we do and even develop some of the skills themselves, because data in biology is only getting bigger and so bioinformatics is only going to become more important in future. So let’s not get elitist and look down on the bench biologist trying to analyse their data in Bioconductor, but applaud them for trying and give them a bit of help and encouragement.

  4. Interestingly While talking to people in the industry I see that they really appreciate exactly these kind of skills and are willing to pay for it.

  5. One surprise I had recently was another comp biol telling me that “bioinformaticist” referred to those doing bioinformatics as a service, rather than the scientists (who were genomicists, modellers, or comp biologists). Has anyone else seen this?

  6. I am the first author of the opinion piece discussed here. I follow, since the beginning, all the buzz on twitter and blogs about my letter. I am incredibly surprised by all the reactions and by persons qualifying my letter as “Navel-gazing”. My goal was and is still not to include or exclude anybody from the bioinformatics field.

    The problem is that many scientists in the biological field simply perform a couple of blast on the NCBI website and qualify themselves as bioinformaticians. And so what you will say? If every person performing a bunch of blast could add in their CV that they are bioinformaticians in addition to a lot of “wet-lab” skills, it will be hard for “real” bioinformaticians to stand out. A bioinformatician is able to use tools AND to understand really how they work. A bioinformatician not just uses blast, he or her understand how it works.

    Moreover, as indicated in the opinion letter, it is important for job descriptions (for the bioinformaticians and their employers). Bioinformaticians are not informatics technicians!

    It is clearly indicated in the letter that gray zones exist. I do not pretend to be able in 1000 words to cover all exceptions and to go deep in the subject. Many persons can be considered as bioinformaticians without fitting perfectly in the definition provided by the letter.

    Finally, the main goal of the letter was to start a discussion on this neglected question of “Who qualifies to be a bioinformatician?” It seems obvious that it is a sensitive topic based on the reactions. So the next question would be why it is so delicate?

  7. “Being a bioinformatician means crafting an exquisite pipeline that has to be subtly changed with each run because every dataset is a special little flower that needs bespoke treatment”
    Exactly!!! I work on NGS data, and each dataset is unique. You need to fine tune the normalization, feature selection, and etc..all the time. I almost feel bad about myself being not able to make a general purpose pipeline until I realize there is nothing “general purpose” and good

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