From dlondon at ebi.ac.uk Thu Jan 20 12:58:59 2005 From: dlondon at ebi.ac.uk (Darin London) Date: Thu Jan 20 13:11:52 2005 Subject: [Bioperl-announce-l] BOSC 2005 Message-ID: <20050120175859.GA7254@parrot.ebi.ac.uk> {Please pass the word!} MEETING ANNOUNCEMENT & CALL FOR SPEAKERS The 6th annual Bioinformatics Open Source Conference (BOSC'2005) is organized by the not-for-profit Open Bioinformatics Foundation. The meeting will take place June 23-24, 2005 in Detroit, Michigan, USA, and is one of several Special Interest Group (SIG) meetings occurring in conjunction with the 13th International Conference on Intelligent Systems for Molecular Biology. see http://www.iscb.org/ismb2005 for more information. Because of the power of many Open Source bioinformatics packages in use by the Research Community today, it is not too presumptuous to say that the work of the Open Source Bioinformatics Community represents the cutting edge of Bioinformatics in general. This has been repeatedly demonstrated by the quality of presentations at previous BOSC conferences. This year, at BOSC 2006, we want to continue this tradition of excellence, while presenting this message to a wider part of the Research Community. Please, pass this message on to anyone you know that is interested in Bioinformatics software. BOSC PROGRAM & CONTACT INFO * Web: http://www.open-bio.org/bosc2005/ * Email: bosc@open-bio.org FEES TO BE ANNOUNCED. Watch the bosc website for more information. SPEAKERS & ABSTRACTS WANTED The program committee is currently seeking abstracts for talks at BOSC 2005. BOSC is a great opportunity for you to tell the community about your use, development, or philosophy of open source software development in bioinformatics. The committee will select several submitted abstracts for 25-minute talks and others for shorter "lightning" talks. Accepted abstracts will be published on the BOSC web site. If you are interested in speaking at BOSC 2005, please send us before April 26, 2005: * an abstract (no more than a few paragraphs) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. Abstracts will be accepted for submission until April 26, 2005. Abstracts chosen for presentation will be announced May 12, 2005 (before the ISMB Early Registration Deadline). LIGHTNING-TALK SPEAKERS WANTED! The program committee is currently seeking speakers for the lightning talks at BOSC 2005. Lightning talks are quick - only five minutes long - and a great opportunity for you to give people a quick summary of your open source project, code, idea, or vision of the future. If you are interested in giving a lightning talk at BOSC 2005, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. We will accept entries on-line until BOSC starts, but space for demos and lightning talks is limited.
SOFTWARE DEMONSTRATIONS WANTED! If you are involved in the development of Open Source Bioinformatics Software, you are invited to provide a short demonstration to attendees of BOSC 2005. If you are interested in giving a software demonstration at BOSC 2005, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * Internet connectivity requirements (e.g. website Application served on the world wide web, or web based client application). We will accept entries on-line until the BOSC starts, but space for demos and lightning talks is limited. ** Because the mission of the OBF is to promote Open Source software, we will favor submissions for projects that apply a recognized Open Source License, or adhere to the general Open Source Philosophy. See the following websites for further details: href="http://www.opensource.org/licenses/ href="http://www.opensource.org/docs/definition.php SESSION CHAIRS WANTED If you would like to be involved BOSC 2005, we invite you to chair a session. This will not require much of your time. You will be given a schedule of presenters during your session. You simply introduce each speaker, and manage the time of their presentation (25 minutes for full presentations, 5-10 minutes for lightning talks/demos, depending on the number of entries). If you are interested in chairing a session, please send us your name and affiliation (if applicable). -- cheers, Darin London dlondon@ebi.ac.uk European Bioinformatics Institute, +44 (0)1223 49 2566 Wellcome Trust Genome Campus, Hinxton +44 (0)1223 49 4468 (fax) Cambridgeshire CB10 1SD, UK -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-announce-l/attachments/20050120/9bb1da79/attachment.bin From jason.stajich at duke.edu Mon Jan 24 21:36:39 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Mon Jan 24 21:33:33 2005 Subject: [Bioperl-announce-l] bioperl-1.5.0 released Message-ID: Bioperl 1.5.0 Developer's release is available for download. =============================================== http://bioperl.org/DIST/bioperl-1.5.0.tar.bz2 425ac55ecbb4339b7b532ba6d429bb40 http://bioperl.org/DIST/bioperl-1.5.0.tar.gz 172472f0675de9a583432e21c9b1b5fc http://bioperl.org/DIST/bioperl-1.5.0.zip 3febcd2445a7393c65981a6f9f13a9ed We'll update the website to reflect this new release. The odd-numbered releases are called developer releases and are not deposited on CPAN. Please note that the API in 1.5.0 may change before the 1.6.0 release. which will be consider a stable API. We may do another developer release before 1.6.0 goes out. Lots of people have contributed to this release, I apologize for not naming them all. I'll try to cover some: thanks to Aaron Mackey for getting this release started, Brian Osborne for extensive documentation improvements, Nathan Haigh for volunteering to make a PPM of the release and Barry Moore and Nathan answering