ISCB and IBM invitation to Virtual Conference April 16-17, 2008 ISCB and IBM are pleased to invite you to a complimentary two day Virtual Life Sciences Conference on April 16-17, 2008. The event runs live on those two dates from 10AM - 5PM Eastern. If you can't participate live for all the sessions, due to time zone differences, the sessions will be recorded and available to you for 90 days after April 16 - 17. Please register to get info on both the live event and the replay. Learn More without travel costs and hassles This two day virtual event, focusing on innovation in drug discovery and development, will cover the latest innovations in bioinformatics, biochemistry, imaging analysis and clinical development. You join the event live from your office. Published Apr 12, 2008 - 06:14 PM

From XML BLAST to HTML This python script converts a XML BLAST file into a HTML file. While BLAST can output to HTML (by using -T T), XML is used since it is the best format for automatic parsing. When the user needs the same output to show in a web server, it should run a time consuming BLAST again. To avoid that, I post a script that convert XML blast to HTML. Convert from XML BLAST to HTML by using Biopython and without Biopython (this one requires Python 2.5). Please send bug reports to: sbassi -AT- genesdigitales.com The code is GPL 3.0 Published Apr 02, 2008 - 12:44 PM

GenPept 164.0 available This is to announce the availability of release 164.0 of the GenPept(R) (GenBank Gene Products) Database. GenPept is provided in a format similar to that formerly distributed by GenBank(R) under the administration of Intelligenetics Inc. This GenPept release IS _NOT_ AN OFFICIAL RELEASE FROM THE NCBI-GENBANK, but an attempt to provide a data file format compatible with existing software products. This data format is suitable as an input data file for the GCG program genbanktogcg -genpept. Compatibility with other software has not been tested. Site: ftp.ncifcrf.gov Directory: pub/genpept Files: gprel.txt.gz, gpdat.seq.gz, gpdat.fasta.gz Directory: pub/genpept/divisions Files: 1 file for each GenBank file Directory: pub/genpept/updates (daily, cumulative) Files: gpseq_updates.dat.gz Rel. Date: 20-Feb-2008 If you have questions or comments concerning this data, or you experience any difficulty in downloading the data via ftp, please contact: Gary Smythers gws@ncifcrf.gov 301-846-5778 or Bob Stephens bobs@ncifcrf.gov ================================================================ GenPept (R) and GenBank (R) are registered trademarks of the U.S. Department of Health and Human Services for the GenBank Gene Products and the GenBank Genetic Sequence Data Banks. Published Feb 25, 2008 - 12:00 AM

plone4bio project starts Biodec.com announces: We are pleased to announce a new Plone project: plone4bio. As the name suggest it is intended as a set of products to do bioinformatics within the Plone CMS. Plone4Bio takes advantage of Biopython. What is plone4bio The rationale of the plone4bio project is to provide an integrated environment where it is possible to manage and analyze biological sequences. The plone4bio package provides the possibility to add a new plone content type, called sequence, than can be either written by hand or imported from a FASTA file, and to apply to that sequence a program, called predictor, that gives back a plot of predicted probabilities for the sequence to have a given property (the property that the predictor tries to determine). thus a predictor can try to assess if a protein sequence is trans-membrane, whether a signal peptide exists, and so on. plone4bio.base The plone4bio.base is a package that defines a skeleton predictor: deriving from that it is possible to integrate any other application and visualize all the results together. biocomp.pscoils This is an example predictor, encapsulating the pscoils algorithm by Fariselli et al. available at www.biocomp.unibo.it/ It is intended both as an example on how to integrate one's own predictor in the plone4bio framework. Published Feb 24, 2008 - 05:29 PM

Kaptain GUI for EMBOSS 5.0 The new version of the Kaptain user interface for EMBOSS. EMBOSS.kaptain v.0.98 provides a simple and efficient GUI to use EMBOSS 5.0 and the embossified Phylip 3.6b on the desktop. The GUI depends on Kaptain, a tool to build nice graphical user interfaces for command line applications like EMBOSS. Kaptain is a Qt3 application. Due to problems with it's configure script it got more and more difficult to install on recent systems. To address this, and to make Kaptain a little more future-proof I have ported it to the modern cMake build system and to Qt4. A patch and build instructions are in the EMBOSS.kaptn package. You can find the package, some screenshots, and additional information as usual here: http://userpage.fu-berlin.de/~sgmd/download.html For Mac users Koen van der Drift provides a fink package at: http://pdb.finkproject.org/pdb/package.php/emboss-kaptain Qt4 is availible under various open source licenses for Windows as well. Thus with Kaptain on Qt4 it may be possible to build and use the Kaptain GUI on that OS as well. Published Feb 24, 2008 - 05:18 PM

Biopython 2007 presentation Here is the presentation of Biopython given at BOSC 2007: Published Oct 10, 2007 - 12:27 PM

Plant Ontology Database Release-September 2007 Plant Ontology Consortium is happy to announce the release #0907 of PO database! www.plantontology.org * Ontology update - 1109 PO terms - 32104 annotations visit www.plantontology.org/docs/release_notes/index.html for more details * New version of PO browser (www.plantontology.org/amigo/go.cgi) - New interface - New users guide - New tutorials - New feature: added "GO" (Gene Ontology) associations link to Arabidopsis genes * POC Website updates (www.plantontology.org/) - added "Request PO terms" feature on navigation menu - added "POC Outreach Activities" link in "Documentation" page - Updated "Mail Archives" - Updated "PO website usage statistics" - Updated "Tutorials" Published Sep 08, 2007 - 10:24 AM

