Being a bioinformatician is hard
August 6th, 2007
For instance, if you have a set of data, you have to understand many things. First, you have to know the biological relevance. How was it produced, what does the data mean, and what is the significance? Lab biologists need to know this as well, but a bioinformatician must also know, in addition, how to store the data. What is the best method of representing it, given that the data needs to pulled out and manipulated within computer code. Next the bioinformatician needs to know what’s statistically feasible given what’s available. It’s going to be tricky to get answers from only three replicates of a noisy microarray experiment. Can you use a SVD to filter some of this noise? What about a microarray experiment with 10 different drug treatments. Where do you begin, can you use dimensionality reduction? How about using clustering? How many clusters? Did someone say probabilistic?
Admittedly producing results in bioinformatics is easy. Compared with the wet lab, where gels have to run, and overnight experiments have to be started at 7.30am. We do have it easy in this respect, it’s entirely possible to produce a new figure, or another set of data every day. But this blessing is also a curse; with the ability to quickly produce so many figures and answers, it’s also easy to get swamped, or lose focus on the overall goal. Being a bioinformatician you need to be disciplined, not because the web and email is a constant distraction, but because you need to always being thinking about the larger picture. What you’re doing right now, how does it relate to your research question. There’s a always a danger of being pulled down a side track, doing work because it would interesting to see what happens. But unless it’s something that leads towards you writing a paper, you’re wasting your time. It’s tough, but it’s true. We’re judged on publication of papers, and we always need to be focused on the big question.
In addition to discipline, you need to believe in yourself. You’ll never have something that you can hold in your hand and say “I made this”. No gel pictures, or tubes of purified protein. We produce p-values, programs, and figures. When things are getting hard, you need a measure of self belief, and good friends to talk to, because tomorrow you’ll have to sit behind the same desk, at the same screen, and keep plugging away at the same problems, problems only you really understand.
Unfortunately you’ll also need a measure of self confidence because, at the moment, bioinformatics is not taken seriously by the majority of biologists. Our peers in the lab think we sit around all day drinking tea and pushing buttons. What we do is either easy, or not “proper science” because we don’t work in a laboratory. The reason for this, partly our fault, is because most lab biologists don’t understand what we do day to day. Modern day biology uses the computer more and more, and this means having to ask for help from a bioinformatician. Unthinkable for an “old school” biologist.
But it’s worth it. Because bioinformaticians are at the forefront of biological science. The fruits of our work were unimaginable twenty years ago. A tool where you can compare a nucleic acid sequence against all those ever found? Analyse the transcript profiles of 23,000 human genes and pick the handful that are drug targets? Simulate the entire reaction network of a cell and be able to predict the genes that are essential? Other biologists have difficulty understanding what we do, because it’s hard. We’ve put in the time to learn how to program, understand what a support vector machine is, and when to use a t-test or an ANOVA. For me, being a bioinformatician is gruelling, personally as well as professionally. But the satisfaction comes from the zen-like moments, when everything comes together. When problems are broken down mentally, and then computationally using a fast and elegant programming solution. When the black arts of statistics, multivariate analysis, and machine learning are your everyday toolbox.
Creative Commons
The photo used in this post is taken from wiseacre on flickr and used under a creative commons licence.
August 6th, 2007 at 10:41 pm
Yes, it’s easy to feel undervalued as the bioinformatician. There is a subset of biologists who believe that we have it easy; numbers go into the black box, numbers come out. Yet they’re happy to come running when they need to transpose rows into columns, or some equally mundane IT-support style task.
Equally though, there are plenty of biologists who realise the importance of bioinformatics and are happy to give us credit for our skill set. So befriend them and ignore the others! They’ll soon get the message.
It’s also important to stay focused on biological problems and promote what you do at every opportunity, so as the relevance can’t be ignored. You’ll never convince some people of the benefits of R/gnuplot/scripting over Excel but when you casually mention in your group talk: “so, I took all of GenBank, fed it through my pipeline and here are the candidates” (one slide), they’ll see for themselves. Eventually.
August 7th, 2007 at 6:30 am
[...] ponders the life of the bioinformatician. Difficult but ultimately rewarding, he [...]
August 7th, 2007 at 10:44 am
It also depends on the labs. I had the luck of doing my PhD in a lab were a lot of people did a bit of both (bench and programing). It is good for several reasons but one of them is exactly that several people in the lab understood those small little things that make the job not has easy as it looks.
August 7th, 2007 at 1:36 pm
I was reading your post and a work colleague (a lab biologist) said over my shoulder ‘Bioinformatics isn’t hard.’ To which I responded by opening up some recent java code I’d written. His response was ‘Oh well thats just gibberish.’
He gives me a region of interest and I generate a list of interesting candidates…easy! Unfortunately, that is exactly how it appears to most of them. Their appreciation for your coding skills, database knowledge, SVMs, web services, workflows, linux commands and your ability to automate analyses that save them months of time just don’t exist.
