Bioperl: BLAST.pm

[Steve A. Chervitz]

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 
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. 


> 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?

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.).

Steve Chervitz


> On Mon, 24 Nov 1997, Chris Dagdigian wrote:
> 
> > 
> > Everybody I've run across seems to have their own internal Blast/Fasta scripts & modules for 
> > starting, parsing and HTMLifying searches. The problem is that very few of them have been put 
> > into the public domain. The public stuff out there is mostly scattered across individual web 
> > pages and is pretty hard to locate. 
> > 
> > We need to get a Blast.pm and a Fasta.pm into CPAN for the individual scientists who don't have 
> > the time or programming staff to reinvent the wheel.
> > 
> > My group (at GI) has a nice object oriented Blast.pm module that is pretty flexible. I'll put it 
> > up somewhere if people are willing to comment on it. If it seems useful I am confident that I 
> > can get 'official' permission from my company to put it in the public domain.
> > 
> > Even gathering a bunch of similar modules from different people/sources and making them 
> > available via CPAN would be nice. People could then pick and choose what makes sense for them.
> > 
> > Regards,
> > Chris Dagdigian
> > Genetics Institute
> > 
> > 
> > > I am wondering if anyone has started working on a BLAST module.  I am
> > > interested in converting alot of the work I have done into modules and would
> > > like some feedback before I put time into such a project.
> > > 
> > > --Joe Ryan
> > ===== 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
> > 
> 
> 
> ===== 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
> 



===== 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