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What do you call a biologist who uses bioinformatics tools to do research, but doesn’t program?

You don’t know?

Neither does anyone else.

The names we use
People who practice biology are known by many names, so many, that the number of names almost reflects the diversity of biology itself.

Sometimes we describe biologists by the subject they study. Thus, we have biologists from anatomists to zoologists, and everything in between: addiction researchers, chronobiologists, epidemiologists, immunologists, microbiologists, neuroscientists, pharmacologists, physiologists, plant biologists, virologists and many, many more.

Sometimes biologists are described by their favorite tools or technologies, especially in the ‘omics arena. Geneticists, for example, often study biology by making or identifying mutants and messing around with genes. Biochemists do biochemistry. Synthetic biologists synthesize new genes and proteins. And so on.

Of course the techniques and subjects overlap. A cancer biologist might use genomics technologies and immunological tools like antibodies. A biochemist might study the enzymatic properties of mutants. Researchers rarely limit themselves to one kind of assay or tool.

Matching the name to the career
Still, the names of biology subfields are pretty useful for those of us who advise students or write about careers, even when the names are fairly general. The distinctions between fields help students who are researching potential careers and picking a major. It’s fairly straightforward to figure out the difference between a microbiologist and a conservation biologist. Likewise, a student can get an idea what a biochemist might do by picking up a textbook on biochemistry or reading about biochemistry in Wikipedia.

Finding job descriptions for people who work at the interface of technologies is harder. In the case of bioinformatics, it’s also complicated by the name of the field and the lack of a distinction between the people who make bioinformatics resources and the people who use them. Certainly, very few science instructors or even many practicing biologists for that matter seem to know what bioinformaticists actually do.

What is a bioinformaticist?
Over the past ten years, however, if you work in an ‘omics-related field, you can see that a kind of consensus has emerged about bioinformaticists and their jobs. A bioinformaticist is someone who is involved in programming, or creating bioinformatics algorithms, software, or databases. If you were to apply for a job with “bioinformatics” in the title, you might be expected to set up servers, install software, write some shell scripts, and do some programming.

Nevertheless, outside of ‘omics research, people have a strong tendency to confuse tool builders with tool users.

This confusion between the tool builders and tool users (biologists) causes problems for both instructors and students. Bioinformatics education programs can vary widely between colleges and the courses vary as well. For example, if you took either of the classes that I teach, you would learn how to use bioinformatics tools for doing biological research, but you would not learn how to program. I call the courses “bioinformatics” but they are really biology courses without a better name and lots of computer work.

[ Believe it or not, I always seem to get a students who are surprised to learn that bioinformatics involves using computers. We even had a high school teacher complain that a bioinformatics workshop involved too much time in the computer lab.]

Because of the confusion, we find students who want to learn how to program and get disappointed because they they can’t practice those skills and biology students are get scared away from bioinformatics courses that require them to use command line tools. Neither group gets served well when we fail to make the distinction ourselves.

Let’s start a new group and call them digital biologists.
The term “bioinformaticist” has evolved a definition. That’s a good thing.

But what do we call biologists (like me) who use software and other bioinformatics resources as their primary research tools, but do not program?

No one seems to know.

The terms I hear the most are: “user” and “customer

Neither of these terms work. Both are way too general and I’m definitely not fond of “user.” Ever since someone told me that only two groups that call their customers “users” are drug dealers and software engineers, the term “user” has made me cringe.

So I propose we follow the lead that the NIH began at the Digital Biology conference in 2003 and christen the biologists who use digital tools for research, i.e. bioinformatics tools “digital biologists.”

Happy 2010 from a digital biologist.

Comments

  1. #1 Deepak
    January 1, 2010

    I’d argue you’re still a biologist, with a new set of tools. Why can’t we just realize that informatics tools are just part of your everyday toolkit

  2. #2 Sandra Porter
    January 1, 2010

    Happy New Year Deepak!

    I agree with you, but people who don’t work in the field don’t understand this.

    Besides, if synthetic biology can be a subfield, I think digital biology can be one, too.

  3. #3 Ian
    January 1, 2010

    It would be difficult to find a biologist who doesn’t use bioinformatics tools at all. So a digital biologist is defined by the absence of wet lab work? Can the absence of a tool really mark the need for a category? Do we need new names now for biologists who don’t do biochemistry, or biologists who don’t work with lab animals?

  4. #4 Sandra Porter
    January 1, 2010

    I wouldn’t define a type of biologist by the absence of a tool, but by the primary tool they use. So, a biologist that mostly uses bioinformatics could be a digital biologist.

    Consider a biochemist for example, they might use genetics, but would mostly use biochemistry. A geneticist might use biochemical assays, but would primarily see themselves as studying or using genetics.

