BSML

Bioinformatic Sequence Markup Language ( BSML ) is an extensible markup language ( XML ) derived standard that “encodes biological sequence information and includes graphical representations of biologically meaningful objects such as sequences, genes, electrophoresis gels, and multiple alignments”.

A detailed BSML overwiev is available here whereas the FAQ page is here.

The last BSML DTD release ( 3.1 ), the BSML reference manual and tutorial are available here. A BSML presentation is also avaible ( pdf, ppt ).

You can manage BSML file with LabBook Java Genomic XML Viewer, that is freely available, or you can purchase LabBook Genomic Workspace.

BioBar, a bioinformatic firefox plug-in

FireFox, the well known open source web browser, now is useful also for bioinformatic web surfers. Biobar is a new plug-in that provides rapid and easy access to several bioinformatic databases, directly whitin firefox.

"The primary advantage of this tool is that it allows a biologist to browse and retrieve data from Genomic, Proteomic, Functional, Literature, Taxonomic, Structural, Plant and Animal-specific databases".

Biobar also has several links to the major bioinformatics sites including European Bioinformatics Institute (EBI), National Center for Biotechnology Information (NCBI) and DNA Data Bank of Japan (DDBJ) and other important databases for nucleotide, protein, 3D-structure data, sequence, structure alignment and analysis tools.

The complete list of resources currently accessible through biobar is listed here.

You can install the latest biobar release ( 1.4 ) from here.

Events and Courses

Several interesting events and courses are listed below.

Today is the early registration deadline for the two-day 3Dsig Structural Bioinformatics and Computational Biophysics Satellite Meeting within the Annual meeting of the International Society for Computational Biology ( ISMB ) ( with the same link ) in Fortaleza, Brasil, August 6-10.

At Inst. Gulbenkian de Ci\u00eancia in Oeiras, Portugal, there is course titled “A Primer on Molecular Evolution, Phylogenetics and Phylogenomics” ( July 24th – 28th, 2006 ).

Kerala University invites applications for 3rd batch of MPhil Bioinformatics (To start in January 2007). Application forms and bochures are available from here and the last date for application is 30 Sept 2006. The programme admits postgraduate students from engineering, computing and life sciences or allied streams.

At the Pasteur Institute a course will be offered in “Informatics in Biology“. The next session will take place from the 8th of January to the 27th of April 2007.

A second level international master in “COMPUTATIONAL AND SYSTEMS BIOLOGY” is aveible at the Università di Trento in cooperation by The Microsoft Research. The Course will start in November 2006 anf the deadline for application is August 14, 2006. Applicants will receive notification by September 18, 2006. More information on the Master Course and how to apply can be found here.

BioRuby

Four months ago BioRuby 1.0.0 has been released. You can download the tar.gz file here and here you can view changelog list.

BioRuby is one of the newest bioinformatic programming languages and this project aims to implement an integrated environment for bioinformatics with a Ruby language library and with a powerful interactive shell.

BioRuby currently allows you to work with sequences for several task as traslation, splicing, similarity search, multiple alignment and sorting and also more. You can also connect with several databases as GenBank, RefSeq, EMBL, TrEMBL, SwissProt, MEDLINE, PROSITE, TRANSFAC, KEGG, FANTOM and PDB.

A first BioRuby on-line tutorial can be found here and here. A comprensive BioRuby shell documentation is also here.

Enjoy programming.

Wellcome to bioTAG

 

bioTAG is the new Italian Bioinformatic Weblog whose aims is to inform about bioinformatic trends in softwares, researches and tecnologies, for scientists and students.The posts will fall in several categories :

bioTAG news: news about bioTAG blog
bioprogramming : news about bioinformatic programming languages
webtools : news about bioinformatic web-based tools
molecular modeling : news about molecular modeling softwares
sequence analisys : news about sequences analisys softwares
biostatistics : news about biostatistics softwares
biosoftwares : news about other kind of bioinformatic software
papers : news about papers, researchs and books about bioinformatic
events : news about bioinformatic events
instruments : news about scientific instruments

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