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

J.W. Bizzaro bizzaro at geoserve.net
Mon May 29 10:23:59 EDT 2000

Brad Chapman wrote:
> 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
> better.

Especially being a poster, I think one address will do.  You can put an
asterisk next to my name and below write...

* Corresponding author:
Bioinformatics.org: The Open Lab
c/o Department of Chemistry
University of Massachusetts Lowell
Lowell, MA 01854
jeff at bioinformatics.org

> Now for your reading pleasure...

I don't have any major changes, just some spelling corrections, etc.

> Distributing Bioinformatics Application with Piper


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

Dominic Letourneau and 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

analysis or analyses [?]

> 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

...existing programs...  [Piper is not designed FOR bioinformatics]


Piper provides a wrapper around existing 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 remote computers so that... [no comma]

> on faster, dedicated systems.

[Since we use "system" to describe Piper, should we use something else here?]

...on faster, even dedicated hardware.

> Piper is designed as a modular system using
> CORBA connectivity protocols as the backbone to link the modules. This
> design allows multiple user interfaces

...allows multiple and different kinds of 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 

...well suited to automate high-throughput...


...well suited for automating high-throughput...


...well suited 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.

                      |           J.W. Bizzaro           |
                      |                                  |
                      | http://bioinformatics.org/~jeff/ |
                      |                                  |
                      |        BIOINFORMATICS.ORG        |
                      |           The Open Lab           |
                      |                                  |
                      |    http://bioinformatics.org/    |

More information about the Pipet-Devel mailing list