Bioperl: BLAST.pm

[Georg Fuellen]

Hi,

> SteveB wrote:
> 
> > I certainly agree with this as well.  I think that just putting all of
> > these modules in a public place (even if they aren't integrated or related
> > to each other or Bioperl) would have immense value.
> 
> As for a "public place", how about creating a Blast Module Development 
> page at the Bioperl site? This site could link to sites maintained by 

OK with me!

> the different developers and would therefore always be up-to-date. (The 
> developer's sites would link back to the Bioperl site as well). This 
> should be considered a temporary situation until a standard module 
> emerges.
>
> > The only difficulty is a naming scheme.  Perhaps Blast_Ryan.pm, and
> > Blast_Dagdigian.pm, etc.?   
>
> Seems reasonable. To further indicate their beta status we could prefix
> them with "Pre" as done for PreSeq.pm. The surname suffix might be 
> sufficient, though. 

I wonder whether the developers would go through a name change at all !
(From my experience renaming Bio::Aln to Bio::UnivAln, it's not just
one editor command; all the dependent code, test scripts, etc, need updating.)
Could we code this into the version number instead ? (Not sure... there may 
be some other trick, too. [Use 5.004's SUPER/can() ??]) 

> > Once the existing code is "out there," we could try looking at it and
> > think about combining the best aspects to make an "official bioperl"
> > module.
> 
> I'm wondering how such a collective development would proceed. For the 
> other modules, there is typically a designated "chief pumpkin holder" who 
> acts as a single point for handling bug reports, upgrades, testing, 
> ensuring the module is in a consistent state, creating a Makefile, etc.  
> Perhaps this would be the person who first creates a combined Blast 
> module?

Any volunteer ???!!!:-):-):-)

> This seems like the perfect topic to be discussed at a Bioperl workshop. 
> Perhaps we should think more seriously about holding such an event and 
> the specifics (where, when, why, who-attends, who-sponsors, etc.).

We need to get serious-- 
I'll most likely be at ISMB98, and we could try to have an event there ?!
http://www-lbit.iro.umontreal.ca/ISMB98/accueil_en.html

> Steve Chervitz

best wishes,
Georg Fuellen,
Univ. Bielefeld, Research Group in Practical Comp. Science
http://www.techfak.uni-bielefeld.de/bcd/welcome.html


===== Bioperl Project General Mailing List Message Footer =======
Project URL: http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl.html