Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

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    GNAT GPL 2008 is now available

    12th June 2008

    We are pleased to announce the release of GNAT GPL 2008, the Ada Toolset for Academic users and FLOSS developers.

    It introduces hundreds of enhancements including:

    • Availability on the Windows .NET platform
    • Upgrade of the debugging engine
    • Improvement in robustness and efficiency for Ada 2005 features
    • Many new warnings & restrictions to help programmers detect errors earlier
    • Companion tools such as gprof, gcov, gnatcheck, gnatpp and gnatmetric are being enhanced to support a wider variety of needs, coding styles, and coding standards
    • Support for Pre/Post conditions

    GNAT GPL 2008 comes with version 4.2.1 of the GNAT Programming Studio IDE and GNATbench 2.1, the GNAT plug-in for Eclipse.

    It is available on the GNU Linux (32 and 64 bit), .NET, and Windows platforms.

    GNAT GPL 2008 can be downloaded from the “Download GNAT GPL Edition” section on https://libre.adacore.com/

    Posted in Ada, Programming | No Comments »

    Drupal theme development: where to start

    8th June 2008

    Simplest way to develop your custom Drupal theme is to start with some skeleton/wireframe theme.

    In this post, I’m briefly reviewing 4 themes (atck, blueprint, framework, and zen), made specifically to serve as theme developer’s starting point. All 4 are listed with their features (as per Drupal project page of each one), with my personal “impressions” (not based on actual use experience, yet). There’s also my choice and order of preference for the 4 candidates at the end.
    Read the rest of this entry »

    Posted in Drupal, Links, Notepad, Software, Web, XHTML/CSS | 8 Comments »

    Ad Unit Guidelines

    7th June 2008

    When either consulting on a new website design, or actually designing one, keep in mind Ad Unit Guidelines if the website is going to use advertising. The list is far not exhaustive, but sufficiently standard.

    Posted in Links, Notepad, Web, XHTML/CSS | No Comments »

    An alternative to shared hosting

    4th June 2008

    Personal communication resulted in a link to slicehost, who provide VDS/VPS services at prices as low as 20$/mo, which is comparable in price to good shared hosting plans, and is cheaper than Dedicated plans.

    I’m considering a move from shared hosting, and found Slicehost attractive. For 20$/mo, you get guaranteed 256MiB RAM, 10GiB disk and 100GiB traffic, which is sufficient to host several under-1k-per-day sites.

    The only thing which isn’t spoken aloud is the guaranteed CPU speed. Based on the numbers provided: 16GiB total RAM per server, quad-core CPU, and CPU quotas set equivalently to RAM quotas, I came to a conclusion that 20$-plan guarantees ~125MHz of CPU (take 16 GiB, multiply by 4 20$-plans – you get 64 “slices” – virtual servers; quad core CPUs were quoted as 8+GHz – I assume that’s the sum of the core frequencies, thus 8GHz divided by 64 slices gives as little as 125MHz guaranteed per slice).

    The better slice you buy – the more CPU is guaranteed, so for 1024-RAM slice you’d have a minimum of 500MHz of CPU.

    However, slicehost describes their CPU-clamping system as the one allowing “bursted” performance, if others aren’t actively using their CPU shares. So it must be much better than what I’m calculating here. And even if it’s not, then for some applications it’s better to have a 125MHz-clamp on CPU, than have a 20-seconds maximal CPU time limit.

    Still, I’m looking for reasonably-priced collocation services in Ukraine – e.g. those (currently unavailable) from Volia, starting at 40$/mo for the rented physical VIA C7-based server with enough traffic included.

    Update: I now have my own server collocated in Ukraine. This blog still lives on a shared hosting, but I’m considering the move to own server (where I have the biomed half-dead site and resource-hungry COTRASIF tool).

    Posted in Hardware, Links, Notepad, Web | No Comments »

    Self-making machine: RepRap

    4th June 2008

    A year, maybe two ago, I came across the news that someone’s constructing a “building printer”, in the sense that it is first filled with liquid concrete, and then – given the schematics of the building – “prints” concrete, producing almost-any-complexity architectural forms. Unfortunately, the names and links to that instance of object printing was lost and forgotten.

    However, I have just stumbled upon the news item about RepRap, which is claimed to be “self-reproducing”. Clearly, this isn’t true, but RepRap – replicating rapid prototyper – is able to produce (some?) of the components necessary to build another RepRap.