many of the windows related questions, Allen Day & Scott Cain & Steffen Grossmann for the work on FeatureIO, GFF3, and SeqFeature::Annotated, Chris Mungall for the work with Unflattener to merge GenBank annotations into GFF3 objects. Please see the AUTHORS file for a complete list of contributors. Jason Stajich on behalf of the Bioperl developers. Here is the info from the Changes file. 1.5 Developer release o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics provide Jukes-Cantor and Kimura pairwise distance methods, respectively. o Bio::AlignIO support for "po" format of POA, and "maf"; Bio::AlignIO::largemultifasta is a new alternative to Bio::AlignIO::fasta for temporary file-based manipulation of particularly large multiple sequence alignments. o Bio::Assembly::Singlet allows orphan, unassembled sequences to be treated similarly as an assembled contig. o Bio::CodonUsage provides new rare_codon() and probable_codons() methods for identifying particular codons that encode a given amino acid. o Bio::Coordinate::Utils provides new from_align() method to build a Bio::Coordinate pair directly from a Bio::Align::AlignI-conforming object. o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils. Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's web service using standard Pubmed query syntax, and retrieve results as XML. o Bio::DB::GFF has various sundry bug fixes. o Bio::FeatureIO is a new SeqIO-style subsystem for writing/reading genomic features to/from files. I/O classes exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO classes only read/write Bio::SeqFeature::Annotated objects. Notably, the GFF v3 class requires features to be typed into the Sequence Ontology. o Bio::Graph namespace contains new modules for manipulation and analysis of protein interaction graphs. o Bio::Graphics has many bug fixes and shiny new glyphs. o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file indexing for HMMER reports and FASTA qual files, respectively. o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are new objects that can be placed within a Bio::Map::MapI-compliant genetic/physical map; Bio::Map::Physical provides a new physical map type; Bio::MapIO::fpc provides finger-printed clone mapping import. o Bio::Matrix::PSM provide new support for postion-specific (scoring) matrices (e.g. profiles, or "possums"). o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now be instantiated without explicitly using Bio::OntologyIO. This is possible through changes to Bio::Ontology::OntologyStore to download ontology files from the web as necessary. Locations of ontology files are hard-coded into Bio::Ontology::DocumentRegistry. o Bio::PopGen includes many new methods and data types for population genetics analyses. o New constructor to Bio::Range, unions(). Given a list of ranges, returns another list of "flattened" ranges -- overlapping ranges are merged into a single range with the mininum and maximum coordinates of the entire overlapping group. o Bio::Root::IO now supports -url, in addition to -file and -fh. The new -url argument allows one to specify the network address of a file for input. -url currently only works for GET requests, and thus is read-only. o Bio::SearchIO::hmmer now returns individual Hit objects for each domain alignment (thus containing only one HSP); previously separate alignments would be merged into one hit if the domain involved in the alignments was the same, but this only worked when the repeated domain occured without interruption by any other domain, leading to a confusing mixture of Hit and HSP objects. o Bio::Search::Result::ResultI-compliant report objects now implement the "get_statistics" method to access Bio::Search::StatisticsI objects that encapsulate any statistical parameters associated with the search (e.g. Karlin's lambda for BLAST/FASTA). o Bio::Seq::LargeLocatableSeq combines the functionality already found in Bio::Seq::LargeSeq and Bio::LocatableSeq. o Bio::SeqFeature::Annotated is a replacement for Bio::SeqFeature::Generic. It breaks compliance with the Bio::SeqFeatureI interface because the author was sick of dealing with untyped annotation tags. All Bio::SeqFeature::Annotated annotations are Bio::AnnotationI compliant, and accessible through Bio::Annotation::Collection. o Bio::SeqFeature::Primer implements a Tm() method for primer melting point predictions. o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML, InterProScan-XML, TIGR-XML, and NCBI TinySeq formats. o Bio::Taxonomy::Node now implements the methods necessary for Bio::Species interoperability. o Bio::Tools::CodonTable has new reverse_translate_all() and make_iupac_string() methods. o Bio::Tools::dpAlign now provides sequence profile alignments. o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF). o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report parsers. o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl) for designing small inhibitory RNA. o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building methods based on a distance matrix. o Bio::Tree::Statistics provides an assess_bootstrap() method to calculate bootstrap support values on a guide tree topology, based on provided bootstrap tree topologies. o Bio::TreeIO now supports the Pagel (PAG) tree format. -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ -------------- next part -------------- A non-text attachment was scrubbed... Name: PGP.sig Type: application/pgp-signature Size: 186 bytes Desc: This is a digitally signed message part Url : http://portal.open-bio.org/pipermail/bioperl-announce-l/attachments/20050124/502b810f/PGP.bin