Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

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    Archive for the 'Links' Category

    Interesting and relevant links I found.

    Generate .mood moodbar files for your whole music collection

    10th April 2011

    Amarok moodbar wiki page has 2 nice scripts to generate .mood files for your whole music collection (to be displayed by amarok when playing).

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    Posted in *nix, Links, Notepad, Software | 3 Comments »

    Debunking the widespread myth of 2^32=4GB being the architectural limit

    10th April 2011

    Quite a number of people are aware of the PAE which can extend the addressable space from 32bit up to 36-48-52bit (depending on the implementation; as I understand, Windows PAE extends to 36 bits, or 64GB of addressable space). However, overwhelming numbers of internet pages continue insisting that a not-more-than-4GB limit for the 32bit Windows is the consequence of 2^32 = 4GB architectural limit.

    There is an excellent, in-depth, well-argumented article by Geoff Chappell on the issue. Highly recommended in its entirety to those who want a complete understanding (additional side-reading and facts verification might be necessary).

    A single citation to get you started:

    There is already on the Internet and elsewhere an awful lot of rubbish to read about this question. Hardly any of it would be worth citing even if I didn’t want to spare the authors the embarrassment. A surprising number of people who claim some sort of attention as expert commentators would have you believe that using more than 4GB of memory is mathematically impossible for any 32-bit operating system because 2 to the power of 32 is 4G and a 32-bit register can’t form an address above 4GB. If nothing else, these experts don’t know enough history: 2 to the 16 is only 64K and yet the wealth of Microsoft is founded on a 16-bit operating system that from its very first version was designed to use 640KB of RAM plus other memory in a physical address space of 1MB. Some remember this history and add seemingly plausible qualifications that exceeding 4GB is possible only at the price of nasty hacks that require everyone—well, all programmers—to jump through hoops. Fortunately, Intel’s processors are a lot more advanced than the 8086 from all those years ago.

    P.S. Unfortunately, patching the kernel won’t help make Windows XP see more than 4GB RAM: even though the kernel itself does support more RAM (with PAE), starting with SP2 the HAL was modified in a way prohibiting access to any RAM beyond 4GB. Patching may only be suggested to devoted geeks with Vista’s and 7′s.

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

    Amazonia! 6462 human microarray datasets

    6th March 2011

    Amazonia!Amazonia! – explore the jungle of microarray results

    Paradoxically, the tremendous downpour of microarray results prevents a simple use of expression data. Therefore, we propose a thematic entry to public transcriptomes: you may for instance query a gene on a “Stem Cells page”, where you will see the expression of your favorite gene across selected microarray experiments related to stem cell biology. This selection of samples can be customized at will among the 6462 samples currently present in the database.

    Every transcriptome study results in the identification of lists of genes relevant to a given biological condition. In order to include this valuable information in any new query in the Amazonia! database, we indicate for each gene in which lists it is included. This is a straightforward and efficient way to synthesize hundreds of microarray publications.

    A special feature of Amazonia! is the field of human stem cells, notably embryonic stem cells.

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    Posted in Bioinformatics, Links, Science | No Comments »

    Introduction to Python for bioinformatics

    25th February 2011

    This overview presentation is two years old, but still a highly valuable resource: modules and tools mentioned are alive and useful.
    I think this is the second presentation by Giovanni I’m embedding (first one being about GNU/make for bioinformatics).

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    Posted in Bioinformatics, Links, Python, Software | No Comments »

    MySQL as NoSQL with HandlerSocket: 750000 qps

    25th January 2011

    HandlerSocket provides a direct access to InnoDB storage, bypassing SQL interpretation layer. With in-RAM data, it may raise MySQL performance to 750000 queries per second.

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    Posted in Links, Software | No Comments »

    MongoDB is web-scale

    25th January 2011

    Disclaimer: don’t take this video seriously.

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    Posted in Links, Misc | 2 Comments »

    Light web-based collaborative project management tools

    10th January 2011

    Updated on the 5th of March, 2010 (added flowdock and pivotal tracker, and also personal experience using a few of the previously described tools).

    Back in 2007 I wrote a brief review of web-based project management tools. After that, I started using dotProject for personal projects management. I’m still using it, but for collaborative project management, communication, and tasks/milestones tracking dotProject isn’t perfect.

    I need a tool, which is

    • collaborative
    • web-based (to allow effective collaboration)
    • preferably free
    • has concise per-project activity log
    • minimal required functionality: tasks, milestones, files, and status updates.

    After trying a few things, our small team settled for now on using github + pivotaltracker jira + confluence + flowdock.

    Here’s a full list of tools briefly reviewed. I’ve been already using ProjectPier, so I’ll start with this software.
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    Posted in Links, Software, Web | 11 Comments »