Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    Archive for October, 2010

    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.

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    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.

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    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.

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    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.

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    Posted in Links, Misc, Notepad | No Comments »

    Installing DeadBeef music player on Debian

    16th October 2010

    In my previous post on CUE sheet support in Linux music players I mentioned DeaDBeeF. Unfortunately, DeaDBeeF is not yet available as a Debian package.

    Fortunately, Alexey Smirnov (the author of DeaDBeeF) maintains a github repository deadbeef-debian which has simple instructions on installing DeaDBeeF in Debian (citing with minor edits): Read the rest of this entry »

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    Posted in Links, Software | 3 Comments »

    International salary survey in sciences (2010)

    14th October 2010

    Nature published the said survey based on responses of over 10000 employees in science. It has lots of multi-axis data to explore, and some major trends are discussed in the special report. Highly recommended for anyone considering science career changes.

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    Posted in Links, Science | No Comments »

    Old news: flying cars get real!

    3rd October 2010

    You should already know that my preferred city vehicle is VentureOne (now called PersuHybrid, and still far from mass production – while Carver One, the original tilting three-wheeler, is now bankrupt/dead). It might be more realistic to go for Campagna’s T-Rex, which is in production since 1996.

    Now, welcome the Terrafugia’s Transition transformer flying car! It can drive as a car (and is sized as a car with wings folded), and it can fly as an air-plane! Now your trip to anywhere looks like “drive to the airport – fly – land – drive to gas station – repeat as needed”. Terrafugia claims that (on average) there’s a suitable airport every 60 miles in the US. And you can fit Transition into your average garage!

    That doesn’t (yet) feel like something from the future – and maybe that is why their prototype already had test flights, and they plan mass-production for 2011, and already have over 80 pre-orders.

    If only it had vertical take-off… :)

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    Posted in Misc | No Comments »