    And, many molecular biologists, for that matter, grow E. coli for cloning and sequencing studies, but they’re definitely not microbiologists.

  5. #5 Gustavo
    January 1, 2010

    I’m kind of surprised at not seeing here mention of the very common term “computational biologist”.

  6. #6 Sandra Porter
    January 1, 2010

    Hi Gustavo!

    From the NIH, the definition of computational biology is: The development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems.

    I guess I do apply the methods, but it’s always seemed like this definition applied more to the computer scientists, and researchers like you, who are developing new algorithms and statistical methods.

  7. #7 Comrade PhysioProf
    January 1, 2010

    I am Doctor Douchebaggio of the Department of Douchebaggiomicology!

  8. #8 Coturnix
    January 1, 2010

    I have quite a strong dislike for defining disciplines by technique, as they tend to lock the students in as practitioners of a technique which, in a few years, will become obsolete.

    I much prefer to define oneself by the questions one asks. If you are interested in the workings of a cell, you are a cell biologist no matter which techniques you use. I expect you to adopt new techniques as they become available over the years if they are appropriate for the kinds of questions you are interested in asking. The same goes for ecologists or any other discipline – think about concepts, choose techniques according to the appropriateness for answering your questions.

    Having computers and cool bioinformatics software expands the range of techniques. But if you don’t need them, don’t you use them just because they are fashionable. Ron Prokopy made fundamental discoveries without having any electricity in his lab, and that was already at the time when his colleagues were running gels. There is a reason why the word “bandwagon” has a derogatory sense to it….

  9. #9 Janne
    January 1, 2010

    If they’re just using bioinformatics tools then they’re not really bioinformaticists, are they? A agree with Deepak that they’re “biologists” (or whatever subfield they work in).

    A “Bioinformaticist” or “Computational biologists” or whatever is, to me, someone who’s actually working on the tools themselves. A biologist that does computer programming (and related mathematical analysis) if you will.

  10. #10 Grant
    January 1, 2010

    It’s one of the reasons I use the term computational biologist by preference and I disagree with your, or rather the NIH’s, definition of the term. In particular, you can’t properly develop good method without understanding the science at hand. Computational biologist = biologist who uses theoretical methods developed on computers as their mainstay. (Think: biophysicist, mathematical biologist, theoretical biologist.)

    I use three terms:

    computational biology (the specialists, focusing on developing and applying
    theoretical biology)

    bioinformatics (developers/advanced users of informatics tools that “happen”
    to manipulate biological data but really have little actual biology in them)

    biologists (who routinely use bioinformatics tools; I guess you could call these
    people if that’s what they mainly do)

    I’ve nothing against those working on informatics tools, but there is difference in developing, say, data pipelines of existing computational biology tools, as to developing the computational biology tools themselves. The former mostly involves a knowledge of computing, as opposed to computer science and generally little real knowledge of biology. (Witness the relatively easy influx of people from other fields into this sphere.)

    The more important difference to my mind, characteristic of computational biologists, is an in-depth understanding of theoretical biology in the particular area of interest. Good theoretical biology is what underpins computational biology, not the computer science (or statistics or physics or whatever), which are just the tools for expressing or encoding that understanding in a useable way.

    This and that, as you put it “very few science instructors or even many practicing biologists for that matter seem to know what bioinformaticists actually do”, is the reason I’ve wrote a couple of (longish) articles loosely on this theme in 2002, see the link on my name for one example that I’ve recently re-published). The earlier article brings up my definition of bioinformatics from memory.

    Personally I prefer a historical view. Earlier “bioinformatics” work (e.g. mid 1960s to mid 1980s) relates more closely to what I’d term computational biology with most of it driven from a biological question that needed to be resolved and people developed the methods they then applied to address their question. (I’m simplifying and generalising, of course.)

    I’ll stop here to save boring people: those who are obsessive enough to want more can just read my articles after all!

  11. #11 Sandra Porter
    January 2, 2010

    Coturnix: I don’t think including a technology as part of a job description is a bad thing. Look at all the statisticians, biochemists, geneticists, x-ray crystallographers, electron microscopists, NMR spectroscopists, etc.

    The technology name gives teachers an idea of what people do in those kinds of jobs and the skills that they would need to learn.

    Names that are too general like “biologist” aren’t helpful when one is trying to explain to teachers what bioinformatics is and what it isn’t. I’ve had a challenging time this year trying to explain to some collaborators that genetic counseling isn’t bioinformatics and to others that many biologists are able to use bioinformatics resources without having to learn Perl. Thus, the need for a new name.

  12. #12 Sandra Porter
    January 2, 2010

    Thanks Janne

    I agree with you. That’s why I proposed the new name.

