Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    Archive for May, 2008

    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.

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    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 »

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    Posted in Science | No Comments »

    Gene regulatory network reconstruction from microarray data

    20th May 2008

    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 :)

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    Posted in Bioinformatics, Links, Science | No Comments »

    COTRASIF: conservation-aided transcription factor binding site finder

    20th May 2008

    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.

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    Posted in Bioinformatics, Links, Science, Software, Web | 6 Comments »

    Enabling special buttons (keys) on laptops under Linux

    8th May 2008

    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.
    Read the rest of this entry »

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    Posted in *nix, Links | 4 Comments »

    Flash video in Drupal (links)

    6th May 2008

    Some things to be aware of when enhancing Drupal site with FLV video playing/conversion features.

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    Posted in CMS, Drupal, Links, Notepad, Software, Web | No Comments »