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

Dong Gregorio biophp-dev@bioinformatics.org
Sun, 06 Apr 2003 01:12:32 +0800


On Fri, 4 Apr 2003 23:53:03   

>mail-lists+biophpdev wrote:
>It's probably about time I figure out how to get CVS going - that >means some thought is called for at this point on how to structure >things, at least initially...
>Every developer with their own subdirectory?  Broken up by purpose?  >Some combination?
>Any thoughts?
>And about XML:

Until we adopt a common framework, I think it's best to have
separate folders for each developer. It wouldn't be good for
readers of our code to see two version of, say, the Sequence
object in the same package.  At least, if you see that some-
one's already written a parser for say, a PDB file, and it's
okay, you'd think twice, thrice, n times before writing your

That's where the efficiency of working as a group comes in. 
We don't waste time writing code that's already been written 
by others.  And we could proceed faster by adopting a "divide 
and conquer" strategy to future work.

However, even without a grand framework, we always discuss
and agree on a per function/method/module basis.  In which 
case, the output can be stored in a SHARED folder.

>I am at this point working with the NCBI BLAST query module and the >EUtils modules.  I have this feeling that I "ought" to be using the >XML-parser capabilities in PHP, but as I keep looking at it I keep 

Do you have some links/materials on this?  I can't comment 
until I've read up on it.  Also, would you happen to have
a list of bioinformatics software/tools, and which among 
them can be accessed online, in a purely interactive manner,
or via some sort of remote procedure call, SOAP/web service,



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