Autarchy of the Private Cave

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    Archive for November, 2008

    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…


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

    Software development schedules

    22nd November 2008

    image from joelonsoftwareJoel Spolsky has an interesting (and useful) post on evidence-based scheduling, as he calls that approach. The post discusses an approach to estimate project volume and key dates (such as milestones and release) based on prior performance of each of the project developers. As Joel argues, this approach provides several benefits, and – among others – allows releasing the software product on the date planned.

    I would recommend learning more about “evidence-based scheduling” to anybody who is somehow involved into software development.

    Also, for me personally it was useful to read the preceding article by Joel (called painless software schedules), which summarizes some basic ideas you should keep in mind while trying to develop some piece of software (mostly from the manager’s viewpoint). If you are going to read that “obsolete” article – better do so before reading evidence-based scheduling.


    Posted in Notepad, Programming, Software | No 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

    Posted in Bioinformatics, Science, Software | No Comments »