However, there are the select few that do and they are the ones that have made an effort to understand your area of expertise. Where would we be without bioinformatics?
Claiming it is ‘not proper science’ is drastically inaccurate as science by its very definition means ‘to know’, it is about knowledge acquisition through observation and experimentation. This is why bioinformatics is a rigorous, intensive, multidisciplinary ’science’.
August 7th, 2007 at 4:50 pm
“We produce p-values, programs, and figures”…
There is one angle to this, the bioinformatics boom also came through the Structure based drug design [ http://staffnet.kingston.ac.uk/~ku33185/BioModule/struclife.pdf ].
August 7th, 2007 at 5:41 pm
[...] life of a bioinformatician… Just finished reading a very good post over at BioInformatics Zen which underscores several issues many informatics-based researchers face. One of the predominant [...]
August 8th, 2007 at 5:07 pm
Bioinformatics is not all about the code and figures - it’s often about deep understanding from many different points of view the system you are working on. And it usually demands both: coding skills and extensive biological knowledge.
I definitely agree that people doing bioinformatics are at the forefront of the biological sciences - being able to look at the problem at all possible levels of molecular organisation is a valuable skill.
August 10th, 2007 at 4:16 pm
After writing this post, I and a few other people in the department had a bit of group discussion: we went to the pub and just let everything out. One thing that came up was how wet/dry collaborations are a one way street. If you spend three days doing work for a lab biologist, you would be lucky to get into the acknowledgements. On the other hand, if you managed to persuade someone in the lab to do three days of work for you, you can imagine the vitriolic rant if you failed to put them as an author in the paper. One person I spoke to said that he’s started refusing to do work for lab biologists now because, in the majority they either have no understanding of the effort it takes, or just treat bioinformatics researchers as a service.
Pedro and Neil both said that there are lab biologists who do appreciate bioinformatics, but my personal opinion is that they are in the minority. Though as both say, when dry and wet work together the results are more than the sum of their parts.
Another interesting point of discussion was about the time it takes to do bioinformatics work. If you do some work for a biologist, if it only takes you a few hours does that mean it’s easy? I think the answer is no, because you’ve put the weeks, and months in learning how to do the analysis correctly. Getting good enough to do the analysis, so that it looks like it’s easy should still mean that you get credit for it, after all have much time have you saved the biologist. Or could they even be able to do it themselves? I think this is something similar to what Kieren was saying.
This is turning into a bit of rant, however I think the political issues that are preventing more wet and dry lab people working together is a bit a waste. Which is in turn usually a waste of public money.
I’d also like to say that person in the picture is not me. A few of my friends have asked this, Kieren in particular asked if I had photoshopped a beard onto myself? I’m also not married either, i.e. there’s a wedding ring on his finger. Maybe that’s why he’s sad? Having said that, I’m not opposed to marriage, it’s just that I’ve had a few bad relationships in the past. Time to stop writing.
August 14th, 2007 at 5:22 am
Is the similarity between “bioinformatician” and “technician” only a coincidence?
While I admit that we are often misunderstood and many wetlab people do not appreciate our work, I believe the blame is on our side too. I see many times people who forget that there’s a “bio” prefix in here, and neglect the biological side of their work. How can we deserve a respect if there are cases where bioinformaticians don’t distinguish between two beta-barrels with different number of strands or treat DNA sequence as protein sequence with limited alphabet (for more inspiring examples see archives of journals focused on biocomputing/bioinformatics)?
It’s not only politics, high self-importance of wetlab people, but also work called “bioinformatics” that’s too often of questionable quality. I believe all three contribute significantly to that problem.
May 20th, 2008 at 4:58 pm
i want to be a bioinformatician so would you say doing the folowing courses are useful:
cell and molecular pharmacology
bioinformatics
gene cloning and expression
protein structure and design
October 11th, 2008 at 5:21 pm
The scope of work involved in Bioinformatics is endless,infinite…..
However debating on issue i.e “Who shall be credited for the reseach work involved whether Wet or Dry Lab gigs” is a Vicious circle of self suicidal attempts to the bright, healthy and beautifull WORLD.
I believe we are all a part of Team…If respected oldage Wet Lab scientists do play such games…..then they themselves become the reason to streatch the fruitfull Results in thier favour only…
We are all PROUD to be Bioinformaticians ( Next to God Father )…
October 12th, 2008 at 4:02 pm
@Susan
I can’t really answer what courses are the best for you. Having an interest in both computers and biology is the most important thing. If you enjoy both of those, I’d say you probably won’t go far wrong.
@Nitin
I agree, I’m sure the best research comes from people working together in both the wet and dry lab. I’m going to hug the next person I see wearing a lab coat.