[Biophp-dev] Updates

Serge Gregorio biophp-dev@bioinformatics.org
Wed, 04 Jun 2003 03:45:52 +0800

Hello all!

>>Nico: I'll try them out.  It might be a good idea to 
>> include some 'test' scripts`, as a demonstration <SNIP>

Yes, and it can attract the interest of "passers-by" 
to the project who might be too timid to actually look at the code.

>> Nico: and as a starting point for people to write >> their own scripts.

Yes, and the effort gives a lot of lessons in how
to continually improve the underlying codebase. For
instance, by writing the Amateur Gene Finder script,
I found out it was very tedious using GenePHP 1.0 
to work with individual codons.  And so, I promised
myself to make up for this inadequacy next release
by writing a bunch of methods like get_codon(), next_codon(), prev_codon(), etc.

>Sean: where these modules fit in the genephp scheme >of things so I can move them.

I think they can fit nicely into the I/O section that you and Nico are working on (Parsing being half of it).

>> Nico: seqIOWrite section, that would be great.  I >> am very busy doing real biology right now, and I 

Well, maybe you'd like to share a little about your "real biology" work?  That would be a welcome break from all the coding stuff we've been discussing 
the past few weeks.

Are you working on re-creating dinosaurs a la Jurassic Park? =)  Speaking of which, there's this guy I saw on Discovery channel who's actually doing that on preserved (fossilized?) microorganisms?  Cool!

>Sean: Serge - will you be doing any work on the seq >object over the next 7-10 days or so?  If not, I can >also e.g. add interface methods and perhaps one or ?>two other functions while I'm on the road and upload
>the changes when I get back.

I'm deep into the parsers right now.  You're welcome to add interface and other methods.  We (a.k.a. the "Design Committee") can all review them later on.   


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