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    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 »

    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.
    Read the rest of this entry »

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    Posted in Links, Software, Web | 11 Comments »

    Microsoft’s perspective on OpenOffice.org

    26th December 2010

    On the 24th of September 2010 Microsoft posted a video showcase titled “A few perspectives on OpenOffice.org”. Here’s the page with the video: http://www.microsoft.com/showcase/en/US/details/faaf9eb8-77c6-4bed-bc08-c069a7bfbb04. It asks to install silverlight, and if you don’t want that – look for the Watch as WMV direct videostream link.

    Just a single quote from Glyn Moody, Computerworld UK:

    The criticisms made in the video are not really the point – they are mostly about OpenOffice.org not being a 100% clone of Microsoft Office, and compatibility problems with Microsoft’s proprietary formats. The key issue is the exactly the same as it was for the Mindcraft benchmarks. You don’t compare a rival’s product with your own if it is not comparable. And you don’t make this kind of attack video unless you are really, really worried about the growing success of a competitor.

    See also what Savio Rodriguez (Infoworld) has to say about that video.

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    Posted in Misc, Software | No Comments »

    How to relay outgoing postfix emails via another mail server (e.g. your ISP)

    4th December 2010

    Here’s a simple and clear guide for gmail, which also definitely works with other relay hosts. I’ve used it to configure my ISP’s mail relay (they block outgoing port 25) on a Debian Squeeze laptop.

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    Posted in *nix, how-to, Links, Notepad, Software | No Comments »

    How to replace newlines with commas, tabs etc (merge lines)

    16th November 2010

    Imagine you need to get a few lines from a group of files with missing identifier mappings. I have a bunch of files with content similar to this one:

    ENSRNOG00000018677 1368832_at 25233
    ENSRNOG00000002079 1369102_at 25272
    ENSRNOG00000043451 25353
    ENSRNOG00000001527 1388013_at 25408
    ENSRNOG00000007390 1389538_at 25493

    In the example above I need ’25353′, which does not have corresponding affy_probeset_id in the 2nd column.

    It is clear how to do that:

    1. sort -u *_affy_ensembl.txt | grep -v '_at' | awk '{print $2}'

    This outputs a column of required IDs (EntrezGene in this example):

    116720
    679845
    309295
    364867
    298220
    298221
    25353

    However, I need these IDs as a comma-separated list, not as newline-separated list.

    There are several ways to achieve the desired result (only the last pipe commands differ):

    1. sort -u *_affy_ensembl.txt | grep -v '_at' | awk '{print $2}' | gawk '$1=$1' ORS=', '
    1. sort -u *_affy_ensembl.txt | grep -v '_at' | awk '{print $2}' | tr '\n' ','
    1. sort -u *_affy_ensembl.txt | grep -v '_at' | awk '{print $2}' | sed ':a;N;$!ba;s/\n/, /g'
    1. sort -u *_affy_ensembl.txt | grep -v '_at' | awk '{print $2}' | sed ':q;N;s/\n/, /g;t q'
    1. sort -u *_affy_ensembl.txt | grep -v '_at' | awk '{print $2}' | paste -s -d ","

    These solutions differ in efficiency and (slightly) in output. sed will read all the input into its buffer to replace newlines with other separators, so it might not be best for large files. tr might be the most efficient, but I haven’t tested that. paste will re-use delimiters, so you cannot really get comma-space “, ” separation with it.

    Sources: linuxquestions 1 (explains used sed commands), linuxquestions 2, nixcraft.

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    Posted in *nix, Bioinformatics, how-to, Notepad, Software | 2 Comments »

    How to record Skype calls on Linux: use free Skype Call Recorder

    11th November 2010

    Just came across Skype Call Recorder – an awesome in its functionality+simplicity tool to record skype calls. Highly recommended!

    It worked immediately for me, and default settings are good enough not to bother tweaking. Well, I know that because I did tweak a few to get more nerdiness, but normal people don’t need that.

    SCR download page has packages for Ubuntu, Debian/i386, Xandros, RPM-based distributions, Gentoo – and as its free, you can of course just use the fsource, Luke!

    At the time of writing, a package for Debian/amd64 was not available, but it is really easy to build one.
    Here’s mine: skype-call-recorder-debian_0.8_amd64.deb

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    Posted in *nix, Links, Software | 1 Comment »

    Overlaying gene expression data onto pathways from databases

    5th November 2010

    Superimposing gene expression data onto pathways from databases is a common task in the final steps of microarray data analysis – that is, biological interpretation and results discussion.

    I have found many tools which claim to facilitate this procedure. Some of them are reviewed below (in no specific order).
    Read the rest of this entry »

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    Posted in Bioinformatics, Links, Software | No Comments »