The Microarray package provides some basic tools for microarray functionality. It was started by Allen Day and may need some more work before it is a mature product.

BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl.

BioPerl is licensed under the same terms as Perl itself which is the Perl Artistic License (see http://www.perl.com/pub/a/language/misc/Artistic.html or http://www.opensource.org/licenses/artistic-license.html).

Use the module Bio::Tools::Run::StandAloneBlast. It will give you access to many of the search tools in the NCBI BLAST suite including blastall, bl2seq, blastpgp. The basic structure is like this.

bioperl-ext is a package of code for C-extensions (hence the 'ext') to BioPerl. These include interfacing to the staden IO library (the io_lib library) for reading in chromatogram files and Bio::Ext::Align which is a Smith-Waterman implementation.

The GUI package provides a Graphical User Interface for interacting with sequence and feature objects. It is used as part of the Genquire project.

The Pedigree package was started by Jason Stajich and provides basic tools for interacting with pedigree data and rendering pedigree plots.

We have a universal version number for a release. This is set in the module Bio::Root::Version which is universally applied to every module which inherits from Bio::Root::RootI. To check the version, just use the following one liner: perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"' Now when we use version tuples that are not just decimal numbers, Perl converts these silently to Unicode representations.

We suggest the following. Post your idea to the appropriate mailing list. If it is a really new idea consider taking us through your thought process. We'll help you tease out the necessary information such as what methods you'll want and how it can interact with other BioPerl modules. If it is a port of something you've already worked on, give us a summary of the current methods.

BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl.

Yes! The solution lies in Bio::Biblio*, a set of modules that provide access to MEDLINE and OpenBQS-compliant servers using SOAP. See Bio::Biblio, Bio::DB::BiblioI, scripts/biblio.PLS, or examples/biblio/* for details and example code.

We are trying to build a standard starting point for analysis application which will probably look like Bio::Tools::Run::AnalysisFactory which will allow the user to request which type of remote or local server they want to use to run their analyses. This will connect to the Pasteur's PISE server, the EBI's Novella server, as well as be aware of wrappers to run applications locally. Additionally we suggest investigating the BioPipe project, also known as bioperl-pipeline, at http://www.biopipe.

Are you sure io_lib is installed where you think it is, and that the install path is seen by Perl (did you answer the questions during perl Makefile.PL ?)

Ewan Birney has answered this a few times on the Ensembl mail list. In short (in this thread): Ensembl doesn't make heavy use of Bioperl anymore - most of the critical things we re-wrote, mainly due to speed/memory issues. I think the short answer is that it _probably_ works with 1.5, but we don't have a strong desire to move up as certainly there are no problems with the 1.2.3 release we are using.

The Pedigree package was started by Jason Stajich and provides basic tools for interacting with pedigree data and rendering pedigree plots. -->

First, you must contact a GCAT scanning center one week in advance to verify the time is acceptable. You must inform the scan center how many microarrays you intend to send and what type of microarrays you are sending. Keep in mind that each microarray takes approximately 30 minutes to scan, so it is helpful to space out your microarrays rather than sending more than 5 at a time. When you pay $20 per microarray, you have paid for the scanning service.

bioperl-ext is a package of code for C-extensions (hence the 'ext') to BioPerl. These include interfacing to the staden IO library (the io_lib library) for reading in chromatogram files and Bio::Ext::Align which is a Smith-Waterman implementation.

The GUI package provides a Graphical User Interface for interacting with sequence and feature objects. It is used as part of the Genquire project.

Well, the perl.org guys granted us use of bio.perl.org. We prefer to be called Bioperl or BioPerl (unlike our Biopython friends). We're part of the Open Bioinformatics Foundation (OBF) and so as part of the Bio{*} toolkits we prefer the Bioperl spelling. But we're not really all that picky so no worries.

We have a universal version number for a release. This is set in the module Bio::Root::Version which is universally applied to every module which inherits from Bio::Root::RootI. To check the version, just use the following one liner: perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"' Now when we use version tuples that are not just decimal numbers, Perl converts these silently to Unicode representations.

BioPerl is licensed under the same terms as Perl itself which is the Perl Artistic License (see http://www.perl.com/pub/alanguage/misc/Artistic.html or http://www.opensource.org/licenses/artistic-license.html).

Use the module Bio::Tools::Run::StandAloneBlast. It will give you access to many of the search tools in the NCBI BLAST suite including blastall, bl2seq, blastpgp. The basic structure is like this.

The Technical Director of the KUGR Facility, Dr. Gavin Pickett (ggpickett@salud.unm.edu) is an expert at analyzing Affymetrix GeneChip data using GeneSpring, a high-end microarray data analysis software package from Silicon Genetics. The facility Director, Dr. Scott Ness, has analyzed results from hundreds of microarray experiments, has written review articles and book chapters about microarray data analysis, and is available for consultation.