Autarchy of the Private Cave

It has been over 18 months, since I started this post. As a result, it has gone through some (though not really extensive) internal reviews and modifications. I have no doubts there will be more comebacks and reviews and edits to this topic.

On Sunday, the 10th of December, 2006, the grandmother of my wife died - almost three days after she had a cardiac infarction.

She was a kind, calm, warm-hearted old woman. She was just a little bit over 79 years old.

What did she leave behind?

She had brought up and educated her children and grandchildren to be People. None of her offspring went the way of crimes, or even disrespect towards others. The likes of her children could form a quasi-ideal ethical society, with no exaggeration - given she would be able to teach and bring up all of them.

She served the society well, working as a psychotherapist at a hospital. She helped people regain peace of mind, she cured mental diseases in the best way she could. She happened to meet her old-time patients in the street from time to time, and they expressed gratitude for her help.

She left a memory of a good, reliable, helpful person. This memory lives with all the people who were lucky to know her.

———

Death is the final evaluation for the person’s deeds during life.

What are the measures for this evaluation? What is really important? What matters after death?

First, it appeared to me that human memories are what matters. Memories of good deeds, memories of helping others, memories of being valuable for the society and mankind. “To put the mark on history” and “to be placed on record” are the expressions of the desire to have people remember someone even after death.
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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/

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.
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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.

100 legal sources for free stock images (via maxon’s delicious bookmark)

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.

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.

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.

Fairly 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).
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The title of this post is my current - “forthcome”, as in “done” - field of interest.

First article on topic: Fast network component analysis (FastNCA) for gene regulatory network reconstruction from microarray data.

Another one, on combining different high-throughput data sources to get higher-quality results: Uncovering signal transduction networks from high-throughput data by integer linear programming.

I’m especially interested in time-series network reconstruction algorithms. If you have a good advice to share with a newcomer to the networks field - don’t hesitate

With this post, I’m finally announcing the opening of the (mostly) functional COTRASIF web-tool, created for the genome-wide identification of promoter regulatory sequences (transcription factor binding sits, TFBS). You can learn more from the About and Help pages. For an example of use, see the Supplement page (article is currently being prepared; as soon as it’s ready, I’ll make it available).

If you are interested - have a look at the News page, where there is information on joining COTRASIF Google group. For non-public enquiries, please use my contact page.

Note: the problem of identifying eukaryotic transcription factor binding sites stays acute for many years in a row - see e.g. the most recent Eukaryotic transcription factor binding sites - modelling and integrative search methods.

Note, that under Gnome I only had to use a single system-wide utility to bind volume buttons to volume control. Under KDE things were a tad tougher.

First, you may want to look for kmilo (if you don’t have it yet). It has several plugins e.g. for ThinkPad and Vaio laptops, as well as “generic” plugin. I didn’t try this solution, though.

If you need more than kmilo can offer: keyTouch could help. keyTouch should be good also for non-laptop multimedia keyboards. However, this also wasn’t the solution I used.

If you want to know how to map your special keys to functions yourself - then read on.
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Some things to be aware of when enhancing Drupal site with FLV video playing/conversion features.

• Setup wizard for the free JW FLV Media Player (and the JW FLV Media Player itself)
• Flash Video in Drupal 5: A complete multimedia tutorial to the flashvideo module
• actual flashvideo module page on drupal.org

If you had some programming experience - read it here. Otherwise ignore, it’s targeted for a narrow group.

I’m providing regularly updated compiled linux and freebsd ffmpeg binaries, and also described how to use ffmpeg on shared hostings if not all the required libraries (like libmp3lame) are present. However, the solution recommended might not “fit all”, so here is another one - simpler and even more portable/universal than setting LD_LIBRARY_PATH.
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NicEdit - lightweight inline configurable rich-text editor for the web. Can fit where both FCKEditor and TinyMCE are too clunky and monstrous.

As an update to WordPress anti-spam plugins, I highly recommend Spam Karma 2. For a time, it seems to be the ultimate protection. I turned off all the other anti-spam plugins (including Aksimet), and everything’s just perfect! SK2 gathers up to a thousand spam comments/trackbacks during a single week on this blog, and I never had a complaint from blog visitors on their inability to add a comment (though some did have to fill in captcha to post a comment with links).

And SK2 still works under WP 2.5! (SK 2.3 was released to support WP 2.1)

Kudos to Dave!

It would be a pity if this excellent plugin is abandoned and stops functioning in one of the upcoming WP releases.

This post provides several links which would be useful for the beginning Drupal developers, or developers deciding which CMS to use as the base for their next project. Also, strengths of Drupal are highlighted.

Intensively working with Drupal during the past two weeks, I find it to be an excellent tool, and also much more than a YACMS.

Now I think that Drupal is also a framework - providing invisible to developer caching, session handling, access control, theming, localization, and more. The minimal effort required to extend already huge Drupal functionality is to write your own module - and, if done right, your module will immediately benefit from all the bonuses Drupal provides.

But Drupal also really shines as a CMS! You can start with a free design theme, and without any PHP knowledge have your custom portal built within a week - with your own hands, if you desire! (Note: “within a week” is true, but only if you already know what exactly you should be doing; learning time is short, but it’s not within that same week.)

What makes Drupal so powerful? I’d say that beautiful core and numerous modules.

What Drupal has to offer?
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4 seasons (23 episodes) of highly enjoyable British comedy. Excellent playing by Stephen Fry (Jeeves) and Hugh Laurie (Bertie Wooster). Good stories by P.G. Wodehouse. Highly recommended!

P.S. “Jeeves and Wooster” differs strongly from the IT Crowd I had written about before. IT crowd is an every-day-situational-comedy, while J&W is genius-serving-the-idiot, with most laughs at Wooster’s plans and deeds.

If taken out of [Ani]Matrix context, and filtered through internal “over-exaggeration removal”, then this exact 9-minute animation (episode 2 of 9) is quite coherent with soon-possible problem to face humans.

Yes, I do believe the creation of sentient machines is within perceivable future. And yes, I do think that the problems of “robot personality” will be acute.

In support of my view - cloning is an unresolved ethical problem, which also grows into legal and social problems in the case of human cloning. When even the possibility of having two genetically identical humans arises, this leads to debates and disagreements (to clone or not to clone?). What could be said about a machine claiming it’s right for life?

Claiming other human rights?

Racism and xenophobia are characteristic for some countries even nowadays, and it can be even said that there is no country where the number of xenophobic or racist citizens is equal to zero. And that’s human-human relations problem.

In other words, I did enjoy The Second Renaissance, Part I (except for the clearly contradictional last two minutes of it).

Overall The Animatrix is good.

And the message I was trying to express is that mankind better be prepared to live side-by-side with machines - develop some realistic co-existence model. SciFi writes will help here . Just let’s avoid the fake, insincere model tried in The Animatrix: Matriculated (episode 9, the last one).