    Grant:

    I agree pretty much with your definitions of bioinformaticists and computational biologists. I don’t think they’re much different from the original NIH ones.

    But, the name “biologist” is just too general for the reasons that I outlined in the post. If you call all non-programmers “biologists” you miss the reality that many biologists spend lots of time doing wet bench work and very little time doing computational analyses. You also misses the diversity of biologists, who do many different kinds of experiments and use very diverse techniques depending on their field and specialty.

    I have been using bioinformatics for 25 years, starting with GenePro in 1984 on a DOS computer, before “bioinformatics” was described as field.

    Much of what we did then was to search for strings of text (i.e. nucleotides). In fact, in 1984, we assembled sequences in Word. We also looked for restriction sites, identified signal sequences, used GenePro to generate plots of hydrophobic and hydrophilic regions, looked for transcription and translation start sites, and used translation programs to predict protein sequences. We still do those things, but those activities don’t require you to be a physicist or mathematician to search for a restriction site or translate a protein in six reading frames and compare sequences.

  13. #13 Don Smith
    January 2, 2010

    Actually, more ancient programmers would call them lusers.

    ;)

  14. #14 Salvatore
    January 4, 2010

    Sorry Jane, but I have to disagree! (with a very unscientific exclamation mark too)

    I have seen the term “digital biology” used to describe the use of computers to model biological systems – as in a “digital cell” to model cell behavior, so I’m not sure that this will just add yet more confusion to an already bewildering babel of biological career labels.

    I disagree with using the technology to describe the job, and especially I hate the idea that biology is becoming more fragmented by methodology rather than by specialty.

    We study life, in all it bewildering and awe inspiring intricacy, and I for one am not interested in defining myself by any, or even all of, the ever growing number of niche tools. They are all there to be used as appropriate. I’ll dip into each of them and find somebody with appropriate expertise and experience to help me understand what the tool does and if it is the right tool for the job at hand.

    What is wrong with defining the job by what you really are interested in understanding, elucidating, or improving – as in cancer, environment, evolution, development, your favorite disease, cheese, wine, aging, etc. Then string them all together to show what you are really trying to solve:

    I study epigenetics of adult stem cells differentiation in cartilage repair, and some might consider what I do “regenerative medicine”, “molecualr biology”, “epigenetics” or “systems biology” depending on what I’m focused on at that moment. But none of these says what I am really doing – “looking for what stops cartilage from repairing itself properly in osteoarthritis”. That is something that even a non biologist can at least get a handle on, and something a little more interesting and inspiring to a potential biologist than something that will take them several years of study to realise is just a way of describing which tools you use most often.

    It is very easy to paint yourself into a box if you define yourself by the tools. In my previous career in IT, I saw a lot of people get stuck (and sunk) because they became wedded to a particular manufacturers technology (as in “Novell Certified Engineer”). This is not what biology is about – I don’t want to work in an industry which sets up 6 week courses and hands out technology certificates to satisfy the ever growing demand for skilled biologists. Do we want to have “Certified Celera Genomicists” or other such meaningless and transient labels applied to us?

  15. #15 Sandra Porter
    January 4, 2010

    Gosh Salvatore, have you never heard of Cold Spring Harbor Courses?

    On a more serious note, scientists have been describing themselves and their academic departments by their preferred technologies for several decades. That’s why we departments with names like: biochemistry, genetics, and bioengineering.

    Maybe it’s better to think or career descriptions like ontologies with professions and activities best described by multiple ontologies that overlap. Maybe the two best ontologies could be a subject ontology and a technology ontology?

    Anyway, I’m still not seeing an answer to the question I asked in the title of the post.

  16. #16 Chris
    January 4, 2010

    If you are interested in the workings of a cell, you are a cell biologist no matter which techniques you use.

    Right. We don’t have “microarrayists” – that’s silly, because it’s just another tool in the arsenal. The fact that you specialize in a certain subset of the available tools is relevant to someone who is hiring you or wants a deep understanding of your job.

    In general, you’re looking for biological answers. The rest is just details.

  17. #17 Grant
    January 5, 2010

    Sandra,

    I’ve been doing bioinformatics from the same time, but with PDP-11s as my main computer at that time (and a larger lab machine and access to a Cray, which I gave up on; it’s long story and went back to the PDP-11).

    I don’t think you’ve quite got what I was after ;-)

    I hope you don’t mind me clarifying.

    I don’t recall calling “all non-programmers “biologists” “, in fact I recall pointing out the many of the earlier “biologists” came from other fields ;-) You’re stretching far past my intended meaning!

    I merely wrote that using bioinformatics methods is routine, that it’s not some obscure thing that few do; I didn’t say that biologists spent lots of time doing it (although a few do) or “missed” your other “explanations” of what biologists do.

