Autarchy of the Private Cave

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    Archive for the 'Bioinformatics' Category

    Bioinformatics is a general term which refers to using computers and computational/math methods in applications to biology.

    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:

    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:

    spoken-only, informal short form of high-throughputomics

    Putomics is also conveniently similar to “computation” (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: Accessed: 2008-07-16. (Archived by WebCite® at


    Posted in Bioinformatics, Science | 1 Comment »

    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.


    Posted in Bioinformatics, Misc, 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 :)


    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.


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

    Using Cytoscape from behind an HTTP proxy which requires authentication (authorization)

    14th September 2007

    Cytoscape 2.5.1 supports proxies, including HTTP proxies, but there is no support for HTTP proxies requiring authentication/authorization. It’s easy to use Cytoscape in the authentication-requiring proxy scenario; below is one possible method.

    Note, that exactly the same method can be used to allow any software, which supports proxies but not proxies with authentication, to be able to access the internet.
    Read the rest of this entry »


    Posted in Bioinformatics, Notepad, Science, Software | 1 Comment »

    GeneDoc: DNA editing, alignment, analyser and shading software

    25th June 2007

    Full Featured Multiple Sequence Alignment Editor, Analyser and Shading Utility for Windows.

    Small and convenient. Can do sequence alignments (I recommend to limit the length to 2kb for alignments).

    Latest version I found: updated July, 2001, GeneDoc version # 2.6.02.

    Drawback: windows only (but has GNU-licence sources).


    Posted in Bioinformatics, Science, Software | 2 Comments »

    Choosing cell modelling software: Virtual Cell, Cytoscape, CellDesigner, E-Cell

    10th May 2007

    I’m planning to reconstruct (based on literature and some original research) a specific cellular regulatory network. For this I decided to use some specialized biological modelling software. The requirements I had were pretty simple:

    • must have SBML support. SBML appears de-facto standard for biological model notation;
    • must be fairly frequently updated;
    • should be feature-packed and easy to use. However, this requirement can only be checked after some use, and I was pre-selecting, not reviewing.

    Software put into the title of the post was found to be the most mature and interesting from the usage perspective. However, there are more than those mentioned software tools reviewed. Reviews are based primarily on the information from official websites and documentation; some tools (like VirtualCell) are reviewed somewhat more thoroughly.
    Read the rest of this entry »


    Posted in Bioinformatics, Science, Software | 2 Comments »