Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    Good hands-on explanation of differences between Spearman’s and Pearson’s correlation

    22nd April 2014

    Linear correlation vs. Rank order correlation: drag 11 data points around the plot and observe how both Spearman’s and Pearson’s correlation measures change. But first follow the Next button at the bottom-right for a guided tour of data manipulations.

    Posted in Links, Science | No Comments »

    Stopfake.org: journalists fight against pro-war, anti-Ukrainian propaganda in Russian state mass-media

    27th March 2014

    Since December 2013 Russian state mass-media were supporting the former president of Ukraine V. Yanukovych and his criminal, authoritarian kleptocracy.

    Manipulating and distorting facts, and even making up fictitious “events”, Russian state mass-media (and personally Dmitri Kiselyov) tried very hard to depict protesters in the least favorable light possible – as violent gangsters, thugs, fascists, attackers of innocent policemen. (Dmitri Kiselyov, apparently for his fervent propaganda services, was promoted by Putin to become the head of the newly-created Russian state news agency.)

    Russian state mass-media never reported about kidnapped and tortured and murdered protesters, protesters who lost eyes after being shot to the head with rubber bullets, heavily beaten protesters with broken ribs and internal organs rupture.

    They also somehow failed to notice that after the night of November, 30, 2013, the protests were no longer about the EU association treaty, but about the responsibility of those guilty of badly exceeding authority during the night beatings of protesters in Kyiv.

    Further escalation of the crisis and street protests was always the (delayed) consequence of authorities using illegally excessive force against the protesters. After the “Party of regions” tried to basically forbid the entire protest movement with a set of laws in mid-January (while the president-controlled police and prosecutors office were opening hundreds of criminal prosecution cases against the protesters), Euromaidan, out of well-understandable desperation, escalated into open fighting with the now-disbanded “Berkut” special police forces. The Russian propaganda machine was omitting causal events, while depicting the protesters’ response to (unrevealed) oppression, and this was probably the least disgusting technique used.

    Further Yanukovych actions made crystal-clear the primary reason for strong Russian media support: Yanukovych response to the protests was fully coordinated with (and, highly likely, suggested or even ordered by) Moscow. Multiple pieces of evidence support this claim, I’ll only mention two:

    • according to, if I remember correctly, Inna Bohoslovska (member of parliament, the former president’s “Party of regions” faction), every time after tension-decreasing agreements were negotiated and nearly finalized between the former president and opposition leaders (who were representing protesters), the phone call to Moscow followed, after which negotiations were aborted without finalizing any agreements;
    • when the EU officials had a night-long negotiation with Yanukovych, discussing ways out of the crisis, Yanukovych interrupted negotiations to call Putin.

    Clearly, Yanukovych was good for Putin because he was, in fact, a nearly-puppet “president”. Had Yanukovych survived the crisis, the 2015 presidential elections in Ukraine would be as clear and honest as the Crimean referendum, most likely extending Yanukovych presidency for the 2nd term. He could have then followed in the steps of the presidents of Belarus or Kazakhstan (who keep being presidents for many years and even decades). A controllable president of Ukraine was a clear win for Putin, and he didn’t care (and still doesn’t care, of course) about the citizens of Ukraine.

    But I digress, as there is indeed a lot to write on the subject. When the Russian military invasion into Ukraine started at the end of February, Russian mass-media kept generating propaganda; now it had the goal to help Putin gain support inside Russia, to brainwash the citizens of Russian Federation (and, to a certain extent, the Russian-speaking Ukrainian citizens who haven’t yet realized that Russian mass-media are poisonous) into believing in (totally ungrounded) scary tales about the hardships and life-threatening conditions of Russian-speaking people in Ukraine.

    To counter Russian propaganda, a group of journalists and volunteers created an anti-propaganda, anti-lies website StopFake.org, which collects lies from Russian mass-media and finds materials proving those are indeed lies.

    Rule of thumb: don’t trust Russian media.
    Especially when they are talking about Ukraine.