    I’d like to think I’m quite aware what biologists do, I’ve spent quite a bit of my life around them ;-) (FWIW, I consider myself a biologist, albeit one who happens to use a computer.)

    I accidentally dropped a bit in my writing (might be related to some keyboard issues I’m having): the bracket portion elaborating on my definition for biologist should have read: “(who routinely use bioinformatics tools; I guess you could call these people digital biologist if that’s what they mainly do)”.

    I meant the last mainly as compromise to your ideas, although I have to admit I generally label “advanced (full-time) users” bioinformaticians, e.g.—answering your question—biologists who mainly use, but don’t develop, bioinformatics methods.

    Regards your writing about (your?) older work, you seem to be confusing different sets of people with respect to what I was writing about. It’s a long story and I’d rather not repeat what I’ve already written about on my blog here…

    There may also be an element of a trans-Atlantic difference too. (I’m more familiar with the English side of the ditch as I was based over that way.) There is also the difference that I include the theoretical work on molecular structures, which makes for a larger picture than if you look solely at early sequence work.

    Your writing splits developers and users. I have strong feelings that the best developers are those that develop in response to trying to solve a biological problem for themselves by having a strong knowledge of both the relevant computer science (etc.) and the relevant biology, i.e. are computational biologists. [An exception can be "pure" informatics methods.] (I have an up-coming post about this, but I’ve a lot on my plate so it might be a few days off.)

    Likewise, I have strong feelings that most computational biology problems, unless they’re routine, are best deal with by someone (or at least co-ordinated by someone) with a strong understanding of both the computational methods and the biological methods. (But then, I’m biased as I’m a computational biology consultant, so I guess I would say that.)

    The common “language” between these two is theoretical biology. My article draws an analogy of a bridge in the latter stages to explain this; I’ll stop here to avoid writing even more…!

    In any event, I want to emphasise a key point for me is that theoretical biology is often overlooked, yet it’s a key element of good computational biology.

    In a sort-of parallel with Coturnix’s comment (although more with respect to teaching that giving a job title) I prefer a focus on the underlying knowledge. In the case of computational biology I consider an important underlying element is theoretical biology.

    There’s a difference between a job title (temporary thing that any one job is!) and a description of a field/career/what-have-you, too. What you’re looking for, for a job title sounds fine to me, but for the name of disciplines I’d prefer to lean to the underlying knowledge, rather than the particular tools of the day, which will change as coturnix was saying (and Chris, too).

    Salvatore: I’m interested in epigenetics myself, from a computational structural biology / chromatin angle + gene regulation angle.

  18. #18 Thomas Joseph
    January 5, 2010

    In silico biologists.

  19. #19 Grant
    January 5, 2010

    Anyway, getting back on topic…

    Bioinformatics analyst?

    (Remembering that I’m thinking of this as a job description, not a discipline.)

  20. #20 Sandra Porter
    January 6, 2010

    Thomas: I like “in silico” but I want a name that will make sense to a larger group of people. I’m afraid there are too many people who won’t know what “in silico” means.

  21. #21 Sandra Porter
    January 6, 2010

    Grant:

    I don’t think you’ve quite got what I was after ;-)
    I hope you don’t mind me clarifying.

    I don’t mind. I don’t think you quite understood what I wrote either. It’s probably just the language differences on the other side of the Pacific (I’m on the West Coast).

    You are closer, though, to what I was getting at with considering job descriptions.

    My idea is that the description: “digital biologist” is similar to description used by people I know who call themselves “mathematical biologists.” Where mathematical biologists use math to study biology, digital biologists study biology by using software to analyze biological data.

    Hopefully, I described my idea better in this post.

  22. #22 Grant
    January 8, 2010

    My idea is that the description: “digital biologist” is similar to description used by people I know who call themselves “mathematical biologists.”

    I got that the first time actually, but thanks for the concise summary. (e.g. In my correction to my original comment I wrote “I guess you could call these people digital biologist[s] if that’s [bioinformatics analyses are] what they mainly do”.)

    I know I wasn’t very clear, but I do get what you are after! I have every sympathy for wanting to be able to define what you do. (I have a parallel local problem with the distinction between computational biology and bioinformatics.)

    Anyway, three answers, one short, one long and one in between.

    Short: someone who does bioinformatics analyses = a bioinformatics analyst.

    Long: see http://sciblogs.co.nz/code-for-life/2010/01/08/more-on-what-is-a-computational-biologist-and-related-disciplines/

    In between:

    I’ve leave it for now. I seem to have written way more than on than is sensible given I’m easy about what people call themselves in the end of the day (provided they don’t over-inflate their skills).

    One thing though: I’ve nothing against the overall idea of wanting to be able to name a line of work or research, don’t get me wrong on that account.

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    July 8, 2010

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