pyrimidine

• Website: bioperl.org
• About: I blog about Perl (and biology).

Recent Actions

• Commented on what to know about aligning
  Saying this as a BioPerl core developer, I highly suggest looking at C/C++ based options; pure Perl-based solutions are technically possible using purely Perl but not recommended due to the overhead (memory used, length of time, etc). Particularly if you...
• Commented on Perl in Pop Culture
  Another one for you, the band Cracker mentions Perl in one of their latest videos (it's around 0:38, and note the book strangely enough is mod_perl)....
• Commented on [UPDATED] Beginning Perl For Bioinformatics
  Speaking as the maintainer of BioPerl, I partially agree (and gladly welcome any help with the code!). If you can specify exactly what you find that is terrible then maybe we can focus on tackling those areas first....
• Commented on Rethinking smart matching
  I do like the idea of having this in a separate module like Smart::Match (as mentioned about), possibly with explicit method calls as alternatives. Re: deprecation (or, going the way of pseudohash 'dodo'): how would this affect the given/when switch,...
• Commented on Workflow, part 3
  Very good set of posts, was hoping to see the next in your series!...
• Posted BioPerl in the Google Summer of Code (2011 Edition) to pyrimidine

  BioPerl is again part of the Google Summer of Code! The Open Bioinformatics Foundation, which also includes BioPython, BioRuby, and others, has been accepted into the Google Summer of Code for 2011. We are actively looking for students interested in OBF-related bioinformatics projects; new ideas…

• Commented on Perl memory management...
  I'm a BioPerl core developer, so I don't necessarily think it's a rathole. ;) However, I agree re: efficiency, it's not great, and there are lots of potential improvements (reducing the inheritance hierarchy, breaking up the monolithic install, etc etc)....
• Commented on Perl memory management...
  Re: 'RAM is cheap', yes I agree, it's a copout under many circumstances. BLAST in particular is an example of something that is ridiculously easy to run in parallel, particularly when running multiple queries or checking parameters; simply batch out...
• Commented on Perl memory management...
  I don't think anyone should be surprised if they run out of memory when working with next-generation sequencing data (or any other large biological datasets) on the equivalent of a laptop's memory, even with 4-8 GB of memory. Don't try...
• Commented on Introduction to wirting readable and maintainable Perl
  Not to be the spelling police, but I would like to ironically point out... wirting => writing...
• Commented on Database Wiki's
  There are many defined schemas available for the life sciences. I’m curious (being a BioPerl developer) as to your take with GMOD and Chado, which is meant to be an extensible database schema. Or, for a more sequence-centric one, BioSQL....
• Commented on No More Excuses
  In the next release iteration of BioPerl we will be modularizing the monolithic core distribution (which is anything but 'core' at 800+ modules), something that's been waaaay overdue. So, having a more automated way of releasing code to CPAN, either...
• Commented on Perl 6, Surely but Slowly
  That would be BioPerl 6. Bad link, my fault....
• Commented on Perl 6, Surely but Slowly
  I have started up the beginnings of a BioPerl port to Perl 6 and have been running into the same problems, actually. That's not stopping me from dabbling in Perl 6, but it is making me hesitate from jumping in...
• Commented on version.pm: just say no
  Take that back, looks like it isn't actually required for core code (and isn't listed in Build.PL as required). It is used with an optional tool (the Deobfuscator) that comes with the distribution....
• Commented on version.pm: just say no
  Ick, just noticed BioPerl on that list. That might be worth looking into....
• Posted BioPerl has migrated to GitHub! to pyrimidine

  For the full details, see here!.

  (and yes, I'm too lazy and tired to type that again...)

• Posted Spam and the Iron Man to pyrimidine

  Perl Iron Man has been getting hammered by spam the last couple of days. Any sign of of a let-up?

• Posted BioPerl and the Google Summer of Code to pyrimidine

  In addition to The Perl Foundation being accepted into GSoC 2010, BioPerl is now also part of the Google Summer of Code! The Open Bioinformatics Foundation, which also includes…

• Commented on What are BioPerl's weaknesses?
  It would be great to turn these recipes into a cookbook in the BioPerl distribution. I'm not doing much bio stuff at the moment, but I (and I think other BioPerl outsiders) would be happy to write up our attempts...
• Commented on What are BioPerl's weaknesses?
  Over-engineered design and poor documentation were the main points. I think removing Bio::Structure from BioPerl would be the easiest solution. The loss of intended functionality would suck, but it's too poorly implemented to be useful now. Overall I tend to...
• Commented on What are BioPerl's weaknesses?
  That was about Bio::Structure::IO. I did manage to read it before it went bye-bye. I do remember agreeing with pretty much everything you mention, just can't recall specifics (slowness and design were two maybe?). The problem (though it's not an...
• Posted What are BioPerl's weaknesses? to pyrimidine

  (Note: this is a repost due to some of the beta-ness of the site).

  BioPerl is a commonly-used toolkit for bioinformatics, but it does have it's share of problems. As educated_foo has p…

• Commented on Migration Issues
  It's an odd issue. My last post still shows up on my account but isn't in the blog roll. Maybe they're not dead (just pining for the fjords)?...
• Commented on Hello (cruel) world!
  All depends on what your particular need is. If I just want the number of sequences in a large file or want to simply split up sequences for repeated analyses, I could just write simple one-off scripts. However, if I...
• Posted Hello (cruel) world! to pyrimidine

  I'll be posting a bit or two on Perl and Biology for the masses, including my attempts at refactoring bits of BioPerl.

Comment Threads

• Gábor Szabó - גאבור סבו commented on Rethinking smart matching

  Oh, right there could be a ref in the given() variable. Anyway, I still don't see uses of ~~ outside of given/when but as I wrote I hardly ever used 5.10 or newer due to client limitations.

• Holy Zarquon's Singing Fish commented on [UPDATED] Beginning Perl For Bioinformatics

  Scientific programming by its nature is a messy enterprise compared to the more production oriented commercial projects that most programmers are used to. On the other hand I saw a text mining with perl book that while useful on the scientific aspects of NLP programming encouraged some pretty awful perl practices. I think it's the job of us perl literate scientific programmers to provide exemplars of good practice in our fields wherever possible.

• ms commented on what to know about aligning

  Thank you all for your comments.

• ms commented on what to know about aligning

  Thank you all for your comments.

• https://www.google.com/accounts/o8/id?id=AItOawlcDTR-3XTXKJMjOd9EuTjv2gGqrZeSUEE commented on Rethinking smart matching

  You say "time to go the way of pseduohashes." Pseudohashes were removed because they slowed down Perl not because they made the spec too hard for a few simple minds to codify.