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

Brad Chapman chapmanb at arches.uga.edu
Sat May 27 18:08:53 EDT 2000

Hello all!
    Jeff and I (at least) are planning on going to BOSC
(http://ismb00.sdsc.edu/bosc2000/) and ISMB (http://ismb00.sdsc.edu/) and
presenting a poster. Towards this end, we wrote up an abstract targetted at
the use of Piper (was Loci) in bioinformatics research for these
    We were hoping we might be able to get some feedback from everyone
about the abstract--any comments: good, bad or indifferent would be
*extremely* appreciated. The deadline for the abstracts is in a few days (May
31st--of course we're doing this at the last minute)...
    Anyways, below is the abstract. Thanks in advance for your time.


Piper: A Distributed Platform for Linking Bioinformatics Programs

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 process 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 to link bioinformatics
programs. 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 more robust
equipment. Piper is designed as a modular system using CORBA connectivity
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 an open-source model, allowing contribution and
design feedback from individuals in multiple area of bioinformatics.
Applications of Piper in comparative genomic mapping and phylogenetic
analysis are discussed.

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