    I’d like to point out that

    “Think of RepRap as a China on your desktop.”

    by Chris DiBona, Open Source Programs Manager, Google Inc., is an offensive and unacceptable phrase, which shouldn’t have been put at the top of the quotes. I’d hack down that RepRap website for this single quotation, and would feel vende vindictive towards Chris, if I were Chinese. But that’s not a long time to wait to see China rising and this kind of jokes vanishing.

    That was a side note.

    Continuing on RepRap, I do find it’s uses intriguing. For the best of everybody, there’s a how-to build reprap page.

    First uses which came to my mind were… a new plastic cup, and a custom notebook/PC body/case, to put standard components into and enjoy the benefits of the perfect custom design :)

    Apart from simple things like cups and actually “fast prototyping” (which does depend on the precision of RepRap), there aren’t that much uses for the SOHO owner of RepRap. But as soon as some small-scale silicon-growing/cutting machines become available, that would definitely open up the whole new world of custom gadgeteering and home-brewed electronic wonders. Also, the level of global and local espionage activities will explode, and Big Brothers will grow like mushrooms after raining cats and dogs.

    Posted in Hardware, Links, Misc | No Comments »

    Xname is down again

    25th May 2008

    As mentioned here and here, XName is a popular DDoS target.

    Although I did enhance reliability of my other domains with a total of 3 secondaries, I forgot to do so with the most visited bogdan.org.ua. Thus, when yesterday bogdan.org.ua stopped resolving from ns0 and ns1 of XName, the site actually became unaccessible. Other XName-hosted domains, but with more secondaries, are resolving finely even 24 hours after the primary ns failure…

    Little research based on the list of free DNS services helped me find this comparison, and made me think this way:

    • zoneedit has 18 servers, but had very unfavourable user feedback from it’s users
    • everydns has 4 servers and very good user feedback
    • editdns has 3 servers, could be a backup
    • xname has only 2

    There is also freedns.afraid.org, but there was nothing substantial about this service I could find (except for the note that if you’re using one of their subdomains, it might not be visible to Google).

    To remedy the problem, yesterday I modified the domain record to contain two more NS. This seems to have helped now. I suspect that I’ll remove XName’s secondary NS from the record, and will replace it with some other secondary NS, and then add one more secondary to get a total of 5 independent NS for the domain.

    Update: according to my blog uptime monitor, total domain downtime exceeds 33 hours. Problems started yesterday with two short downtimes (33 and 38 minutes), then domain name went down for 32 hours. Now domain is up, but that could be only because of adding more non-XName secondaries.

    Update 2:

    XName infrastructure was under heavy attack since friday 8PM (GMT+2).
    Until sunday 1PM, despite efforts of our different transit providers, www , ns0, and our internal mail server were unreachable. ns1 was reachable, but not very responsive (about 30% of DNS requests were answered). ns2 was unaffected.
    From Sunday 1PM to monday 3AM, ns0 was reachable with a responsiveness of about 50%. ns1 was fully responsive, as ns2. www and internal mail were still heavily affected.

    Posted in Misc | No Comments »

    Sirtuins, aging, and disease: longevity webinar

    22nd May 2008

    BiosymposiaFairly recently I did enjoy the webinar by Biosymposia. Dr. Leonard Guarente made a presentation first, and then there was a Q&A section.

    After taking WIPO‘s distant learning course in IP, I started paying more attention to distant learning techniques. In the long run, I assume that more and more structured knowledge (whole courses and learning programs) will be made available to the public for free.

    WIPO’s IP course was as a matter of fact a collection of textual and audio materials presented in a specific order, and interspersed with self-assessment questions to control learning progress, with a final exam at the end. Acknowledging the difference between the distant learning program and a webinar, Longevity webinar felt more like a tele-auditorium, with live-seeming (though actually pre-recorded) streaming presentation and video (side-by-side) by Dr. Leonard Guarente. It was just like attending a lecture :). The Q&A felt more like a TV show, in that listeners could write their questions during and a bit after the presentation, for the webinar hostess to ask Dr. Guarente those questions.

    Longevity is a question which bothers most of the people at some point in their lives. Amrita, the elixir of life, is one of the dominant topics of the Medieval Ages (alongside the any_metal-2-gold transformation idea).
    Read the rest of this entry »

    Posted in Science | No Comments »