Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    Archive for September, 2008

    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 »

    Which Hosting Control Panel to use for a Debian server?

    27th September 2008

    To cut the long story short: for the final evaluation, I had this line of control panels:

    SysCP: looks good to me (though demo isn’t functional), has customer billing module. Unsure as to where it is used, but most probably sponsors are also the users of SysCP. Majority of support forums are in German.

    DTC: has no demo, only some screenshots. Has a set of packages for Debian lenny (which is a huge plus for maintenance and future upgrades). DTC is being developed by GPLHost, and is also used by GPLHost – so this is a live (used) distribution. Seems quite feature-rich.

    Virtualmin claims to be the “world’s most powerful and flexible web server control panel”. Virtualmin offers 4 means to control it: Web, mobile device, command line, and remote API. There are both screenshots and demo. Has both GPL and Professional versions. GPL version has a number of limitations, comparing to Pro version. From what I’ve read about Webmin (all three – Virtualmin, Webmin, Usermin – are just different “layers” of server control), it is a framework with a number of “interface scripts”, which allow to control various services. As such, it is easily extendible, but is not monolithic – in the sense of module inter-dependencies and action triggers.

    RavenCore was a promising CP.

    GNUPanel is a year-old control panel, but has a news item on the front page (dated August, 17) promising new, completely rewritten release somewhere in October. By the feature list, looks promising. However, I need the panel right now, and even in October, that will be quite a rough release, not really used/tested anywhere, so not a good option as well. But GNUPanel is a panel to check in half a year for progress.

    As the final choice, I had ISPConfig (which seems to be the best by people’s comments), and which is also quite widely used, and is easy to install onto Debian (at least the Perfect setup: Debian Etch says so), and DTC. I discarded Virtualmin (for the poor functionality of the GPLed version), RavenCore (for the lack of current descriptions and non-functioning demo), GNUPanel (which just isn’t ready yet), and SysCP (because ISPConfig seems better ;) ).

    As DTC has Debian packages (and will be easier to maintain/upgrade), I decided to try it first. I already have it installed (that’s easy, esp. if you first read the DTC Debian Express Setup). Later I might post my impressions from using DTC.

    Update: DTC is indeed easy and pleasant to use. I had problems allowing FTP and SSH access using MySQL authorization, but at least FTP was an easy one to fix (SSH access with MySQL authorization is still unconfigured, but that’s a low priority for me). There is a minor concern about the files and directory permissions setup, but thanks to chrooted environment that is only minor concern. Use of a single Apache installation for hosting admin and serving user sites might be a sub-optimal decision, but it works. Traffic and disk space accounting are plain superb! Server memory use for the dtc-toaster installation is troublesome, but for a powerful RAM-my server that is not a problem (I now have about 800-900MiB RAM occupied, but that includes the XCache’s cache, quite big MySQL cache, and loads of Apache and PHP modules).

    But I’m still willing to try other control panels. As I expected, GNUPanel hasn’t released anything yet; Ravencore‘s online demo is still unfunctional; ISPConfig has recently released RC (and their demo is working as it should and as it used to); SysCP is also up and running fast. If my little hosting service starts pouring in some cash, then I’ll try SysCP on my second server – to compare it with DTC, and choose one of them for further support/extension/localization.

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    Posted in *nix, Notepad, Software, Web | 17 Comments »

    How to ssh through the unconfigurable NAT/firewall

    20th September 2008

    There’s a how-to on the topic at howtoforge.com.

    Note, that for the suggested solution to work, NAT/firewall should be “transparent” for outgoing ssh connections.

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    Posted in *nix, Links | No Comments »

    Russia vs Georgia: no comment

    17th September 2008

    2008 South Ossetia war

    russia-vs-georgia

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    Posted in Society | 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).

    Read the rest of this entry »

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

    Vista Ultimate has a Linux benefit

    12th September 2008

    One of the benefits, offered exclusively by the Windows Vista Ultimate (not even by the Windows Vista Business), is

    running UNIX applications (via SUA, Subsystem for UNIX Applications) , which provides higher flexibility for Windows workstations.

    Where is the world going? :)

    And how soon will all the Windows users (not only Ultimate Users) benefit from the higher flexibility by running UNIX applications? :)

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    Posted in *nix, Humour, Misc | No Comments »

    Google Chrome is not for Linux?

    4th September 2008

    I’ve tried it already under Windows, but as my main OS is Debian, I can’t use it :(

    You can sign up for updates on Linux version.

    After reading the Google Chrome book, it is a long time waiting for it to be released for Linux….

    Also, I’m looking forward for the plugins to enhance Chrome. Although it did import my settings/passwords(?!)/bookmarks from Firefox, but it has no Foxmarks, AdBlock and some other goodies I’m now used to on all the computers I regularly use.

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    Posted in *nix, Links, Misc, Software, Web | No Comments »