Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    Archive for July, 2008

    Iceweasel/Firefox 3: how to work-around random/erratic right-click action

    19th July 2008

    Update: as of FireFox/IceWeasel 3.0.14, this bug appears to be fixed.

    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 work-arounds (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.)

    Alternative workaround (found at the bug report page): install the mouse gestures add-on, and restart firefox. Tested: works for me.

    This bug/behaviour is otherwise unsolved.

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    Posted in Misc, Web | 8 Comments »

    Gnome, NetworkManager, and FireFox/IceWeasel 3 starting in Offline mode (also: Pidgin Waiting for network connection)

    19th July 2008

    For some reason, my IW 3 is now starting in Offline mode each time, despite my attempts to remove that checkbox every time. Also, Pidgin says “Waiting for network connection” in the status drop-down.

    Update: as suggested by Donny Kurnia (based on the recent post by Hobgoblin), the simplest and the most correct way to fix the problem for FireFox/IceWeasel is to go to about:config and set toolkit.networkmanager.disable to true.

    The simplest workaround for Pidgin is to open Accounts -> Manage, then remove and then set again the checkbox near the account you wish to get connected. This has to be done every time you start pidgin :( .

    Below you will find other (worse and obsolete – for FireFox/IceWeasel, but good for Pidgin) solutions.
    Read the rest of this entry »

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    Posted in *nix, Web | 19 Comments »

    New bioinformatics term: (high-) throughputomics

    16th July 2008

    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)

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    Posted in Bioinformatics, Science | 1 Comment »

    debian.org.ua: universal Ukrainian Debian mirror

    15th July 2008

    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.

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    Posted in *nix, Links | No Comments »

    Internet Explorer 6 for Linux

    13th July 2008

    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:

    IE6 under Linux screenshot

    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:

    IE6 under Linux: high CPU use

    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.

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    Posted in *nix, Links | No Comments »

    Concise guide to CPU frequency scaling in Linux

    11th July 2008

    Debian HOW-TO: CPU power management / frequency scaling

    Also as a PDF: Debian how-to: CPU frequency scaling and power management.

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    Posted in *nix, how-to, Links | No Comments »

    BGRS-2008 conference in Novosibirsk, Russia

    10th July 2008

    International Conference on Bioinformatics of Genome Regulation and Structure logo… 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.

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    Posted in Bioinformatics, Misc, Science | No Comments »