EMBOSS 4.1.0 EMBOSS 4.1.0 is available for download from: ftp://emboss.open-bio.org/pub/EMBOSS/ It contains: a) Two new applications, edialign and wordfinder b) Improvements to other applications e.g. coderet can now write non-coding regions to a file. c) Bugfixes, including all those supplied for the previous release. See the attached ChangeLog file for full details. Please remember that you should not install a new release over the top of an existing one. Also remember that the associated EMBASSY packages (e.g. MEME/PHYLIP/etc) are specific to a given release i.e. download them again if you wish to install them. A version for Microsoft Windows is also available at: ftp://emboss.open-bio.org/pub/EMBOSS/windows/ Published Mar 07, 2007 - 03:55 PM

NCBI Special Announcement: Beta test of new BLAST interface NCBI is holding a beta test for a new BLAST interface design. We invite you to try these pages and send us your comments and suggestions. One major improvement is a new "Recent Results" feature that provides links to all of your recent BLAST search results. Another is "Saved Strategies", which allows you to save BLAST forms with their parameters and use them later. Saved Strategies requires a free MyNCBI account, and is compatible with existing accounts. Signing in to MyNCBI also makes your Recent Results available from any browser. Other improvements include: - Easier navigation - Simplified BLAST program selection - Easy access to genome searches - Improved Organism selection with species name auto-complete - Automatic parameter adjustment to optimize for short queries - A user-specifiable title for each BLAST job The Beta test is available at: Published Mar 07, 2007 - 03:51 PM

NCBI COURSE: NCBI PowerScripting *** ANNOUNCING AN NCBI COURSE: NCBI PowerScripting *** NCBI PowerScripting The National Center for Biotechnology Information (NCBI) presents NCBI PowerScripting, a 4-day course including both lectures and computer workshops on effectively using the NCBI E-utilities within scripts to automate search and retrieval operations across the entire suite of Entrez databases. Dates: January 30 - February 2, 2007 Location: Lister Hill Center (Bldg 38A), NLM, NIH, Bethesda, MD For more information and to apply for the course, see the course web page at http://www.ncbi.nlm.nih.gov/Class/PowerTools/eutils/course.html The course is free but an application is required. Space is limited to 20 participants, so apply now! ****************************************************************** Published Dec 05, 2006 - 12:00 AM

Workshop "Storage and Annotation of Reaction Call for participation Workshop "Storage and Annotation of Reaction Kinetics Data" Heidelberg, May 21-23, 2007 http://projects.eml.org/sdbv/events/workshop2007/index_html The main objective of the workshop is to discuss issues regarding the generation, storage, integration, annotation and usage of kinetic data of biochemical reactions in the context of systems biology. The workshop will be divided into four sessions, namely: - Data generation - Data storage and integration - Data annotation - Data usage We will have 3-4 invited speakers for each of these sessions (see below), allowing us to leave sufficient time for questions and discussion. A poster session is also planned as part of the workshop. Additionally, 3-5 posters will be selected for short oral presentations of 10 minutes each. Published Dec 04, 2006 - 12:00 AM

Announcing Pfam Release 21.0 Pfam 21.0 is now available from the Wellcome Trust Sanger Institute. The latest release contains 8957 protein domain families, matching 74% of sequences from UniProt 8.0. This release includes 669 new families and 8 families have been deleted since the last release. http://www.sanger.ac.uk/Software/Pfam/ Published Dec 03, 2006 - 04:28 AM

Reactome 19 released The Reactome Knowledgebase team (Lincoln Stein's group at CSHL and Ewan Birney's group at European Bioinformatics Institute) is proud to announce the release of Reactome Version 19, accessible at http://www.reactome.org! Reactome is a curated knowledgebase of biological processes in humans. It covers processes ranging from basic pathways of metabolism to complex events such as hormonal signaling and apoptosis. The information in Reactome is provided by expert bench biologists, and edited and managed as a relational database by the Reactome staff. New material is peer-reviewed and revised as necessary before publication to the web. Reactome entries are linked to corresponding ones in NCBI, Entrez Gene, RefSeq, OMIM, Ensembl genome annotations, UCSC Genome Browser, KEGG, ChEBI and Gene Ontology (GO). Two way links between HapMap and Reactome have been enabled from this release. Published Nov 22, 2006 - 12:00 AM

Entrez PubMed 2007 DTD changes The PubMed Team announces: We anticipate switching to the PubMed 2007 DTDs on December 11, 2006. 2007 DTDs are available using the same naming convention as the 2006 DTDs listed on the Entrez DTD page: http://eutils.ncbi.nlm.nih.gov/entrez/query/DTD/index.html Change the date from 06 to 07, e.g., http://eutils.ncbi.nlm.nih.gov/entrez/query/DTD/pubmed_070101.dtd The following changes were made in the nlmmedlinecitation_070101.dtd: Added PartialRetractionOf and PartialRetractionIn to the CommentsCorrections element Published Nov 21, 2006 - 10:37 AM

EMBOSS explorer 2.2.0 EMBOSS explorer 2.2.0 has just been released, after a long delay. It has been updated to work with EMBOSS 4.0.0 (though it should continue to work with EMBOSS 3) Visit http://embossgui.sourceforge.net for more information or to download. Report any problems using the bug tracker (available from the website above), or by email to mccarthy@users.sourceforge.net Published Nov 14, 2006 - 06:20 AM