Collection of updates -- Pubmed and biblio; Gbrowse tracks; menu links

We have been pushing a number of efforts in parallel, and many of them are reaching milestones at the same time. Thus there are several updates that we hope will make the overall site more usable and useful to the avian research scientist.
The Drupal biblio and entrez modules were added and configured, so that when we give due credit to others' great work, we can do so with a full set of authors, the abstract text, and direct link to the article, all just by entering the Pubmed ID. We'll be updating links on the site to use this method instead of having to search for the proper URL and hotlinking it manually.
We are continually adding data and reconfiguring the Gbrowse genome browser, and trying to smooth out your daily routines.

• Updated all gene annotations for the ZebrafinchOligoarray
• Posted updated GAL files on the ZebrafinchOligoarray web page here (and at http://songbirdtranscriptome.net.) The files include: cloneid, clusterid (aka gene locus), subclusterid (aka transcript variant), gene symbol, and gene description. It is in the exact order for the Agilent zebra finch oligoarray, but is tab-delimited and can be merged directly with any dataset.
• Updated the zebra finch clones text in Gbrowse.
• Changed the top tab from "Genome Views" to "Genome Browser" and linked to the browser instead of another page about the browser.
• Promoted numerous changed from "New Development" to "Production" including:
• Added Budgerigar (parakeet, Budgie, or Melopsittacus undulatus) genome sequence tracks for the overview, region view, and details view.
• Confirmed with
• The track "contigs" shows the individual 454AllContigs contigs, which are a subset of the overall scaffolds (and to some extent the individual reads. I need to update the % of reads which are found in contigs overall and post it here.)
• The track "scaffolds" similarly shows the 454Scaffolds sequences, aligned with zebra finch genome. Notice how it looks very spotty and disconnected? The next track addresses this observation.
• The track "scaffolds (extended)" shows an expanded scaffold view which shows the alignments to finch and in between them it shows where unaligned sequence is available but did not align above the alignment threshold.
• Added improved balloon hover text for many of the tracks, including the Clones and xenoRefGene tracks. More will come this week, including the finch EnsEMBL genes, the 454 cross-species cDNAs, and of course the Budgie genome sequences.
• Changed some of the track names to be more user-friendly, and more definitive by including species name so it is more self-documenting. More balloon help text is coming to each track, which will describe its composition and the glyphs in more detail.
• Added an apple-touch-icon for anyone creating a shortcut on their iPhone Home Screen. Turns out it's pretty easy, and definitely better than the default screenshot. (Easiest method is just to create a 125x125 PNG file. iPhone will do the rest.)