Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

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    Archive for August, 2006

    Contact me page using WP-ContactForm plugin

    26th August 2006

    Citing RyanConnect: “WP-ContactForm is a simple drop in way for users to get in touch with
    you. Its easy for any WordPress user to add this functionality to their
    site. Just upload two files and change a few options in your admin
    panel and you’re set.”

    I can only prove the citation. So now you can contact me, too :).


    Posted in WP PlugIns | No Comments »

    How to compare promoter structure of several genes

    16th August 2006

    I needed to find out common transcription factor (TF) binding sites (TFBS) in the structure of the promoters of interferon-regulated genes. I tried several different approaches – starting from the simplest sequence-sequence comparisons using BLAST, ClustalW alignments, and searching each of the promoters for transcription factor binding sites – to compare and find common.

    But the easiest way was to use Genomatix’s “Gene2Promoter” tool. With it, the whole procedure is extremely simple:
    Read the rest of this entry »


    Posted in Bioinformatics | No Comments »

    Selecting notebook model to suit your needs

    13th August 2006

    Here I will list parameters you will most probably consider when bying a new notebook. I hope this post will help you choose what you really need.

    Weight: ranges from under 2kg (1.6 for yet-fully-functional notebook) and up to 6 kg (DTR). Most of the notebooks you’ll encounter weigh around 2.5-3 kg. If you want less kilos – you’ll have to pay noticeable extra for portability.

    Screen size: ranges from approx. 12″ up to 20″ (is that still a ‘notebook’ with 20″, how do you think?). The most common screen sizes are 14.1-15.4 inches. As for any other LCD display, the most important features are the reaction time (pixel on/off times), brightness and contrast. Usually you will not get those details in notebook specs; so you have to see for yourself. I just should note that cheaper notebooks (those in 600-800$ range) usually come with noticeably worse displays than more expensive laptops.
    Read the rest of this entry »


    Posted in Hardware | 5 Comments »

    Which CMS is better

    3rd August 2006

    When you have a new web-project just about to be started, you frequently face the problem of the CMS selection – ‘Which CMS is better’? There’s a hundred and more various CMS out there. To name just a few – PHP-Nuke, PostNuke, Mambo, Joomla, Drupal, e107, XOOPS, Nucleus, Typo3, Xaraya, YACS! (visit for much more and try for yourself).

    If you gooogle this problem, you will get loads of forums discussing topics like ‘Mambo vs Drupal’, ‘PHP-Nuke vs PostNuke’ etc. But, to be sure, this ‘source’ of information is not likely to really help you choose. What you need is a good in-depth overview of the systems.
    Read the rest of this entry »


    Posted in CMS | 3 Comments »

    WordPress Related Entries

    2nd August 2006

    This is the plugin you may find useful if you want to keep visitors to your blog for more than just one-post-reading-time. This plugin will provide to the user entries, which have some common/similar words in the post/page title.

    Installation is as always easy. Most probably you will want to put these ‘related entries’ into yours ‘sidebar.php’ or ‘right-sidebar.php’ (if you have one), and your code may well look like this (I assume that in ‘Plugins’->’Related Posts Options’ you set the pre/post tags to ‘<li>’ and ‘</li>’):

    <?php if ( is_single() || is_page() ) { ?>
    <li><h2>Related entries</h2></li>
    <?php related_posts(); ?>
    <?php } ?>

    The block of PHP code above the actual insert determines whether blog visitor is on the post page or blog page – this way ‘related entries’ will not be shown in listing pages. If you want, you can leave only is_single() in place, for related entries to appear only in posts, and not in pages.

    Finally, plugin home is:

    If you want your visitors, arriving from the wrong or just outdated links to find what they might be looking for, it will be a good idea to check Related posts for your 404. That plugin adds an extra function related_posts_404(), which you should put into your ’404.php’ template file. Now, when someone gets to your 404 page, they might as well get a list of close hits from your blog, and stay longer.


    Posted in Notepad, WP PlugIns | No Comments »

    On the importance of early detecting your main interest and inclinations

    2nd August 2006

    This essay is primarily targeted at the teenagers up to 17 years old, but can also be helpful for up to 25 years (in the extreme cases). I did realize the things I am describing here quite late – only somewhere in the third year of my bachelor diploma studies. The following text is based on my own experience, and may not be appropriate for everyone.

    From my early childhood, I did not want to specialize. I just didn’t like the idea of doing only some limited portion of work, when there are so many interesting things to do. Becoming a specialist a priori seemed the way to boring life, because as a specialist you must do only the small subset of things related to you profession.

    Opposite to becoming specialized in some field, I imagined doing that and this for some short periods of time, and eventually becoming a ‘specialist in everything’ (which pretty much equals to a ‘specialist in nothing particular’).
    Read the rest of this entry »


    Posted in Life, Misc, Society | No Comments »