[Bioperl-l] RemoteBlast [was: (no subject)]

Wed Feb 8 05:16:44 UTC 2006

Paul,

I think that most core Bioperl folks have long since moved away from
RemoteBlast and are using the functionality in StandAloneBlast to run their
own local servers. More importantly, they are, in general, researchers who
are coming to Bioinformatics from the life sciences side, and are
particularly tired of dealing with the technical issues that RemoteBlast
consistently generates due to changes in the text-formatted BLAST reports. 

They aren't code-for-code-sake geeks like me. ;}

When RemoteBlast was written, XML was barely on the technology radar, and
XML-formatted BLAST reports weren't even available. It seems that everyone
recognizes that the XML reports now generated by NCBI's blast server is the
wave of the future, but I think there is still some concern that not every
flavor of BLAST produces XML yet. Even so, the XML parser is considered to
be very strong, and only helps hasten the end of text-formatted support,
since parsing text-formatted reports is the primary source of pain. 

In discussing the shift from old to new, I think the idea of relying on
NCBI's application (and NCBI's issue system and NCBI's developers) entered
the realm of possibility, so as the guy who just showed up to adopt
RemoteBlast, I am trying to air all options and beg for all requirements. 

Personally, I am okay with the idea of maintaining text-formatted report
parsing, but like I said, I'm pound foolish about code sometimes. Additional
foolishness arises from the fact that the first money I earned in
Bioinformatics was on a contract gig where I relied on RemoteBlast (and the
related text parsers).

For my money, I just needed anyone, anywhere, to say they desired a pure
perl implementation to meet my personal threshold. So far, you're the
second. ;}

I do, however, see the advantage in shifting to XML-formatted reporting and
parsing *only* as soon as every BLAST flavor supports it, if not before.
(Anyone - is this still an issue. Please educate me.)

At the moment, I'm leaning towards adding an option to RemoteBlast. The
default (no option) would use a "pure perl" implementation, and the
enhancement (with explicit option) would merely wrap the NCBI executable.
However, there are other issues (queuing, batches) that I don't fully
understand in context, so I haven't zeroed in on a complete recommendation
yet. Additionally, the end of text-formatted reports, while drawing near, is
not yet agreed, although it is pretty clear that the only way text support
will be continued is if I insist on it and then deliver the support myself.
:}

In any case, I am very interested in a pure perl implementation for exactly
the two reasons stated thus far: it's one less thing for a newbie to worry
about, and it will run on every platform that runs perl. 

Thanks much for the input!

Roger Hall
Technical Director
MidSouth Bioinformatics Center
University of Arkansas at Little Rock
(501) 569-8074

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Paul Boutros
Sent: Tuesday, February 07, 2006 7:39 PM
To: BioPerl Mailing List
Cc: Roger Hall
Subject: [Bioperl-l] (no subject)

Hi Roger,

I would definitely prefer a fully Perl-based implementation.  For starters,
I have not 
been successful in compiling the Toolkit that contains netblast for some
platforms (e.g. 
AIX 5.2 w/gcc 4.0).

I haven't been following the discussion: is there some compelling reason to
prefer a 
netblast-based system that's come up recently?  I'm guessing that adding a
new non-perl 
dependency would only be done if there was considerable justification for
this type of 
change, but I'm not clear from your message what that justification is.

Paul

------------------------------ 

Message: 12 
Date: Mon, 6 Feb 2006 20:46:44 -0600 
From: "Roger Hall" <rahall2 at ualr.edu> 
Subject: [Bioperl-l] RemoteBlast users - potentially major changes - 
        please        reply 
To: <bioperl-l at lists.open-bio.org> 
Message-ID: <002001c62b90$bb9dbe00$4301a8c0 at LIBERAL> 
Content-Type: text/plain;        charset="us-ascii" 

To everyone who uses RemoteBlast.pm: 

Would anyone object to RemoteBlast being rewritten in a way that requires 
NCBI's blastcl3 executable? 

Binary downloads of blastcl3 (column "netblast") are available for numerous 
platforms at: http://ncbi.nih.gov/BLAST/download.shtml 

Does anyone require or desire a "pure perl" implementation? If so, please 
explain the advantage you see with such an implementation. 

Thanks! 

Roger Hall 

Technical Director 

MidSouth Bioinformatics Center 

University of Arkansas at Little Rock 

(501) 569-8074 

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