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Frequently Asked Question

Nope, not a typo - there are a number of Questions that have been asked Frequently...but they're really all the same question.

  • Why not just use BioPerl/Perl-CGI(or BioPython/Zope, or BioJava/JSP)?
  • You don't really expect me to replace my BioPerl system with this, do you?
  • Is making web pages really that important to Bioinformatics? That's all PHP is for, right?
  • Do we really need BioPerl re-implemented in ANOTHER language? After all, we've already got BioJava, BioPython, BioRuby, and of course BioPerl itself!
  • PHP is just a stupid toy language! You suck! What's next, BioBASIC?

The important points in response are:

  • Each language has it's strengths and weaknesses. PHP is suited particularly well for certain types of tasks, which is where this project intends to focus.
  • No. That would be silly. This isn't isn't some sort of zero-sum competition, and the point here isn't to "defeat" the other BioXXXXX projects, but to offer another set of Bioinformatics tools for the metaphorical toolbox.
  • PHP is not "for web pages" any more than Perl is "for generating reports". Development of PHP has grown well beyond only web-page functions (though PHP is still best "tuned" for internet-server/web-page related tasks, much as Perl is still well-known for its text-parsing capabilities).
  • This project is NOT intended to "mirror" the capabilities of BioPerl/BioPython/BioJava. Instead, BioPHP is focussed on the subset of bioinformatics tasks for which PHP is best suited. This will result in a certain amount of overlap with other projects, but only where the other projects' languages have similar strengths. (There IS a possibility that PHP's Java support may be used to incorporate access to BioJava's functionality directly at some point, however.)
  • No. No. And No. (Sheesh, one-true-language zealots...)