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Biotech Technology

Supportive Courses for Bioinformatics? 37

Posted by Cliff from the learning-from-others-experiences dept.
Per Christian Henden asks: "I`m aiming for a masters degree in bioinformatics, and I`m uncertain which courses would be good to follow (and my counselor doesn't know, either). There are of course some courses that 'belong' to this degree, and I`ll take those, but I get to choose a number of additional courses. I want to ask people working in bioinformatics 'What (CS) subjects are important or especially useful in bioinformatics?' I`m planning on choosing 'Large Datasets', 'Parallel Programming', 'Image Classification', and 'Subsymbolic AI', because I think those are important, but I`m really not sure what is useful or not in real life bioinformatics." Other Ask Slashdot articles, which have touched on bioinformatics, have dealt with magazines, books and graduate schools.
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Supportive Courses for Bioinformatics? More

Supportive Courses for Bioinformatics?

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  • Take Biology (Score:4, Interesting)

    by biodork ( 25036 ) on Friday June 13, 2003 @08:22PM (#6196391)
    I work for a Bioinformatics company. Biology Biology Biology Biology!!! We have, and they are not doing as well, several people who with more of a CS background. They don't understand what it is that they are writing programs/algorithms about. We have found it easier to take Biologists who know computers and get good work from them than to do the converse. Make sure you get a VERY good grounding in basic biology. If you don't know what the data you are looking at mean, in the biological sense, then you will make the same mistake a lot do. Just because an algorithm is cool doesn't mean it makes sense. Only by understanding the Biology can you understand the difference.

    • Re:Take Biology (Score:3, Interesting)

      by Alan Shutko ( 5101 )
      But remember that having a good grounding in CS is also essential. I've met too many bioinformaticists whose code was horrid.

      Really, I think that it's easier to get good work from a good CS type in close collaboration with a bio type than a bio type who's picked up the usual smattering of CS. My wife (biologist) agrees.

      Your experience may be different, but I'd bet you just haven't hired good CS types. Instead, your company probably hired according to buzzwords (like so many other companies in IT) and i
      • Nope - Not Perl. C++ and Java. Perl won't get it done. Data set sizes are too large and speed too important. Crap code won't sell either (as that feature does shine through), and we are distinctly a 'for profit' entity.

        I would agree that the best stuff comes out of a tight collaboration between developers and Biologists, but both parties involved need to know the others language. We have seen many of the folks coming out the Bioinformatics programs that are just CS people who thought there was money to be
    • I'd have to agree on the biology, but I might go further. As others have posted, where you need to go now depends on where you've been (what have you studied so far?).

      Bioinformatics is a newish field and still defining itself. But there is a need for 'Bio IT' that covers the spectrum... from the basic grunt work of handling *huge* databases (and good user interfaces to them) in an efficient and useful way to ground-breaking chemical/molecular/organism modelling. I think the latter is where we'll make th

  • ask a professor (Score:3, Interesting)

    by Goldsmith ( 561202 ) on Friday June 13, 2003 @09:45PM (#6196774)
    Your first problem is asking a counselor.

    Find a professor at your University doing this, or interested in this, and get his advice. Better yet, start working for him.

    That's just generally good advice for anyone who wants to go to grad school in science or engineering.
    • Yeah, I know. I asked the appropriate counselor, and his predecessor, but they didn't know.

      I've also tried asking the (only) professor I cand find working on bioinformatics at my University, but she's never available and doesn't reply to my email :(
      • It sounds like you're in the wrong place then. If you're an undergrad, I would plan on going to grad school somewhere else. If you're already working on the Master's... well perhaps then you're better off just following other people's advice.

  • BioInformatics for Dummies... (Score:3, Informative)

    by PHAEDRU5 ( 213667 ) <instascreed.gmail@com> on Friday June 13, 2003 @10:47PM (#6197000) Homepage
    subject line says it all.

    No, seriously, this is a good book.
  • First, it would help if you told us what they're going to make you take for the program.

    Second, what is your background. Do you have a CS background? Biology? English?

    As for the courses of those Large Datasets is probably the most useful. Image Classification? Depends. If by 'bioinformatics' your actually talking about Biomedical IS (things like Query By Doodle for retrieving X-Ray information and so on) then yeah, but working on sequence data there aren't any images to classify. Maybe for some of the lab
    • My background is mathematics (with some physics and chemistry) and computer science mostly. I think I know English well enough, all my textbooks are in English.

