Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

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    Archive for July, 2009

    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 »

    Bad memory handling and server stability

    13th July 2009

    The two graphs below (clickable) are for CPU and RAM use during a period of a program going wild between 23:17 and 23:41 (24+ minutes of server’s downtime). The program was run non-root, it just consumed all the memory it could. It was killed by kernel, so the server started responding without any interventions – which were hard to perform, because none of the services (including ssh) were responding during downtime.

    If you happen to be developing a C/C++ program – do use mtrace and valgrind, those are huge helpers against the problems akin to that shown on the graphs.


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

    Harness the power of rsync

    6th July 2009

    I have read manpages of rsync today.
    I feel enlightened.

    I had a dream of rsync being one of the legendary nix Super-Cows.

    A tiny perversive part of self created a PDF version of rsync manpages (43 pages).

    It seems that Super-Cows can damage the brain, when stared at too intensely.


    Posted in *nix | 4 Comments »