Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    • Archives

    • Recent 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.
    Read the rest of this entry »

    Share

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

    Why I love Debian

    4th October 2008


    I love Debian, too.

    Though I prefer ‘testing’ (which is currently codenamed Lenny) over ‘stable’ (aka Etch).

    Share

    Posted in *nix, Links, Misc | 1 Comment »

    Debian, fgl_glxgears: Using GLX_SGIX_pbuffer… Segmentation fault

    1st October 2008

    If you get Segmentation fault when trying to run fgl_glxgears in your Debian desktop environment, most often this would mean that 3D acceleration isn’t enabled.

    For the case of ATI (and ATI Mobility) Radeon series, the easiest procedure would be (doing all as root, or prepending sudo to all commands):

    1. aptitude update, to ensure you’ve got the list of latest packages
    2. aptitude install fglrx-driver fglrx-control fglrx-kernel-src, for the actual driver; I also installed fglrx-atieventsd and fglrx-glx (these are driver-recommended packages)
    3. aptitude install module-assistant, required for building the kernel module
    4. module-assistant prepare, to verify that you have everything needed for the module build procedure
    5. module-assistant update
    6. module-assistant auto-install fglrx, to build and install the fglrx kernel module
    7. depmod -a
    8. modprobe fglrx, to load the fglrx kernel module
    9. aticonfig ––initial, to configure ATI’s device section in /etc/X11/xorg.conf (for more options, see aticonfig ––help)
    10. reboot

    Read the rest of this entry »

    Share

    Posted in *nix | 5 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? :)

    Share

    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.

    Share

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

    debian.org.ua: universal Ukrainian Debian mirror

    15th July 2008

    http://debian.org.ua/ and ftp://debian.org.ua/

    What is on offer (mirrors):

    • backports.org
    • cygwin
    • deb.opera.com
    • debian – stable, testing, sid
    • debian-archive (starting from 1.1!)
    • debian-multimedia
    • installation media (CDs/DVDs)
    • debian-security
    • even debian-volatile is here!

    All this goodness is only 3 hops away from my DSL modem…. (ISP UkrTelecom)

    Gone editing /etc/apt/sources.list :)

    P.S. For non-ukrainian IPs, access might be slow/bandwidth-limited; for Ukrainian IPs, speed might be up to 100MBit/sec.

    Update: some time after publishing this post, debian.org.ua was down for some reason. When it was up, it was serving me packages with a mere 3 kb/sec :( . I found that ftp2.debian.org.ua mirror is faster at the moment.

    Share

    Posted in *nix, Links | No Comments »

    Internet Explorer 6 for Linux

    13th July 2008

    IEs4Linux provides a convenient package of Internet Explorer 5.0, 5.5, 6.0, and (partially supported) 7.0 for Linux.

    It installed and runs fine under Debian Etch:

    IE6 under Linux screenshot

    However, as you could notice from the screenshot above, CPU use is almost 100% while IE6Linux is running. It is better illustrated by the next screen:

    IE6 under Linux: high CPU use

    I didn’t yet bother finding out what’s wrong, but that must have some kind of a fix, as running at 100% CPU on a laptop is … hot.

    Share

    Posted in *nix, Links | No Comments »