Giovanni Dall’olio has recently posted a presentation on using make.

Although it has “bioinformatics” on the title page, this is a good and very easy to understand make intro.

Original post is here.

The following sites are available:

http://bacteria.ensembl.org
http://protists.ensembl.org
http://metazoa.ensembl.org

During summer, two more sites – for Fungi and Plants – should be made available.

Learn more about Ensembl Genomes project.

First, learn about custom CDFs and why they are needed.

The aroma.affymetrix R package google group has a how-to: create a CDF annotation file from scratch.

Also useful: how to convert CDF into an R package, which has all CDF data available (as a PDF with more details).

If you were a frequent user of GNF SymAtlas, then you’d better bookmark BioGPS – Your Gene Portal System. BioGPS is basically the same gene expression atlas, but with a completely different interface, and more flexible ideology (e.g. expression atlas is now just a “plugin”, and more of those can be plugged in).

There are also some easter-egg-like features: try hovering the BioGPS logo in the top left corner several times…

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 some period of time, I had to switch to my Windows installation when writing articles with references, because I keep my references database there and there is an extremely convenient add-on for MS Office to insert citations and format bibliography on the fly.

However, it is quite inconvenient to make/run programs/scripts under Linux, and then switch to Windows to describe the obtained results in the article-like form. Thus, I briefly investigated available citation managers for Linux.
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CLANS (CLuster ANalysis of Sequences).
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