Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

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    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 »

    Outlook 2010: MAPI was unable to load the information service gwmsp1.dll

    24th November 2013

    If you try starting Outlook 2010 and get an error like this:
    “Outlook 2010 cannot open your default e-mail folders. An unexpected error has occurred. MAPI was unable to load the information service gwmsp1.dll”

    you can easily fix this problem by going to Control Panel, clicking on Mail, then Show Profiles button.
    Remove everything that’s there. Now start outlook again.

    Note: removing all the mail profiles will disable your Novell Groupwise client.
    If you still want to use non-Outlook email profiles, then the better solution is to manually create a new mail profile for Outlook.

    Source: CNET forums.

    Posted in Misc, Notepad | No Comments »

    The list of spammers emails

    13th November 2013

    All sane people agree that spam is a blight of the internet, be it email spam or comments spam or forum spam or any other form of unsolicited, blatant, shameless, out-of-context advertising. Multiple spam-fighting and spam-stopping systems are being developed.

    With automated spam, automated spam-fighting systems might be the only choice. Sending rightfully angry emails to ISPs to notify about their customers violating service agreements is probably a waste of effort (something tells me most of these complaints end up in the trash folder, or even in the… spam folder). However, I get a feeling that some spam is not automated – it appears to have been actually prepared and sent by a human. (Alternatively, spammers behind those spams simply have better software.) Anyway, some spams seem to contain valid contact data of the advertized entity – like an email.

    The resulting idea is very simple and was probably already implemented somewhere by someone: simply publish online contact emails of the entities which, apparently, had chosen spam as the primary means of advertising. These emails will be sooner or later harvested by spammers, added to spam databases, and will start getting progressively more spam.

    There are a few drawbacks to this approach:

    • knowing spam-collection points enables “black PR”-like mass-mailings in the name of one’s competitor, double-hurting the innocents; I do not see a clear method of preventing this, other than by concealing spam collection methods;
    • human intelligence is required to identify if the contained email truly belongs to the advertised entity; this is fairly time-consuming, especially when scaled up; a possible solution (with its own problems) would be to build an online gateway for submitting curated spam samples, thus distributing the workload to all the participating volunteers;
    • the next logical step is actually harvesting and then publishing all the emails from the advertised website;
    • the biggest drawback, however, is low efficiency of this approach; increasing spam percentage will only be a mild nuisance, which isn’t likely to propagate high enough to affect spam-deciders; also, indirectly spamming someone’s mailbox will result in the loss of time, which could have been otherwise used for facebook and other important activities :)

    What do you think? Should such a method be used?

    Below I provide a few sample records from real spam comments, which had true-looking emails. I’m including some extra meta-data. Ideally, this should be stored in some kind of a database.

    Submitted on 2013/11/13 at 15:23 GMT
    Author : Виктор (IP: 95.134.110.37 , 37-110-134-95.pool.ukrtel.net)
    E-mail : aionind@yandex.ru
    E-mail : sale@aion-industry.ru
    E-mail : info@aion-industry.ru
    Submitted on 2013/11/26 at 8:53 GMT
    Author : Виктор (IP: 95.134.146.235 , 235-146-134-95.pool.ukrtel.net)
    E-mail : kvazargr@yandex.ru
    E-mail : info@kvazar-gr.ru
    Submitted on 2013/11/28 at 7:24 GMT
    Author : Виктор (IP: 95.134.117.155 , 155-117-134-95.pool.ukrtel.net)
    E-mail : relevater@yandex.ru
    E-mail : info@relevate.ru
    E-mail : support@relevate.ru
    E-mail : billing@relevate.ru

    There’s definitely a need for a public database, API keys, and quorum algorithms…

    Author : casinoworka (IP: 91.207.4.201 , 201.4.207.91.unknown.SteepHost.Net)
    E-mail : pharmacywork7777777@gmail.com
    E-mail : info@prowessmedical.com

    Posted in Misc, Web | No Comments »