Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

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    Archive for October, 2006

    Ring of the Nibelungs (2004)

    31st October 2006

    I classified this movie as an “epic fairy tale” from the very first seconds. I even suspected that main events might be happening “nowadays”, but fortunately I had to throw away both this assumption and the “fairy tale” from the definition. Despite some drawbacks, the movie is definitely good.
    Read the rest of this entry »


    Posted in Movies | No Comments »

    List of free DNS services

    28th October 2006

    Information taken from:

    1.; 5 names; A, MX, NS; mail forwarding, web forwarding
    2.; 20 names; A, MX, NS; web forwarding, dynamic domains
    3.; 3 names; A, MX, NS; web forwarding, mail forwarding, backup MX
    4.; unlimited names; A, MX; web forwarding, paid mail forwarding
    5.; no limit; A, MX, NS (I keep several domains there; quite good as for a free service)
    6. (UA-IX only); unlimited names; A, MX, NS; primary only
    7.; unlimited names; secondary only
    8.; unlimited names; secondary only
    9. (suggested in comments; looks promising – I now have one domain there)

    Posted in Links, Web | 8 Comments »

    Gliwice stay is getting pleasant

    27th October 2006

    Since the 16th of October I am on bioinformatics training in Gliwice, Poland, at the Comprehensive Cancer Centre Maria Sklodowska-Curie Memorial Institute, Gliwice branch. I am training in microarrays data analysis, with focus on R + BioConductor usage for analysis.

    I am already more-or-less comfortable with Polish – though understanding is still a much easier task than expressing own thoughts, thus most commonly I address colleagues in English, and perceive responses in Polish :)

    Here there is an excellent lunch location – Bar U Piotra (“At the Peter’s”). For 6.5 PLN (roughly 2.2 USD or 10.4 UAH) you get soup, meat with some garnish, and – not always – some salad. However, 6.5 PLN is a special price, available only if you buy at least 7 (or 10?) meals ahead. Food is simple but tastes like home-cooked, and helpings size is well sufficient for me – which means “more than sufficient” for an average person.

    I still cannot get used to other people coming to work at 8 a.m., but the idea of leaving at 4 p.m. adds a kernel of good sense to the early-rising idea.

    Generally, Gliwice is not a bad place to stay, at least for up to 2-3 months. Autumn here is beautiful – see my gallery for some samples of what is looks like here at the end of October.


    Posted in Notepad | No Comments » down: largest DDoS they ever had

    27th October 2006

    Yesterday (October, 26, 2006) I found that the nameservers for my blog (, are not responding.
    Today the following message appeared on

    XName currently DOWN

    XName is temporarily closed since 08:00PM CEST yesterday evening. We were experiencing the largest DDoS we ever had on both ns0 and ns1 IP addresses, forcing our upstream providers to cut off XName servers in order to preserve their other customers.

    We’re working hard in order to have at least one DNS server answering ASAP, and we already negotiated with a premium transit provider to host one of our DNS servers shortly.

    Currently my blog is back online, available by its name, and not by IP.

    But I am looking for other free NS-record hosting servers (xname-like). I would appreciate if people comment with their experience on managing this problem. I temporarily allowed comments for anyone without registering (but with moderation).

    Meanwhile there are two places for Russian speaking folks to register secondary DNS:, Soon I’ll register secondaries there, leaving primary on xname, which was a stable service up until yesterday’s DDoS attack they had.


    Update: Sat. 28. 12:00 – ns0 is up and running, serving all zones correctly

    update 2:

    Update: Mon. 30. 18:00 CEST – ns1 is up and running, reachable from Association Kazar’s network peers (ns1 IP is still blacklisted on upstream transits backbones)

    update 3: is back online, fully functional.

    update 4:
    See the List of free DNS services.
    I’m staying with xname, though did add a couple of secondaries for better fault protection.

    update 5:
    See the comments to this post for new technical information about the DDoS attack, including IP addresses of the attackers and some packet statistics. Thanks Boris for the new information.

    new attack. On the 14th of January, 2007, I got the following letter from XName team:

    DDoS attack on both DNS servers
    Our both DNS servers IPs – and – are under heavy DDoS since 5PM CEST today.
    Consequently, both of them are unreachable – except very intermittently.
    We’re working with our transit providers to solve this ASAP.

    Next day (2007-01-15), XName was up and running:

    Resuming normal operations
    Since 2AM CEST both ns0 and ns1 were answering correctly – many thanx to
    our transit providers for their help on this issue.

    the total outage of our service was 7 hours…

    one more attack on the 1st of October 2007 (started on the 30th of September):

    both ns0 and ns1 DNS servers are under DDoS attack since 10PM (gmt+2) yesterday (September, 30th), ns0 is unreachable since 6AM this morning (October, 1st: total saturation of our uplink).
    ns1 is fine but was off 3 hours today (October, 1st), between 2PM and 5PM.

    I wonder what kind of a mentally sick person would attack the free service…

    For any further X-Name attack updates and history, please refer to the comments below.


    Posted in Notepad, Web | 11 Comments »

    Homology and similarity

    23rd October 2006

    In bioinformatics and biology, the “homology” term is used quite often, and quite often it is mis-used. So what are “homology” and “similarity”, and how can one use these terms correctly?
    Read the rest of this entry »


    Posted in Bioinformatics, Science | No Comments »

    Flag as a symbol of language – usability or convenience?

    23rd October 2006

    Probably a month ago I came across this forum thread (which, in turn, references original article), where the idea of using a country flag on the web-site to represent one of the site’s language versions is discussed in terms of ‘stupidity’ and ‘insult’. Fortunately, in the forum thread, there are also sound comments, which do show the inconsistency of the idea that flags must not be used as language shortcuts.

    Adding my five cents, I should note the following:
    Read the rest of this entry »


    Posted in Society, Web | 4 Comments »

    HTTP caching: request and response headers

    18th October 2006

    In this post: some caching-related HTTP request and response headers discussed.

    Modern websites are “dynamic” by nature – content you get depends on a number of variables and conditions. The simplest example – being a “guest” or a “registered” user of some forum; in both cases you get content generated by the same script/program, but it differs because of your “registered” state.

    Another example – web-photogallery. By design, it is wise to always keep the original photo (the largest and presumably of the highest quality). When gallery visitor’s browser requests any smaller version of the photo – we can dynamically resize (often downsize) the original and feed the resulting photo to the browser. This scheme works OK until your gallery gets more and more visitors – CPU load climbs up and increases wait time when accessing your gallery. Evidently, caching is needed.
    Read the rest of this entry »


    Posted in PHP, Programming, Web | 1 Comment »