      I have a detailed list at http://www.stud.ntnu.no/~perchrh/courses.html

      I'm not going for Computational Chemistry.
    • For the question about subsymbolic AI:

      The field of AI is divided into subsymbolic and symbolic AI, where the symbolic AI guys are working with formulas in logic and programming in prolog, typically, and the subsymbolic AI guys are programming in Lisp and working on neural networks, genetic algorithms and genetic programming.
  • You can learn enough about programming language later on to write programs to do what's needed. Learn about as much biology as you can, as well as as much as you can about algorithms (e.g., phylogenetic methods, alignment methods, micro-array analysis methods, and lots and lots of statistics). In your spare time, learn Perl.
  • I am constantly confused by what is bioinformatics. I always thought it was data relating to organisms. That's a pretty damn broad definition of it, however in my experience, using bioinformatics in a search engine rarely gets what I want.

    Population pharmacokinetic and pharmacodynamic modelling is a huge field. I have a masters degree in it and as a pharmacist I can tell not a lot of knowlegde in biology is really required (if that is a problem for you). If you want cutting edge stuff there are clinica
  • It depends what you mean by bioinformatics, which in itself is a broad and fairly uninformed decision. Most of the time these days people mean molecular biology, so for a good overview of what it means in molecular biology have a look at this [nih.gov]. Then it really depends on what you want to do. Do you want to administer the systems, identify new software and try to maintain and improve a toolset? In that case you need some computer science. Also it's also a hell of a lot easier to be a self taught computer p
  • Univ Calif, Irvine's CS dept has a Bioinformatics specialty/emphasis for graduate students.

    UCI's Institute of Genomics and Bioinformatics [uci.edu]
    UCI ICS Informatics in Biology and Medicine [uci.edu]

    They just got a $4.2M grant from the NIH [uci.edu] to strengthen and consolidate their Bioinformatics group. Maybe they'll offer scholarships.

  • You Need Biology (Score:3, Insightful)

    by JunkDNA ( 123288 ) on Saturday June 14, 2003 @02:26AM (#6197801)

    I work for a huge Bioinformatics department at a major pharmaceutical company. One thing you need to understand is that the lion's share of Bioinformatics would probably be considered "run of the mill" stuff as far as the rest of computer science is concerned. The biggest problem in Bioinformatics is that our IT people lack sufficient understanding of the underlying biology. If I had to pick an ideal candidate for a position with us, I would look for the following (in order of importance):

    Biology background that includes some of the following undergraduate courses: molecular biology, genetics, evolutionary biology, biochemistry/biophysics, virology, & microbiology

    Computer background that includes many of the following: Perl, Java, relational databases, XML, Visual Basic (lots of stupid stuff uses it) & general UNIX skills

    Preferably some kind of lab experience

    Any background in statistics (the more the better)

    What we really need are people capable of integrating large amounts of data (DNA sequences, protein structure info, gene expression results, biochemical pathways, clinical data, etc...). This stuff all needs to tie together somehow. While this doesn't require massive programming heroics, it does require an attention to the underlying science or else the wrong assumptions can be made and a total disaster created.

    Now, that's not to say that people with experience in areas such as artificial intelligence, image analysis, or natural language processing wouldn't be assets, but to be honest, we're just not at that point yet. Some actual Bioinformatics companies and organizations (TIGR, Celera, Affymetrix, Rosetta, etc...) may (and probably do) have a need for these specialized skills more than us. But do yourself a favor and take as much biology as possible. It's invaluable to my "office karma score" to be able to discuss the latest on Slashdot with our programmers, and two minutes later talk about an article from Nature with our biologists.

  • Take more stats than I did! (Score:2, Informative)

    by h3 ( 27424 )
    Depending on exactly which area of bioinformatics you're looking to get into, statistics may be an important aspect and is often overlooked. Not just your basic stats 101, but understanding what hidden Markov models, Monte Carlo simulations, and Bayesian analysis are good for.

    I didn't take enough stats and have no real good grasp of the above :p.

    -h3
  • I`m aiming for a masters degree in bioinformatics, and I`m uncertain which courses would be good to follow

    So take a Master's degree in Bioinformatics [bbk.ac.uk]. What's to be uncertain about?
    • Perhaps he doesn't want to go to England just to get a degree? (And pay a lot of money in the process.) The knowledge exist in other parts of the world too, there might just not be an established curriculum.
      • Perhaps he doesn't want to go to England just to get a degree? (And pay a lot of money in the process.)

