Autarchy of the Private Cave

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    The 9th ICSB-2008 in Gothenburg, Sweden

    12th September 2008

    It has been quite a time since my last serious and long post. On the one hand, summer is vacations time – so I’ve been to one in Turkey; on the other hand – the long-awaited ICSB-2008 conference finally took place in Gothenburg, Sweden, on August 23-27 (or 22-28, counting in tutorials and workshops).

    Update: it appears that conference domain name http://www.icsb-2008.org/ was not maintained after the conference, so I had to remove all the links to that website (which now appears to be owned by someone not related to ICSB). However, there seems to be a mirror of ICSB-2008 at http://www.gmm.gu.se/groups/icsb08test/.

    Synopsis: in this post I present a personal-perspective report on the 9th ICSB (with a condensed ICSB-2008 photo-report in my gallery).

    Read the rest of this entry »

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    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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    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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