Flags and Lollipops - Bioinformatics Blog: Some tips I wish I'd been told

Friday, August 05, 2005

Some tips I wish I'd been told

I started working in bioinformatics without much knowledge of biology or genetics; my background is in vanilla computer science. I knew that I wanted to get into bioinformatics - I'd already dabbled in some relevant open source projects - but my knowledge of the field as a whole was pretty much restricted to what I'd gotten out of a copy of Developing Bioinformatics Computer Skills (which unfortunately is aimed more at bench biologists uncomfortable with computers rather than programmers uncomfortable with bench biology). On top of that I entered academia from industry.

Anyway, some things I wish that I'd been told when I first started:

You don't need a qualification in the life sciences to work in bioinformatics : it takes the same amount of time for a biologist to learn the relevant computer science skills as it does a computer scientist to learn the relevant biology.
Don't expect perfect solutions : I reckon that the sweet spot for accuracy in bioinformatics is 60-70%. Protein structure predictions work for 60-70% of genes. 60-70% of regulatory regions can be detected with the more recent methods. 60-70% of gene names can be successfully culled from large sets of Pubmed abstracts. Biology is complex. Current knowledge is far from perfect. Don't get into bioinformatics if you like clean, elegant solutions.
Learn Perl : You can try and get away with just Java or C but I assure you that at some point you're going to have to embrace Perl. Twas the language of the original bioinformaticians and thus shall remain ever so.
Stay well informed : As in computer science, you have to keep your skills current to survive. Unfortunately you also need to keep up to date with current scientific thinking on top of that. Sign up to the RSS feeds or table of contents alerts from the big bioinformatics journals (some are listed on the sidebar to the right).
Offer your services : your job probably involves helping out bench biologists anyway, but be on the lookout for ways that informatics could help the work going on in your lab; sometimes you'd be surprised. What might take you a couple of minutes with a simple script could be taking an unfortunate RA days (a real life example: checking a list of a hundred or so SNPs to look for those in conserved regions, running them through SIFT, etc.).

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Neil

Stew

Lei

Stew

Anonymous

Stew

Obi Igbokwe

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8 Comments:

At August 07, 2005 9:59 AM, Neil said...: Interesting points. A few comments:

-heated discussion often ensues as to the best route into bioinformatics - computer science to biology or vice versa. Ultimately I suspect it doesn't matter much, as one of our goals is to eliminate traditional disciplinary boundaries. One thing I would say is: ensure that your methods are relevant and address real-life biological problems. I've seen a lot of examples where someone presents a cute or clever computational technique of which they are very proud, but its application is almost an afterthought. Multiple incremental refinements which allegedly generate more accurate multiple alignments is my favourite example of this. Ultimately, biologists are looking to you to solve their problems - they don't care if algorithm X is better than function Y.

-a lot of biologists are uncomfortable with computers - not to mention maths, statistics, physics, engineering and more or less anything outside of the gene that they are cloning or the organism they are studying. It's a real challenge getting those types of people to realise what they're missing out on. Give them lots of simple, practical examples and they'll get it eventually.

-biology is indeed complex. But biological processes are also consistent and reproducible. Again, the challenge is getting biologists to understand that physical processes cause what we observe, as opposed to something mysterious and peculiar to biological systems. Some biologists also confuse "lots of data" with "complex data". A microarray experiment may generate a matrix with many thousands of rows, but that's not complex data - it's a lot of data. And handling a lot of data is what computers do.

-I'm with you on Perl. Simply because a lot of data formats and program outputs are plain old ASCII and Perl was designed with text processing in mind. And of course, because of Bioperl which is just fantastic and makes my life inestimably easier every day.

