Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    • Archives

    • Recent 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

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

    Blatant dewlance.com SEO, thrustvps, and HEAD attacks

    6th November 2010

    Update 4: there are claims that these HEAD-attacks were coming from a malicious dewlance.com customer, and have nothing to do with dewlance itself.

    Noticing weird narrow spikes in server load graph, I decided to investigate the most recent one – at 03:50 GMT+2 on Nov. 6, 2010.

    The reason was simple: someone issued a few hundred HEAD-requests over a 30 second period to a PHP-based web-application.

    All the requests were coming from IP 109.169.59.139, which belongs to the IP range of thrustvps.com:

    inetnum: 109.169.58.0 – 109.169.59.255
    netname: ThrustVPS_1
    descr: Thrust::VPS
    country: US
    admin-c: RF5058-RIPE
    tech-c: RF5058-RIPE
    status: ASSIGNED PA
    mnt-by: RAPIDSWITCH-MNT

    However, it is the referrer string which is more interesting: in all those requests, decorated with varying UserAgents and even operating systems, there was only one referrer – www.dewlance.com.

    Initially I thought that was a test of a new DoS attack – really, who would issue dozens of HEAD requests to the same page over a few seconds? However, after seeing that “referrer” string, I now think this is a cheap, blatant, poor and ugly SEO performed by dewlance. It relies on some sites displaying a box of ‘recent visitors’, sometimes including their referrer URL as a “page where this visitor came from” – this would give dewlance.com some free link-love. Or maybe dewlance.com expects administrators to investigate log files, notice that referrer string, and happily order some services from dewlance? No way :)

    I’ll file a complaint with thrustvps if I see that kind of misbehaviour again. All that started on Nov. 4, so there’s still hope people behind this dumb SEO implementation will get fired.

    Update 1: they do this every 4 hours since November 4, 2010 (Thursday). This results in loads up to 22, with ~50 apache processes struggling for a few CPU cores:
    Read the rest of this entry »

    Posted in Misc, Web | 8 Comments »

    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 »

    Posted in Bioinformatics, Links, Software | No Comments »

    Batch-retrieve EntrezGene homologs using NCBI’s HomoloGene and R’s annotationTools

    27th October 2010

    1. Install the annotationTools R package:
      source(“http://bioconductor.org/biocLite.R”)
      biocLite(“annotationTools”)
    2. Download full HomoloGene data file from ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/current
    3. library(annotationTools)
    4. homologene = read.delim(“homologene.data”, header=FALSE)
    5. mygenes = read.table(“file with one entrez ID of the source organism per line.txt”)
    6. getHOMOLOG(unlist(mygenes), taxonomy_ID_of_target_organism, homologene) [alternatively, wrap the call to getHOMOLOG into unlist to get a vector]

    It might be easier to achieve the same results with a Perl script calling NCBI’s e-utils.

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

    The world’s shortest marketing plan (4P cheat sheet)

    24th October 2010

    Source: Kelly’s think tank.

    Posted in Links, Notepad, Startups | No Comments »

    ask.debian.net: stackoverflow for Debian with Shapado

    19th October 2010

    ask.debian.net is a StackOverflow-like Q&A website built with OSS Shapado.

    That’s my first encounter of Shapado, so it was interesting to read Shapado authors’ justification and a related question on meta.SO.

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

    Workplace or gamer’s HQ? ;)

    16th October 2010

    Find out more about the depicted office. That would be a nice setup for flight and/or space simulators, I guess.

    TinEye Firefox extension helped finding more nice workplaces.

    And Stefan in his office description provided some more links to multi-display workplaces – Mitch Haile’s and Kevin Connollie’s among others.

    Posted in Links, Misc, Notepad | No Comments »