[Pipet Devel] Take 2--Abstract on Piper/Loci for ISMB and BOSC

Brad Chapman chapmanb at arches.uga.edu
Mon May 29 09:47:08 EDT 2000

Hello again;
 	I got some very helpful comments on the abstract for Loci/Piper and
made a few changes to it, so I thought I would resend it with the new info.
Once again, if anyone has any comments, no matter how small, they would be
much appreciated.
	Also, I need to get address info for everyone mentioned in the
authors so I can get this together, so if you are listed please send me an
e-mail off the list and drop me the info. Or, if Jeff has an idea how we
can just all be referenced as coming from "The Open Lab" that would be even

Now for your reading pleasure...

Distributing Bioinformatics Application with Piper

J.W. Bizzaro, Gary Van Domselaar, Jarl van Katwijk, Jean-Marc Valin, Brad
Chapman, Dominic Letourneau, Deanne Taylor

	A typical problem in bioinformatics research is linking together
multiple programs to analyze a set of information. A common example of this
is in building phylogenetic trees from DNA sequences. The sequences are
intially aligned using a sequence alignment program, are then analyzed in a
phylogeny program to produce trees, and finally the trees are visualized in
a viewer. This process can be further complicated by the fact that the
programs may have incompatible inputs and outputs, as well as extensive
memory and processing requirements. To address these problems the authors
have developed Piper, a distributed platform that can be used to link
bioinformatics programs. Piper is ideally suited to bionformatics analysis
in that it can combine highly specific, modular, data repositories and data
analysis functions together to provide sophisticated and efficient data
processing networks. Piper is designed to provide a wrapper around
exisiting bioinformatics programs so that they can be connected and
executed in an intuitive manner. In addition, individual programs can be
located on remote computers, so that expensive calculations can be executed
on faster, dedicated systems. Piper is designed as a modular system using
CORBA connectivity protocols as the backbone to link the modules. This
design allows multiple user interfaces to control the core processing
engine. In addition, Piper is being developed under the Open Source model,
allowing contribution and design feedback from individuals in multiple area
of bioinformatics. Piper is especially well suited to for automated
high-throughput data analysis like protein fold identification, sequence
condiditioning such as repeat/vector masking and data format conversion,
and customization of batch scripting processes such as building
phylogenetic trees from DNA sequences.

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