Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

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    Convenient design and debugging of regular expressions under Linux

    10th October 2009

    redet-supported languagesRegular expressions (regexps) are powerful indeed. But debugging non-trivial regexps is a burden even if you understand how regexps work, and remember most (if not all) regexp syntax.

    Miscellaneous tools exist to ease this task. This post was inspired by redet’s comparison of regexp helper tools – it could be sufficient to read only that, if you’re going to try the mentioned tools yourself. Otherwise, read on.
    Read the rest of this entry »

    Posted in *nix, Notepad, Programming, Software | No Comments »

    Google barcode day: make one for your site/blog

    7th October 2009

    bogdan.org.ua barcode Today Google celebrates the invention of the barcode.

    To help in this celebration, you can make a barcode with your site’s address (there is at least one more at barcodesinc, but at the moment of writing it is painfully slow).

    I find these parameters nearly optimal:

    • Type: Code 128-B
    • Styles: Draw value text
    • Size: 234×60 (half-banner size)
    • Xres: 1
    • Text font: 5
    • Value: bogdan.org.ua :)

    If you wish, you can also exactly replicate today’s Google logo – which says “Google”, as you could have guessed.

    You can place this barcode on your “souvenirs” – pens, cups, t-shirts. Many phones now have barcode scanners (e.g. Nokia E71), so put this code onto your namecard.

    Read on to learn about matrix barcodes.
    Read the rest of this entry »

    Posted in Links, Misc, Software, Web | 1 Comment »

    IOMMU: This costs you 64 MB of RAM

    30th September 2009

    If you have happened to observe similar messages in your dmesg:

    aperture

    [ 0.004000] Checking aperture…
    [ 0.004000] No AGP bridge found
    [ 0.004000] Node 0: aperture @ 20000000 size 32 MB
    [ 0.004000] Aperture pointing to e820 RAM. Ignoring.
    [ 0.004000] Your BIOS doesn’t leave a aperture memory hole
    [ 0.004000] Please enable the IOMMU option in the BIOS setup
    [ 0.004000] This costs you 64 MB of RAM
    [ 0.004000] Mapping aperture over 65536 KB of RAM @ 20000000

    and you are using AMD-based system w/o AGP video, then my advice is: just leave that as is, do not bother “improving”! Any tinkering with kernel boot options won’t do you any good, as the kernel has already done the best it could.

    Just a note: all those messages at the top of the post should only happen if you have 4 or more GiBs of RAM. If you have less than that, and do have those messages – my experience might be inappropriate for your case.

    Another note: my BIOS does not have any IOMMU settings (or “Memory hole remapping” settings), so I didn’t try that. You should check if your BIOS has IOMMU-related options first, just as kernel message suggests.

    Read on for details.
    Read the rest of this entry »

    Posted in *nix, how-to | No Comments »

    Screem HTML editor dies with ‘GSlice: assertion failed: sinfo->n_allocated > 0′

    20th August 2009

    Screem HTML/XML editor has tag-specific auto-complete, and is a nice editor for web-developers (at least as long as Quanta is not available for Debian testing).

    However, version 0.16.1 is very unstable, and dies with

    ***MEMORY-ERROR***: screem[5527]: GSlice: assertion failed: sinfo->n_allocated > 0

    As a workaround (initially suggested for the highly similar Firestarter crashes), try running screem with this command:

    G_SLICE=always-malloc screem

    Too bad last development version of Screem is dated March 2006.

    Posted in *nix, Software, XHTML/CSS | No Comments »

    DIYbio, biohackers, and Open Source Medicine

    25th July 2009

    DIYbio is

    an organization that aims to help make biology a worthwhile pursuit for citizen scientists, amateur biologists, and DIY biological engineers who value openness and safety.

    DIYbio also has a google group, where a wide range of questions – from bio-patents to DIY gel electrophoresis shopping list and model organisms is dicussed. There is also a DIYbio/biohacking FAQ.

    Today for me is the day of discoveries. I learned about the International Open Space Initiative (to give robotics enthusiasts a way to send their tele-controlled and/or intelligent robots to the Moon and Mars), about the DIYbio and biohackers, about OpenManufacturing (which doesn’t seem to have produced enough content to link to), Open Source Medicine (ouch!), BioBrick Assembly Kit (with an assembly manual), OpenWetWare, and a whole bunch of other awesome and inspiring community efforts, which do not belong here.

    Do you feel the wind of change?

    Posted in Links, Misc, Science, Society, Welfare | No Comments »

    DrupalCamp 2009 in Kyiv, Ukraine: August, 28-29, 2009

    23rd July 2009

    DrupalCamp Kyiv 2009 This will be the 2nd DrupalCamp in Kyiv. Please click the logo to visit the official web-site to learn more.

    Posted in Drupal, Kyiv, Misc | No Comments »

    SciVee.TV: YouTube for science

    15th July 2009

    SciVeeStumbled upon SciVee.TV – an open video upload service for research-related videos.

    I believe it is highly useful. Compare: watching an 8-10 minute video of someone’s research to reading their article on that same subject. For me, those 8-10 minutes make video option a clear winner.

    One of the envisioned uses of SciVee is to upload videos describing peer-reviewed published articles. This has two benefits for the reader: quickly getting acquainted with the essence of the article, and having that article as a complete reference for any questions not discussed in the video. For the author, this gives an additional bonus of higher visibility of his research.

    Personally, I’ve immediately found 3 videos pertinent to my topic. Of those, one was accompayning an article in PloS Biology, one was an hour-long lecture, and one was a poor quality audio recording of someone’s intended research.

    SciVee is young, and that is currently the largest drawback: not much could be found in a narrow research field. But I’m sure it will grow.

    Posted in Links, Science, Web | No Comments »