Perl bioinformatics
in [Perl]
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From: Xho Jingleheimerschmidt on 26 Oct 2009 21:57 J�rgen Exner wrote: > ccc31807 <cartercc(a)gmail.com> wrote: >> I'm not changing jobs, but I've been contacted about some contract >> opportunities that (reportedly) are difficult but seem easy enough to >> me, manipulating genome files to produce various kinds of reports, >> graphs, etc. I have zero experience in this, so I'm just wondering ... > > The usual problem is the huge volume of data that needs processing. > Therefore typically the standard algorithms don't work any more and you > need a really strong background in data processing. Isn't that exactly Perl's strength? > Perl is not necessariy the best choice here. Perl's powerful features > make it easy to write code that seems to do the job, but it won't scale > from the small test samples to the huge actual data set where you really > need special methods and optimizations. If you think about scalability as you write the code, Perl will not present any special scalability issues versus other languages. If you do not think about scalability, no language choice will protect you. I certainly would not implement a heavy duty multiple alignment algorithm directly in Perl, but I certainly might (and have) implement things like that in Inline::C or just link pre-existing C code in via XS, using Perl to handle the book-keeping, memory management, IPC, pre-processing and parsing, post-processing, packing, unpacking, etc. Based on the description of "produce various kinds of reports", I wouldn't think they expect this to cover Smith-Waterman type of things anyway, but only the kind of reports that are very similar to what you would find in non-bioinformatics type work. Xho
From: Xho Jingleheimerschmidt on 26 Oct 2009 22:13 ccc31807 wrote: > > You seem to have a handle on what's going on. Is using Perl for > bioinformatics totally off the wall, or a reasonable option for data > mangling? Not off the wall at all. http://bio.perl.org/wiki/How_Perl_saved_human_genome Xho
From: Dr.Ruud on 28 Oct 2009 04:42
Keith Bradnam wrote: > I co-teach a Unix & Perl course at UC Davis that is aimed at teaching > graduate students how to learn the basics of Perl in a biological > context. We have specifically tried to assume no prior knowledge of > programming as many people who take our course are new to this. > > We have made our course materials (data & documentation) freely > available to anyone else who is interested: > > http://korflab.ucdavis.edu/Unix_and_Perl/index.html > > There is a corresponding Google Group for discussion of issues arising > from the course. We also make regular updates to the documentation. > Hope this might be of use to you. I Like It. -- Ruud |