Autarchy of the Private Cave

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    How to create custom Affymetrix CDF file

    23rd March 2009

    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).

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    Posted in how-to, Links, Science | No Comments »

    BioGPS: by the makers of Gene Expression Atlas

    22nd November 2008

    BioGPS logo 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…

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    Posted in Bioinformatics, Links, Science, Software | 3 Comments »

    Ensembl release 51 is out!

    20th November 2008

    ensembl logoThis 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
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    Posted in Bioinformatics, Science, Software | No Comments »

    Citation and reference managers for Linux: short overview

    29th October 2008

    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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    Posted in *nix, Links, Science, Software | 1 Comment »

    CLANS: CLuster ANalysis of Sequences

    25th October 2008

    CLANS (CLuster ANalysis of Sequences).
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    Posted in Bioinformatics, Links, Science | No Comments »

    Weird orthology species names in Ensembl

    30th September 2008

    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?

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    Posted in Bioinformatics, Science | No Comments »

    The 9th ICSB-2008 in Gothenburg, Sweden

    12th September 2008

    It has been quite a time since my last serious and long post. On the one hand, summer is vacations time – so I’ve been to one in Turkey; on the other hand – the long-awaited ICSB-2008 conference finally took place in Gothenburg, Sweden, on August 23-27 (or 22-28, counting in tutorials and workshops).

    Update: it appears that conference domain name http://www.icsb-2008.org/ was not maintained after the conference, so I had to remove all the links to that website (which now appears to be owned by someone not related to ICSB). However, there seems to be a mirror of ICSB-2008 at http://www.gmm.gu.se/groups/icsb08test/.

    Synopsis: in this post I present a personal-perspective report on the 9th ICSB (with a condensed ICSB-2008 photo-report in my gallery).

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    Posted in Bioinformatics, Science, Systems Biology | No Comments »