Open Source Programming with Bio* Libraries
The Open Bioinformatics Foundation or O|B|F is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics. The mission of the O|B|F is to support the development of open source toolkits for bioinformatics, organize and run the Bioinformatics Open Source Conference (BOSC), and assist in the development and promotion of open source software for the life sciences. The foundation hosts code repositories for a number of open source projects, including four major programming languages that have bio* libraries (which can save a lot of headaches, not to mention coding time).
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BioPerl: The Bioperl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research. The Bioperl server provides an online resource for modules, scripts, and web links. Pro: long history in bioinformatics, can do most anything. Con: awful syntax. |
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BioPython: The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology. Pro: clean style, easy to read. Con: execution can be slow. |
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BioRuby: BioRuby project aims to implement an integrated environment for Bioinformatics with Ruby language. Pro: clean style, easy to read. Con: execution can be slow. |
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BioJava: The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data. Pro: great libraries, fast. Con: verbose and tedious to code. |
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I may have some MySQL and Oracle databases to mine for clinical parameter associations. I asked my social network on FriendFeed tonight which programming language would be best: Python, Ruby or Perl? The comments I received were consistent with what I’ve been reading: Python or Ruby.
It looks like I’ll be spending more time in the FriendFeed room Python for Bioinformatics.
What’s your favorite programming language and why?
Tagged as bioinformatics, Bioinformatics Open Source Conference, biojava, bioperl, biopython, bioruby, BOSC 2010, language, Open Bioinformatics Foundation, programming
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wjjessen (Walter Jessen)
Open Source Programming with Bio* Libraries [link to post]
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To answer your question about favourite programming languages: mine is Perl, because at this point I can write it in my sleep and CPAN has libraries for everything I want to do. I feel increasingly like a dinosaur - my impression is that postgrads and junior postdocs are learning Python/Ruby and a lot of experenced Perl programmers are switching. Perl seems to suit my mindset somehow - or possibly my brain has just been warped by it.
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I'd vote for perl too. Like Tom said CPAN has libraries for everything, and bioperl is perfect for most of the problems. BTW I'm also thinking about learning some python/ruby too.
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Java: many libraries, OO, fast learning curve/coding with eclipse, more job offers.
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Walter seems to be going with Python. I doubt there's much to choose berween Perl/Ruby/Python/Java in terms of libraries for what he's trying to do.
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I use Perl a lot for parsing files, knocking up webpages, talking to databases etc. I'm sure Ruby and Python are lovely, but I don't see how they can compete with CPAN. Having said that, most of my bioinformaticsy stuff involves big datasets (microarrays, next-gen sequencing data etc) so Bioconductor gets my vote for most useful Bio* project.
To answer your question about favourite programming languages: mine is Perl, because at this point I can write it in my sleep and CPAN has libraries for everything I want to do. I feel increasingly like a dinosaur – my impression is that postgrads and junior postdocs are learning Python/Ruby and a lot of experenced Perl programmers are switching. Perl seems to suit my mindset somehow – or possibly my brain has just been warped by it.
This comment was originally posted on FriendFeed
Perl, because at this point I can write it in my sleep and CPAN has libraries for everything I want to do. I feel increasingly like a dinosaur – my impression is that postgrads and junior postdocs are learning Python/Ruby and a lot of experenced Perl programmers are switching. Perl seems to suit my mindset somehow – or possibly my brain has just been warped by it.
This comment was originally posted on FriendFeed
I’d vote for perl too. Like Tom said CPAN has libraries for everything, and bioperl is perfect for most of the problems. BTW I’m also thinking about learning some python/ruby too.
This comment was originally posted on FriendFeed
Java: many libraries, OO, fast learning curve/coding with eclipse, more job offers.
This comment was originally posted on FriendFeed
Walter seems to be going with Python. I doubt there’s much to choose berween Perl/Ruby/Python/Java in terms of libraries for what he’s trying to do.
This comment was originally posted on FriendFeed
I use Perl a lot for parsing files, knocking up webpages, talking to databases etc. I’m sure Ruby and Python are lovely, but I don’t see how they can compete with CPAN. Having said that, most of my bioinformaticsy stuff involves big datasets (microarrays, next-gen sequencing data etc) so Bioconductor gets my vote for most useful Bio* project.
This comment was originally posted on FriendFeed
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