24 carat JABBA awards

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Here is a new paper published in the journal PLOSBuzzFeed…sorry, I mean PLOS Computational Biology:

It's a good job that they mention the name of the algorithm ninety-one times in the paper, otherwise you might forget just how bogus the name is. At least DIAMOnD has that lower-case 'n' which means that no-one will confuse it with:

This second DIAMOND paper dates all the way back to November 2014. Where does this DIAMOND get its name?

Double Index AlignMent Of Next-generation sequencing Data

This DIAMOND gets a bonus point for having a website link in the paper which doesn't seem to work.

So DIAMOnD and DIAMOND are both the latest recipients of JABBA awards for giving us Just Another Bogus Bioinformatics Acronym.

Trying to download the cow genome (again): where's the beef (again)?

Almost a year ago, I blogged about my frustrations regarding the extremely confusing nature of the cow genome and the many genome assemblies that are out there. Much of that frustration was due to websites and FTP sites that had broken links, misleading information, and woefully incomplete documentation.

One year on and I hear a rumor that a new version of the cow genome is available. So I went off in search of 'UMD 3.1.1'. My first stop was bovinegenome.org which is one place where you can find the previous 'UMD 3.1' assembly. But alas, they do not list UMD 3.1.1.

After some Google searching I managed to find this information at the UCSC Genome Bioinformatics news archive:

We are pleased to announce the release of a Genome Browser for the June 2014 assembly of cow, Bos taurus (BostaurusUMD 3.1.1, UCSC version bosTau8). This updated cow assembly was provided by the UMD Center for Bioinformatics and Computational Biology (CBCB). This assembly is an update to the previous UMD 3.1 (bosTau6) assembly. UMD 3.1 contained 138 unlocalized contigs that were found to be contaminants. These have been suppressed in UMD 3.1.1.

This reveals that the update is pretty minor (removal of contaminant contigs which were never part of any chromosome sequence anyway). In any case, the USCC FTP site contains the UMD 3.1.1 assembly so that's great.

But out of curiosity I followed UCSC's link to the UMD Center for Bioinformatics and Computational Biology (CBCB) website. The home page doesn't make it easy to find the cow genome data. Searching the site for 'UMD 3.1.1' didn't help but searching for 'cow genome' did take me to their Assembly data page which lists the cow genome. Unfortunately the link for the Bos taurus genome takes you to 'page not found'. In contrast, the 'data download' link does work and takes you to their FTP site which fails to include the new assembly (but it does list all of the older cow genome assemblies).

Plus ça change, plus c'est la même chose.

More bioinformatics link rot: where is EUROCarbDB?

Update 2015-01-19 15.19: I contacted the corresponding author about this and now the EurocarbDB link in the original paper works.

First published online a few months ago in the journal Bioinformatics (September 12th, 2014):

The name of this resource is not the snappiest name out there. "Oh, you're interested in resources for glycomics, have you tried EuroCarbDB-open parentheses-cee-cee-ar-cee-close parentheses?", but leaving that aside the paper lists the following URLs as part of the abstract:

Availability and implementation: The installation with the glycan standards is available at http://glycomics.ccrc.uga.edu/eurocarb/. The source code of the project is available at https://code.google.com/p/ucdb/.

The first link says that the server is down. The parent page (http://glycomics.ccrc.uga.edu/ seems to make no mention at all of this resource (not that I can find anywhere). Following the second link in the abstract, I found the following text:

An incubator project for the future direction of the EUROCarbDB project. More to follow.... This new project is in it's infancy - please use the original EUROCarbDB site. A new project will be hosted at UniCarb-DB (http://www.unicarb-db.org to reflect the continued work of the developers

I followed the first of these links to the 'original' EUROCarbDB site. This Google Code page in turn told me that the online version of EuroCarbDB is hosted by the European Institute of Bioinformatics.

Following the link for the online version of EUROCarbDB takes me to what seems to be a closed down site at the EBI titled 'What happened to the EuroCarbDB website?' which has this to say:

The pilot project ended in 2009 but efforts to obtain renewed funding have unfortunately not been successful. The EuroCarbDB website was hosted by the Protein Data Bank in Europe at EMBL-EBI but has now been discontinued

So that's all very helpful then.