    Posted in Society, Ukraine | No Comments »

    How to cite PHYLIP

    10th January 2014

    Official PHYLIP FAQ does suggest a few ways to cite the software, but I believe that the best citation is mentioned in the wikipedia PHYLIP article: pubmed reference for PMID 7288891. This PubMed citations seems the best, because

    • it does mention the software tool implementing the maximum likelihood approach,
    • it is likely the earliest mention of the PHYLIP software (which was distributed since around 1980),
    • it refers to a journal indexed by pubmed, and
    • according to Google Scholar, it was already cited over 6660 times :)

    Posted in Links, Science, Software | No Comments »

    Debian command of the day: popcon-largest-unused

    2nd January 2014

    From the Debian squeeze to wheezy upgrade guide:

    Remove packages that take up too much space and are not currently needed (you can always reinstall them after the upgrade). If you have popularity-contest installed, you can use sudo popcon-largest-unused to list the packages you do not use that occupy the most space. You can find the packages that just take up the most disk space with dpigs (available in the debian-goodies package) or with wajig (running wajig size). They can also be found with aptitude. Start aptitude in “visual mode”, select Views → New Flat Package List, press l and enter ~i, then press S and enter ~installsize. This will give you a handy list to work with.

    Posted in *nix | No Comments »

    Fake news imposter website

    1st December 2013

    One of the primary independent news websites in Ukraine is Українська Правда (The Ukrainian Truth).

    There exists, however, an imposter website, which blatantly edits news reports to discredit Ukrainian people disagreement with the recent actions of the president and the government.
    I call this website “imposter”, because they have the same name (but in Russian) as the above-mentioned original website, a similar domain name, and they also use exactly the same short-name (“УП”). Not a single serious news website would do so.
    They, however, only post news in Russian, while the original website is published in both Ukrainian and Russian (with blogs available in the language of the blog’s author). It is clear that the idea behind the fake news website ukrpravda.ua is to influence and manipulate the opinions of the Russian-speaking people unaware of the true nature of that imposter website.

    It should be of no surprise that domain name of the imposter is currently hosted by a Russian web-development company “rossiysky.net”:
    Read the rest of this entry »

    Posted in Society, Ukraine | No Comments »

    Brief comparison: Dropbox vs BitTorrent Sync vs AeroFS vs SparkleShare

    24th November 2013

    Right now I’m mostly using Dropbox, and recently started BitTorrent Sync for my music collection sync between all the PCs and my backups server, as well as for sharing larger files at work (thanks to direct LAN connections, this is much faster with BTSync than with Dropbox, which has to first upload the file to Dropbox server). I’m also considering syncing a TrueCrypt container of my photos archive using BTSync. SparkleShare is potentially interesting, but given my trend to move to free code-hosting services, I do not yet see a need for it.

    Below is a short summary table I’ve used to compare available solutions. Feel free to contribute to the table in the comments – I’ll update the post, then.

    Read the rest of this entry »

    Posted in Links, Software | No Comments »

    The Mysteries of BitCoin

    24th November 2013

    BitCoin logoDid you know that the creator(s) of BitCoin is/are unknown?
    Did you know that the account which generated the Genesis Block is estimated to have up to 0.6-1 million BitCoins?
    Did you know that the creator(s) of BitCoin disappeared from any BitCoin-related discussion and development forums a long time ago?
    Did you know that 3 journalist investigations aiming to identify BitCoin creator(s) all ended up with different results?

    This information is not available in one piece, but there are some of the pieces at the following URLs:

    A mistery hidden in the Genesis Block
    Who is Satoshi Nakamoto?
    Four years and $100 million later, Bitcoin’s mysterious creator remains anonymous
    Ted Nelson Says That Bitcoin’s Satoshi Nakamoto Is Shinichi Mochizuki
    Where in the World is Satoshi Nakamoto?
    The Rise and Fall of Bitcoin

    Below is a huge graphical brief history of Bitcoin, including the continued growth of its exchange rates.
    Read the rest of this entry »

    Posted in Links, Misc | No Comments »