On the scripting skills

19 Aug

The interview with dr Alexei Drummond inspired an interesting discussion. While I agree that some level of training in programming would be very beneficial for the biologists, I think that there’s something more important people working at the bench should learn – using the tools for biological data analysis. The scripting skills are fine, they save often enormous amount of time, however not willing to learn how to do a BLAST search (or any other basic tool in the field) and interpret results, leads to publishing papers with errors (the best case) or with completely wrong conclusions (that is more often). I’m not talking about becoming an expert – this can take years, like in programming and this should be left to people spending the whole day doing data analysis (aka bioinformaticians). I’m talking about “scripting” equivalent of programming and this level is currently taught on bioinformatics undergraduate courses at most of the universities. Such training would save the world from papers comparing multiple sequence alignments from Clustal and… BLAST (if some readers do not know – BLAST at best can produce multiple pairwise alignment; it does not align all the sequences together).
These are my two cents. I hope to hear your opinion on that.


Posted by on August 19, 2007 in Comments, Research skills


3 responses to “On the scripting skills

  1. Deepak

    August 19, 2007 at 17:07

    These are very much in line with my own thoughts. It’s a question of priorities. A knowledge of statistical methods, tools, and being able to use those tools properly is a higher priority IMHO.

  2. freesci

    August 19, 2007 at 17:41

    Thanks Deepak,

    You made an interesting point in your post that a formal training would be beneficial for bioinformatics-turned biologists (like myself). I’d love to hear that couple of years ago when I thought that O’Reilly’s perl cookbook is enough to learn programming.

    I didn’t want to point to the specific examples, but I usually find one, two papers per month (only in my small field) that clearly show that there was no-one around able to run sequence search and understand its results. Unfortunately, these papers get published and mistakes are propagating…

  3. Alexei Drummond

    August 20, 2007 at 23:56

    At the University of Auckland we have an undergraduate degree program in Bioinformatics. Our students learn computer science, biology and statistics/maths all to final year… They are the next generation of biologists, if I have my say. But even so — at the end of the day its the science that matters, not the programming — so the better and more productive the software tools are the less fiddling around all of us will have to do, and the more we can focus on the scientific questions!

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