Autarchy of the Private Cave

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    Archive for the 'Links' Category

    Interesting and relevant links I found.

    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.

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

    I want a physical QWERTY keyboard Android

    27th October 2014

    My motivation is simple, and Kevin Michaluk had nicely written down the benefits of physical keyboards: Why there’s still demand in 2014 for phones with physical keyboards. For many years I’ve been using Nokia E71, and now, after switching to a screen-only Android 4.4.2 device, I dearly miss the physical keyboard (and the compact, durable metal phone body, too, as well as week-long battery life…).

    I really hope that phone manufacturers offer something that:

    • is about the size of E71, possibly slightly higher/wider/thicker
    • has a physical QWERTY keyboard, either E71-style or a slider
    • runs Android Lollipop :P
    • has decent (but not necessarily the best) smartphone hardware (5-8+MP camera, 1.4+GHzCPU, 1.5+GB RAM, 8+GB internal storage, etc)
    • has a good screen, e.g. HD (~4.3-4.7″) for a slider-keyboard version, or half-HD for Nokia-style keyboard
    • is minimally waterproof (can withstand heavy rain for 30 minutes)

    Reasonable price would also be welcome…

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    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.

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    Posted in Links, Science | 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 :)
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    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.

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