Autarchy of the Private Cave

We are pleased to announce the release of GNAT GPL 2009, the Ada Toolset for Academic users and FLOSS developers. It introduces many new features including:

- Ability to generate byte code for the JVM

- Improved support for the .NET Framework

- Addition of the Ada-Java Interfacing Suite (AJIS) that enables native Ada code to be called from Java:
http://www.adacore.com/2008/06/17/ada-java_interfacing_suite

- Availability on the Mac OS X (64 bit) platform

- Automatic C/C++ binding generators

- Addition of the GNAT Component Collection (GNATcoll) providing new APIs that can be extended by the user community:
http://www.adacore.com/2008/06/17/gnat_component_collection

GNAT GPL 2009 comes with version 4.3.1 of the GNAT Programming Studio IDE and GNATbench 2.3, the GNAT plug-in for Eclipse.

It is available for the GNU Linux, Mac OS X (64 bit), .NET, JVM and Windows platforms.

GNAT GPL 2009 can be downloaded from the “Download” section on the new Libre website:
https://libre.adacore.com.

I wonder if the new JVM bytecode generation feature was frequently requested by Ada developers, or is just a move towards popularizing Ada as a highly capable programming language. Either way, it’s good.

Hopefully, I will find time and a matching project to finally learn Ada properly – since a couple of years I believe Ada is a very good programming language. And the D language is better than C and C++ (holy war, anyone? )

This in itself wouldn’t be so exciting, if it were not for the new webcode! If you do visit Ensembl now, you will be definitely surprised with the page loading speed – it is amazingly faster than it used to be! Also, as you dig deeper and deeper, you’ll see that there are a lot more other differences – starting with the new design, and not forgetting the changed page organization logic.

To cut the long story short, here’s the list of changes in the new Ensembl 51 webcode release. Other changes to Ensembl in release 51 are also available.

One of the new features which caught my attention is the ability to add custom tracks in Ensembl (which is a long-available feature in UCSC Genome Browser). Interestingly, you do not even have to be logged in to use this feature. We shall be considering providing the TFBS custom track for several species, as predicted de-novo by our evolutionary conserved tfbs search tool (binding site finder), but this is a long shot, given the already published COTRASIF development roadmap.

There is one more great news which is kinda insufficiently highlighted: the brand-new Ensembl Genome Browser website, which (as planned, it hasn’t yet started operations) will provide access not only to vertebrates, but also to other taxonomy groups. The full list is:

• Metazoa
• Protists
• Bacteria
• Plants
• Fungi

For the COTRASIF tool, I’ve been using the Ensembl Compara database (since release 47) to automatically import into COTRASIF gene orthology mappings.

However, with the E!50 release, the Compara database was dropped.

Looking for another option to get orthologs from Ensembl (using martservice, via biomart.org), I tried using the standard query – selecting “Homologs” group on the “Attributes” page for a single species database, and then selecting appropriate second species to get orthology mappings.

Imagine my surprise, when not only in the interface, but also in the generated XML file I found attribute names like “cow_ensembl_gene” :-O

I only need 11 species at the moment, and excluding the sufficiently unique name mappings like “zebrafish – danio rerio”, there is a number of questionable mappings: “yeast” for S. cerevisiae (could be S.pombe), “rat” for R. norvegicus (could be R.rattus), “anopheles” for A.gambiae (could be some other Anopheles). Other mappings might be also non-unique, especially for people working with different species of the same genus.

Am I missing some system in this naming “convention”, or am I the only one who finds it strange?

Is there a way not to use “common species names” when importing orthology data from Ensembl with the help of martservice?