Autarchy of the Private Cave

When right-clicking many links in FF3/IW3, it quite often happens so that a random action is performed instead of opening the context menu (bug report).

One of the solutions (suggested by Andre Pirard) is to slow-right-click, that is to hold the right mouse button down until the menu actually appears, then - and only then - release it. Or, you can even slow-right-click, move the pointer over the desired menu item, and then release - that will perform the desired action in a single long right click (instead of more common single right click with a following single left click.)

This bug/behaviour is otherwise unsolved.

For some reason, my IW 3 is now starting in Offline mode each time, despite my attempts to remove that checkbox every time.

Little research had shown that the simplest solution is to disable FireFox’s/IceWeasel’s feature to auto-detect if Internet connection is available: go to about:config, find browser.offline-apps.notify and set it to false. After this, FireFox/IceWeasel 3 will no longer try to check if you have Internet connection.

However, this is not a good solution, because auto-detection generally improves user experience (e.g. by automatically using cached page versions for tabs open at startup). The actual reason (in many cases) is the network detection by the NetworkManager - it reports “no connection” although connection is present (bug report).

The simple solution is to remove NetworkManager.

Another simple solution (without removing NetworkManager) is to disallow NetworkManager to notify other desktop application about the presence of the internet connection (slightly edited):

Open the terminal/konsole (Applications–>Accessories—>Terminal), and type gksudo gedit /etc/dbus-1/system.d/NetworkManager.conf (note: path might differ for your Linux distribution - try locate NetworkManager.conf). Then replace all lines

< allow send_interface="org.freedesktop.NetworkManager"/ >
with
< deny send_interface="org.freedesktop.NetworkManager"/ >

Save the changes and either reboot or just stop/kill/restart the running instance of NetworkManager. This change will stop NetworkManager from notifying FireFox/IceWeasel and other desktop applications about the presence/absence of internet connection - and FireFox will no longer start in Offline mode.

(Thanks Nikitas350 from Ubuntu forums for this fix.)

Personally, I did what Nikitas350 suggested, and also removed the networkmanager-gnome package - I’m still able to add networkmanager-kde monitor to Gnome panel, if I want to (and for me, networkmanager-kde works properly).

The even better solution would be to make NetworkManager detect the availability of connection properly. However, I did not dig deep enough to find how to do that - comments and better solutions are welcome.

One of the more complicated solutions (and still not a perfect one) was also found at Ubuntu forums (slightly edited for contextual clarity):

I am using USB modem to connect to internet and the Offline mode issue was also bothering me after upgrading to Firefox 3.

The solution I have found was: disable Network Applet from System -> Preferences -> Sessions, and add the following lines to the file “/etc/network/interfaces”:

auto eth0
iface eth0 inet dhcp

Thus, I guess, Firefox believes that eth0 (i.e. ethernet card) is active, although Internet connection is established via ppp0 (i.e. USB modem).

Just made it up for convenience, stimulated by reading workshop descriptions for the upcoming ICSB 2008 in Gothenburg, Sweden.

Here is formal definition:

high-throughputomics

the term is used to denote/mention any or all of the modern high-throughput techniques (in all of, but not limited to: genomics, transcriptomics, proteomics, …), together with derived/applicable data-processing approaches. All the “networks” things also conveniently fall into the high-throughputomics definition

As this is a general term, it might be even suitable as a conference title (but NOT for ICSB, which I’m waiting for eagerly).

For a shorter and informal (spoken-only) term, putomics can be used:

putomics

spoken-only, informal short form of high-throughputomics

Putomics is also conveniently similar to “computation” (computomics):

computomics

application of computer hardware and software for the analysis of massive amounts of data, obtained using high-throughput methods; this is a research sub-field of high-throughputomics

P.S.
For easier citing:

Tokovenko, Bogdan. New bioinformatics term: high-throughputomics. 2008-07-16. URL:http://bogdan.org.ua/2008/07/16/new-bioinformatics-term-high-throughputomics.html. Accessed: 2008-07-16. (Archived by WebCite® at http://www.webcitation.org/5ZMD9DITU)

http://debian.org.ua/ and ftp://debian.org.ua/

What is on offer (mirrors):

• backports.org
• cygwin
• deb.opera.com
• debian - stable, testing, sid
• debian-archive (starting from 1.1!)
• debian-multimedia
• installation media (CDs/DVDs)
• debian-security
• even debian-volatile is here!

All this goodness is only 3 hops away from my DSL modem…. (ISP UkrTelecom)

Gone editing /etc/apt/sources.list

P.S. For non-ukrainian IPs, access might be slow/bandwidth-limited; for Ukrainian IPs, speed might be up to 100MBit/sec.

Update: some time after publishing this post, debian.org.ua was down for some reason. When it was up, it was serving me packages with a mere 3 kb/sec . I found that ftp2.debian.org.ua mirror is faster at the moment.

IEs4Linux provides a convenient package of Internet Explorer 5.0, 5.5, 6.0, and (partially supported) 7.0 for Linux.

It installed and runs fine under Debian Etch:

However, as you could notice from the screenshot above, CPU use is almost 100% while IE6Linux is running. It is better illustrated by the next screen:

I didn’t yet bother finding out what’s wrong, but that must have some kind of a fix, as running at 100% CPU on a laptop is … hot.

Debian HOW-TO: CPU power management / frequency scaling

… was held on June 22-28, 2008, in Akademgorodok (Novosibirsk), Russia. It was the sixth conference held.

The International Conference on Bioinformatics of Genome Regulation and Structure is the bi-annual event. It features several bioinformatics sections, which IMO cover most of bioinformatics sub-fields.

The Sixth conference, BGRS-2008, was well-organized and had something to offer to everyone. By far the largest section was Genomics and Transcriptomics (at least if judging by the abstracts book and by the posters presented; talks given were distributed more equally between sections). As I did some work in genomics (namely, our COTRASIF tool), I had quite a load of info to digest, and many new potentially fruitful contacts to establish (which I did quite good).

The second section on my scale of priorities was “COMPUTER ANALYSIS AND IMAGE RECOGNITION IN SYSTEMS BIOLOGY”, which had several interesting researches presented in the field of spatial/developmental modelling. There was a very good talk on model reduction (with an actual example) for the purposes of both comparing different models and decreasing the model complexity without sacrificing model-predicted outcomes.

As for the other sections, I didn’t find them interesting enough. Fortunately, there were social program events scheduled for every day, so I visited the Novosibirsk zoo and the Archaeological museum. I did not do as many pictures as I usually do at conferences/schools, because there were two photographers at the conference, and their photos can be freely seen here and here.

Most of the conference participants could speak Russian (I’d estimate the group of Russian-speaking participants at 90% of the number of participants), even though they were coming from e.g. Singapore or USA. But the official conference language was English, and the 10% of non-speakers were far not underprivileged, which goes well with the international status of the conference.

After the conference, there was a BGRS-2008 summer school. As I stayed for some extra days, I managed to attend up to 90% of the school’s events (including the guided tour to Novosibirsk ). For me, summer school was somewhat less useful than the conference, but nevertheless such presentations as on Petri nets and about SABIO-RK/Sycamore were informative and will be used in my future work.

There were 3 prizes for the student presentations; winners are at the end of the page.

Certificates were given after successful school completion. As I wasn’t registered, I can now only print out the empty certificate, which is to signify that I did not attend the last day of the school and thus was disqualified .

Just found that there are also some photos from the organizers.

There was also a football (soccer) game between the ICG team and the school participants team. I’m a fan of neither watching nor playing football, so I skipped this event altogether.

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