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 Applications > 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] or 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 areas > of bioinformatics. Piper is especially well suited to for automated > high-throughput ...well suited to automate high-throughput... or ...well suited for automating high-throughput... or ...well suited for automated, high-throughput... > data analysis like protein fold identification, sequence > condiditioning conditioning > such as repeat/vector masking and data format conversion, > and customization of batch scripting processes such as building > phylogenetic trees from DNA sequences. Cheers. Jeff -- +----------------------------------+ | J.W. Bizzaro | | | | http://bioinformatics.org/~jeff/ | | | | BIOINFORMATICS.ORG | | The Open Lab | | | | http://bioinformatics.org/ | +----------------------------------+