Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

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    Archive for March, 2010

    Tabachnik-inspired remake of Pink Floyd’s Another Brick in the Wall

    31st March 2010

    Dmitri Tabachnik is the Minister of education in the new (Yanukovych team) government.
    He is well-known for his anti-Ukrainian rhetoric and for the denial of everything Ukrainian.

    The other day he canceled obligatory Ukrainian language university entrance exams, proving again with his actions that he does intend to enact his phobia of Ukrainian identity.
    Read the rest of this entry »


    Posted in Society, Ukraine | No Comments »

    R tutorial links

    29th March 2010


    Posted in Bioinformatics, Links, Science, Systems Biology | 1 Comment »

    Good online Python book with code examples

    1st March 2010

    Building Skills in Python: A Programmer’s Introduction to Python by Steven F. Lott (© 2002, 2005, 2007, 2008 Steven F. Lott).


    Posted in Links, Programming, Python | No Comments »

    screen mastery with only 3 keyboard shortcuts

    1st March 2010

    screen is a must-use for anyone familiar with SSH sessions; it saves your time by keeping your console apps running even after (an unexpected) disconnect from the remote session.

    The easiest way to start with screen is screenie – an interface to screen. To use it, you only need to memorize a single keyboard shortcut: C-a d (Ctrl+a, d). This shortcut detaches (hides) your current screen session, allowing to resume later – either with the help of screenie, or by issuing screen -r command.

    After a while, with increased screen (and screenie) usage, you will find it inconvenient detaching every time you need a new screen session. Here comes the second keyboard shortcut: C-a c (Ctrl+a, c), which creates a new window within a current screen session, and switches to it.

    Finally, you will find it tiresome detaching to then re-attach to a different screen. C-a “ (Ctrl+a, Shift+’) will display a list of screen windows for you to select and switch to.

    Screenie, an excellent beginner’s interface to screen, is no longer needed after you memorize these 3 keyboard shortcuts.

    Many will say that this is a bare minimum, and also there is much more to screen than what you present here, and that will be true. However, these 3 shortcuts are sufficient for simple but convenient everyday screen sessions management.


    Posted in *nix, Software | 2 Comments »

    ntfstruncate binary for Debian (resetting NTFS bad clusters counter)

    1st March 2010

    There is an excellent step-by-step instruction on resetting the bad clusters counter of an NTFS partition with linux-ntfs tools. I’ve checked – it works as expected:

    1. Back up important data from partition just in case
    2. Find out size of ‘$Bad’ attribute in $Badclus using ntfsinfo -i 8 partition (partition is for example /dev/sda1). It will be the “Allocated size” value in the “Dumping attribute $DATA (0x80)” (there will be two 0x80 attributes. Only one has an “Allocated size” line). Let us write down (remember) this size as ntfs_size.
    3. Use ntfstruncate partition 8 0x80 ‘$Bad’ 0 to set $Bad’s attribute length to zero.
    4. Use ntfstruncate partition 8 0x80 ‘$Bad’ ntfs_size to set $Bad’s attribute length back to proper value ntfs_size which was recorded in step 2.
    5. Boot into Windows and run chkdsk -f diskname. It will find errors and should fix them.

    However, Debian’s ntfsprogs package does not have the ntfstruncate binary.

    Here’s how you can easily build one yourself (you may need a few extra packages with build tools for that):
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    Posted in *nix, how-to, Software | 3 Comments »