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in reply to Re: Stereotypes about perl
in thread Stereotypes about perl

I was at a bioinformatics presentation yesterday where the term "using Java instead of some crap Perl" came up.

I'm actually very surprised at this.. working in a Bioinformatics area.. we've used Perl quite a bit. Granted, we also use other languages such as ASP, ColdFusion, and Java. I still think you use whatever is best for the job. We don't use Perl for our websites, but it's quite useful in other areas. I always thought Perl was a big item for Bioinformatics... maybe the times are changing..

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Re: Re: Re: Stereotypes about perl
by flyingmoose (Priest) on Feb 24, 2004 at 18:13 UTC
    I didn't think the speaker was very sharp, but I didn't challenge him on the Perl since the audience was (ugh) lacking in Perl experience and laughed at his Perl jokes. Well, he was missing other questions too (he couldn't answer my question about how fiting a model to data in a biased way might violate the scientific method of hypothesis testing through data collection). This java talk was mostly in regard to the "caBIG" (cancer bioinformatics grid -- essentially web services and not technically a distributed computing system) and he was discussing how they were replacing a bunch of random things with Java. The part that didn't drive is that good grids are language agnostic. He also stated there bascially was no room for more Comp. Sci folks in the field now, which I also didn't believe. In fact, I left a little early to get some food -- he was just infuriating me with his language bias :)

    This would be another meditation, I guess, but is bioinformatics actually open to new programmers (compared with "pure software"), particularly in Perl? And how much emphasis is actually placed on biology experience? I was expecting tremendous love of Perl in that room, and what I saw instead was a tremendous love of Java for the wrong reasons.

    Ex: Java w/ matlab. Now there is a cast-heavy bloated syntax I don't want to have to deal with when doing math!

    I don't think times are changing, it's just that some folks have this bad taste in their mouths about Perl, and well...some people are just stupid!

[reply]
      About Bioinformatics being open to new programmers - that might be better off as a thread on it's own. Just to get opinions from others out there. My own experience is very limited to what's going on here.. we have a mixture of CS people and Scientists (course, some of the scientists have CS backgrounds as well.. even a bigger plus!).

      I think Biology does help.. I can't really generalize on this though.. I'm not sure how other Bioinfo Depts. work.. we have a rather large one and it's split to many mini Bioinfo departments. One is Bioinfo Software Dev, which would work for CS majors - you sort of gather Biology information along the way. But, this as I said before is a mixture of Programmers and Scientists/Programmers. It does help to have the Biology background though...
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