Autarchy of the Private Cave

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    Archive for the 'Science' Category

    Need a computer science paper? Try SCIgen!

    9th December 2007

    Quite an entertaining story:
    SCIgen at wikipedia
    SCIgen tool
    SCIgen blog

    Finally, just a useful resource if you need a shiny name for your brand-new 2.0-beta project: anagram server.


    Posted in Humour, Links, Science | 1 Comment »

    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 »

    Practical Artificial Intelligence (AI)

    25th June 2007

    Googling for “practical artificial intelligence” gives only two (somewhat) relevant links:

    Looks like it isn’t widely acknowledged, that AI is, in fact, quite widely used. Though primarily in OCR, TTS, STT :), and NLP (including machine translation).


    Posted in Artificial Intelligence, Links, Programming, Science | 5 Comments »

    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 »

    HIV is not the cause of AIDS?

    24th June 2007

    I added a new video to my Conspiracy theory in gallery.

    I am an advocate of the official position: that is, HIV causes AIDS. In the movie description, I put my comments which dis-approve the point set and mentioned in that movie. I would strongly recommend that you stick to the official position in everything that is related to your health!

    And now, with all the warnings, you may want to see it (326 MiB):
    Read the rest of this entry »


    Posted in Misc, Science, Society | No 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 »

    Nonanticipatory: definition

    5th May 2007

    Nonanticipatory (system or predictor) is a (system or predictor) where the output y(t) at some specific instant t0 only depends on the input x(t) for values of t less than or equal to t0. Therefore these kinds of (systems or predictors) have outputs and internal states that depend only on the current and previous input values.

    In simpler words, nonanticipatory systems can “take into account” only past and present, and cannot base their behaviour/decisions on future expectations.

    Nonanticipatory systems are also known as causal systems.


    Posted in Artificial Intelligence, Notepad, Science | No Comments »