Autarchy of the Private Cave

“We only value what we loose”, they say.

Fortunately, I haven’t lost anything valuable, and don’t plan to. However, I did come to realize that false leads may and actually do obscure some simple happiness bits we fail to notice in our everyday life. Especially when that happiness comes from someone close, someone you literally got used to as to something inseparable from your life – but still fail to give value to.

Take care of your happiness and inner peace – do stop sometimes to thank and praise and value the oh-so-inseparable people around you.

Copyrights note: this is not my image, and I do not know who is the proper copyrights holder. It is used here for illustrative non-profit purposes, with a proper disclaimer. Contact me if you own the copyright and wish this image removed.

Sometimes there is a need to remove all the probesets, which have expression values below the minimal spike-in intensity on the Affymetrix microarray. The reasoning behind this procedure is simple: minimal-expression spike-ins represent the bottom margin of microarray sensitivity, and anything below that margin cannot be reliably quantified – which also means that both fold-change and p-value of expression variance will be unreliable for these probesets.

Here’s a simple R script to do just that. It is abundantly commented, and also contains an optional (commented out) fragment which allows the removal of more low-variance, low-intensity probesets.

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Recently, I have come across the Chandler project. Chandler is a sophisticated organizer, including tasks, calendar, appointments, invitations, and many more.

The project does provide a 64-bit package for Ubuntu 8.10 “Intrepid Ibex”, but it has a dependency on python-zope-interface – which in Debian testing is a virtual package, currently provided by python-zope.interface. That single dependency made my aptitude complain all the time, so I edited the .deb-file, renaming depends/python-zope-interface to depends/python-zope.interface (following nice and simple instructions). After that – no more aptitude complaints, and Chandler works fine.

Download the modified Chandler 1.0.3 Debian testing amd64 package (md5: 239071715977bea2eb75f3bb54491a02).

MathIsFun offers nicely illustrated pages on math, algebra, geometry and maybe more.

For example, there is a step-by-step instruction on calculating variance and standard deviation for a set of measured dog heights, with a final picture (below) illustrating one-sigma distance from the mean. Unfortunately, concepts of normal distribution and %% of data points within each sigma range are not discussed, but that might as well be too much for a nice explanation. There are also animations, like this mean machine. Overall, MathIsFun is a nice resource for younglings.

Just a quick note: upgrading Drupal using a patch file is a really efficient and fast method, especially because diff/patch files are available for different Drupal version combinations.

For about 2 weeks now, I am every day alerted of the suspicious behavior of some computer/server from the Google’s IP range:
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fail2ban has a php-url-fopen rule.

WordPress has a Global Translator plugin, which – among others – uses Google Translate service.

If someone uses Google Translate (e.g. using Global Translate’s mini-language-flags), and goes back to your blog – that someone might get banned by fail2ban (especially if you have set maxretry to 1), as the referrer will contain the php-URL-fopen attack signature. The bad thing is that you will not realize that until after you check one or several translations yourself, as a random site visitor experiencing the problem is highly unlikely to bother reporting this problem – especially when your blog’s Contact page is also inaccessible.

Clearly, Google Translate is not the only legitimate service which will trigger that rule.

Solution: The only solution I have found is to specify the whitelist regex for the php-URL-fopen rule.