-offering your services is both a blessing and a curse. Particularly if as I am, you are the sole source of bioinformatics skills in a department of computer-illiterate biologists. It is satisfying when you provide a script or web page in 30 minutes which saves your colleague weeks or months of work and it may win their admiration and respect. However, it's very easy to fall into the role of service provider, which from a career point of view can be frustrating. Whilst your input is valued and seen as essential, it can also feel as though all you provide is technical support to the bigger picture (think: a string of 3rd, 4th or 5th authorships or even "we thank xxx for computational assistance"). So make sure you keep a couple of your own projects on the boil at all times.
At August 07, 2005 1:44 PM, Stew said...: Thanks for the comments! Good last point about keeping your own projects going, too.
At August 07, 2005 2:34 PM, Lei said...: It's a shame what you guys are saying about biologists being computer illiterate. Unfortunately, even my colleagues who are statistical/genetic epidemiologist don't know much more about computers/Internet beyond what they have to do for work. Still better than some, but not good enough IMO.
At August 07, 2005 8:56 PM, Stew said...: Yeah - I wonder how much of it is just not knowing about what tools are available and how much is, well, not wanting to do any more in-depth training for whatever reason? (which is fair enough; I couldn't do a Western blot and have little enthusiam for learning how to do one at this point).

Maybe it's because most of the software packages designed to make bioinformatics tasks quicker & easier for end users are described by application notes in bioinformatics journals, peer reviewed by bioinformaticians or presented at bioinformatics conferences. They're rarely pitched at the actual target audience of bench biologists...
At August 09, 2005 1:20 AM, Anonymous said...: hey, just wanted to add what great blog you have - and thanks for your tips.

I'm currently thinking about studying bioinformatics as well, but unfortunatelly, i'm not quite sure yet: I've already informed myself about the topics I'm going to learn at university, but I don't have any idea of how my later work will look like:

Of course I've already read about the research going on, but are you guys all working in a laboratory?

Isn't it too hard finding a job in smaller towns? Do I have to move into a bigger city?

Won't bioinformatics be too crowded in a few years time?

So many questions ;) - anyway, keep up the good work!
At August 09, 2005 5:46 PM, Stew said...: Hi anonymous,

Bioinformatics is getting more and more popular but I shouldn't think that you'd need to worry about the field getting overcrowded yet.

Over here in the UK you tend to see labs with one or two bioinformatics researchers attached to them rather than large centres dedicated just to bioinformatics (though those exist too). As such there are bioinformatics positions available all over the place - anywhere there's life science research going on. It depends on the kind of bioinformatics you want to do, I guess.

Having said that, science jobs (at least here) aren't all that common to begin with and bioinformatics is no exception... so you might end up having to move closer to a city where the best chance of getting a job is anyway.

Cheers,
Stew
At September 21, 2005 2:19 PM, Obi Igbokwe said...: You raised some good points, Stew, I get a lot of emails from people asking how they can get into bioinformatics. They also raise the issue of how hard it can be to find bioinformatics jobs. While it possible to find say an IT job from constantly visiting one site, because of the smaller size of the bioinformatics, a more extensive search using several sites is needed, which is why we have developed a bioinformatics jobs aggregator site, Biohealthmatics and we find between 8 to 20 bioinformatics jobs per day in the UK alone and much more in the US.
At October 26, 2007 8:33 PM, Anonymous said...: Hey folks,

A lot of people, including my family, thought Bioinformatics was a joke. Be an accountant. Not my things.

What are the best areas for Bioinformatics - San Diego, St. Louis, Boston, Indianna? I see ads for Bioinformatics that ask for Ph.D's and I know from Washington University that there aren't that many out there. And few people in this country - U.S. - have degrees in it. Many have just ended up doing it because they liked it and were good at it.

Does anyone know how the BioBelt near St. Louis or Chicago is doing?

Too much emphasis is placed on San Francisco, Seattle, San Diego or Boston or Maryland.

Personally, I see this side of the business becoming much more numerous - Doctors, Pharmaceuticals, Dentist, Drug Stores simply will need this kind of expertise in an ever changing world.

Seems that India is becoming a major player here; where is the U.S.?

Walter

Friday, August 05, 2005

Some tips I wish I'd been told

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