Autarchy of the Private Cave

Probably you already know and use it – but I started using it just today.
As expected, this plugin is amazing!

It’s main concept is to allow WordPress administrator to use GUI in the admin panel to place new plugins in the arbitrary locations in sidebars (and not only sidebars, but that requires a bit more work), so you don’t have to modify your sidebar.php with each new plugin installed.

The actual power of Sidebar Widgets (aka WordPress widgets) is not restrained by the sidebar – the “readme” file of the plugin distribution archive provides hints and ideas on how this plugin could be used. I suspect that Widgets might become the base for the further development of many other plugins and WordPress core as well.

So hurry to the WordPress Widgets homepage, grab one, and install as usual. You might need to modify your theme, if it doesn’t support Widgets, but this process is well documented in the “readme” and should be fast and easy to complete.

You will surely enjoy this new experience, if you hadn’t yet!

I am doing some simple statistics now, and had to review some basic concepts like standard deviation.
As a note to myself and anyone interested, here it stays.

The mean is just a sum of all your numerical observations, divided by the number of observations. E.g., if you have measured how tall your 5 children are, and got the values 1.42, 1.56, 1.05, 1.89, 1.92, the “mean height” of your children will be x = (1.42 + 1.56 + 1.05 + 1.89 + 1.92) / 5, x = 7.84 / 5 = 1.568 (all values in metres).

The mean itself doesn’t tell you much, however. If you had this 1.568 mean available, you wouldn’t know even the range of heights.

The standard deviation helps with this. First of all, it is measured in the same units as initial data – i.e. metres in our example. Second, it gives you an idea of how strongly do the measured values differ in your sample – the bigger the deviation, the longer is the value range measured in the sample.
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Sitting late in the night in front of my PC, and doing something boring, I stumbled upon the albinoblacksheep website. The two things I read were Cyber Sex (with a kind of follow-up) and probably old but anyway funny Automation: A Way of the Past – I liked that, so here’re the links .
And if you’re Star Wars fan – you MUST watch ASCII Star Wars, for the Force to stay with you

I didn’t read anything else there, but looks like a funny resource.

Hope you will enjoy

As I previously mentioned, in converting PFM to PWM single variable – [prior] background nucleotide frequency – was ambiguous to me. From other articles I noticed that it is usually set to 0.25 (1/4 – because there 4 nucleotides, thus in “perfectly random” sequence they would appear in 25% of cases each). In that post, I also thought of using “real” background frequency of nucleotides, calculated from the sequence, to which the matrix is to be applied.

I wrote a program to search all the 1000-basepair upstream sequences from all human, rat and mouse genes, present in Ensembl database release 40 (assuming those 1kb upstreams to be “promoters” of genes). For each promoter, only the single best score was returned. Then I draw a graph of the distribution of the number of promoters (y-axis) depending on the best match scores (x-axis). I did the search twice – one with p(b) = 0.25, and one with p(b) set to calculated values of A/C/G/T content in each promoter.
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In the course of my current research, I was dealing with the TFBS (Transcription Factor Binding Sites) search. To perfrom the search, one needs position weight matrix (PWM) for each TFBS. When you refer to the TRANSFAC database of transcription factors (and matrices), you will get position frequency matrix (PFM), and will need to convert PFM into PWM.

I did find a couple of conversion formulas, but that was quite an effort to figure out which one is correct – I had seen two different formula variations. Here I will share what I had found.
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Post last updated: April 18, 2010.

Now there is a Drupal 6.x module available. It is in no way related to the migrate script(s) below.

The newest script version migrates from PHP-Nuke 6.5 to Drupal 5.x.
Download the latest version of the migration script.

In 2002 I set up a PHPNuke-6.0 – based portal. Eventually it died due to the lack of time investments and support from collaborators. Now, when time came to revive the project, I made a search and decided to use Drupal as a base CMS for the portal.
In order to migrate userbase from an old portal to the new Drupal-powered one, and following the topic at drupal.org, I found a script and its modification.
I used it to migrate only users, and made some cosmetic changes:

• added options for custom phpnuke table prefixes
• default user name is now = uname (login), not ‘temp_name’, as before
• I replaced hard-coded links to ‘migrate.php’ with links to $_SERVER['PHP_SELF'], so that if you rename the script you don’t have any problems with that
• now forum topics should not be promoted to the main page (changed 1 to 0 as hinted by Alexis)

Finally, I would like to thank both Karthik Kumar for the original script and Alexis Bellido for the 6.0_to_4.7 modification.
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Sometimes, writing automatic HTML forms processors, you need to post several values with the same name of the form field, e.g.:
collection_gene = str_chrom_name
collection_gene = gene_stable_id

This is against the RFC on form fields design and submitting, but this approach is used – for example, by Ensembl. I spent some time to figure out how to make HTTP_Client and HTTP_Request submit multiple ‘name-value’ pairs instead of one (the latest defined, which overrides the previous). The solution is extremely simple:
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