        England's not that far from Norway, and the EU would probably give him a grant [eu.int] to study. I guess it all depends on how serious he is.
        • Yeah, but if he can get the same from a school he's already attending then it doesn't make much sense to go to England, just because.

          I know I could do the relevant courses here in Sweden, it's just that they haven't made a specific program for it.
    • I am planning to take a one year depth-study of bioinformatics, similar to the programme in London (url), but this one year of study is not much, and I'm thinking I should choose courses wisely to support this specialization in bioinformatics.

  • Learn biology, and specially cybernetic biology, the modern stuff (post-1970s) that most schools won't teach. You probably will have to go to Europe, or perhaps Latin America to find such courses, though.

  • Life Sciences and Statistics (Score:3, Informative)

    by pvera ( 250260 ) <pedro.vera@gmail.com> on Saturday June 14, 2003 @10:05AM (#6198835) Homepage Journal
    I work for a market research firm that focuses exclusively on the bioinformatics market. With a bachelors degree in Mechanical Engineering I am the worst educated employee of the company if you don't count the President/co-owner with his bachelor's in history.

    The main problem we have is that all our employees, regardless of field, need a strong scientific education (there's only 15 people and the company is profitable, so there is a lot of cross-utilization). Even the marketing folks come from a lab background, so they understand what is going on. I am their resident IT geek and in the last year I have been forced to absorb more about biology tools and techniques that I would have even dreamed of, and that's without even trying.
  • University of Illinois at Chicago actually has Bioinformatics programs and their curriculum is available on their website [uic.edu].
  • I have a few papers published in the BioInfo area and so alittle experience.
    i) Biology or BioChem
    ii) Maths or Statistics

    Reaons: Bioinfo is about handling large data sets of Biological information. Therefore unless you have a good understanding of Biology and/or BioChem you haven't a clue what to actually do with the data.i.e. what are you looking for?
    Once you have access to the data and want to extract significant meanings from it you'll need somewhere along the line to use maths/stats to figure out what t
  • I recently visited the Human Brain Project yearly conference at the NIH in Bethesda Maryland. It answers all your questions. There was one computer person giving a talk for every three researchers' talks.

    The big buzzword this year was Bayseian Filtering. People were using it to model probabilities that genetic sequences would correspond to: Behavior, electcrical signals in specific cells, pathology.

    Lots of people were using Java. a few more people using PHP, Python and Perl... no mention of C# or other

  • Computational biology (Score:2, Informative)

    by arn0n ( 675488 )
    I'm studying for a MSc in computational biology myself, and I've found that the most useful courses would be statistics-related, i.e. parametric & non-parameteric analysis, information theory, etc. It may be boring (it IS boring, dammit!), but you have to know how to do it.
    Not knowing how to assess significance of your results can cause you a lot of grief, either if you miss important results, or assign importance to non-signifcant results.

    In the second tier, it is crucial to have a good grasp of th

  • I hope i can shed some light into why i've enrolled in Bioinformatics...

    I chose Bioinformatics Undergraduate course at Birmingham (http://www.bham.ac.uk) because it was a sensible blend of Biology (something I'm 'good' at msyelf and supposed to be inherantly good at with my father being a GP, mom a nurse and grandad a health inspector) and computers, more specifically, perl and databases.

    I've found a love of genetics recently, since embarking on my AS levels two years ago, and today, the eve of my A2 leve
  • I guess the obvious question is whether your school offers any bioinformatics-specific classes. If not, you should strongly consider seeing if you attend a similar class at another nearby university. Trying to piece together the CS and Bio on your own is not particularly efficient! My school here has an excellent computational molecular biology class you can check out the syllabus at

    http://bio5495.wustl.edu/
    there are some books mentioned recommended by the professor at http://www.genetics.wustl.edu/bi

  • Your not going to get far in bioinformatics coming from the CS side. You need a good background in biology and/or biophysics. There is a top notch program at Johns Hopkins which is designed for CS people who want to work in computational biology. (They have a tough time attracting CS types because the pay is lousy, so they are always on the lookout for good people). Check it out at: http://www.jhu.edu/~ibr/bwf/index.html Good luck!

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