[Biophp-dev] Seeking comments on CVS, XML, and other TLA's

Dong Gregorio biophp-dev@bioinformatics.org
Wed, 09 Apr 2003 14:03:16 +0800

Hi again.

>As I once saw in a .sig on Slashdot:
>"The can's already open, the worms are EVERYWHERE..." :-)

Well, maybe I'll just wait till the worms grow into snakes. =)

>I just keep having trouble really CONVINCING myself that
>the apparently complex framework of tag-handling functions
>that you seem to have to build to parse XML with an "official" 
>parser is really any better than easier-to-follow regular expressions
>(DESPITE the fact that on a purely "rational" level I can certainly
>see that at a certain point the complexity of a set of regular >expressions for parsing eventually becomes worse than the XML >parser, but still...)

Same feelings here.  Don't worry, the technology will mature.
I remember the time I used LYNX (text-only web browser), and
told myself, nah, there's got to be a better way to surf the
web.  A year and a half later, Marc Andreesen came out with

>I have to confess my weekend has been spent "slacking off" (well, if 
>you can count manual labor hauling boxes out of storage and such as
>"slacking off") so I haven't yet gotten to looking at the example >code that Greg was kind enough to forward - I'll try to get to that >tomorrow.

Uhuh, and what does that code supposed to do?  Let's take a look
at it.

>> >- Differentiate BioPHP as fundamentally supporting XML

>> >- Why bother with flatfiles ? BioPerl/Python/Java probably do
>> >  these already
>BioPerl/Python/Java/Ruby/Lisp also already deal with DNA sequences...
>should we ignore them as well, then? :-)
>Besides, I'd consider formats such as Phylip, Clustal, ASN.1, etc. to
>be "flat files", and parsers for them will be handy.

Well, that's a whole debate in itself.  To rephrase it:  

Do we work on features that would differentiate BioPHP from BioXXX (and work backwards later on) or do we through the basics first 
(data file parsing, sequence analysis, etc.)?

Taking the first approach would mean developing interfaces to other
BioXXX (because we can't even do the simplest tasks ourselves using
BioPHP).  Taking the second approach means it would take some time
before we earn "bragging rights" vis-a-vis BioXXX.  Bragging rights being, "My dog can sing while standing on its head, yours cant!" 
* Laugh out loud * 



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