Autarchy of the Private Cave

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    R tutorial links

    29th March 2010


    Posted in Bioinformatics, Links, Science, Systems Biology | 1 Comment »

    R script to filter probesets with log-expression values below the lowest spike-in

    27th January 2010

    Sometimes there is a need to remove all the probesets, which have expression values below the minimal spike-in intensity on the Affymetrix microarray. The reasoning behind this procedure is simple: minimal-expression spike-ins represent the bottom margin of microarray sensitivity, and anything below that margin cannot be reliably quantified – which also means that both fold-change and p-value of expression variance will be unreliable for these probesets.

    Here’s a simple R script to do just that. It is abundantly commented, and also contains an optional (commented out) fragment which allows the removal of more low-variance, low-intensity probesets.

    Read the rest of this entry »


    Posted in Bioinformatics, Programming, Science | No Comments »

    DIYbio, biohackers, and Open Source Medicine

    25th July 2009

    DIYbio is

    an organization that aims to help make biology a worthwhile pursuit for citizen scientists, amateur biologists, and DIY biological engineers who value openness and safety.

    DIYbio also has a google group, where a wide range of questions – from bio-patents to DIY gel electrophoresis shopping list and model organisms is dicussed. There is also a DIYbio/biohacking FAQ.

    Today for me is the day of discoveries. I learned about the International Open Space Initiative (to give robotics enthusiasts a way to send their tele-controlled and/or intelligent robots to the Moon and Mars), about the DIYbio and biohackers, about OpenManufacturing (which doesn’t seem to have produced enough content to link to), Open Source Medicine (ouch!), BioBrick Assembly Kit (with an assembly manual), OpenWetWare, and a whole bunch of other awesome and inspiring community efforts, which do not belong here.

    Do you feel the wind of change?


    Posted in Links, Misc, Science, Society, Welfare | No Comments »

    SciVee.TV: YouTube for science

    15th July 2009

    SciVeeStumbled upon SciVee.TV – an open video upload service for research-related videos.

    I believe it is highly useful. Compare: watching an 8-10 minute video of someone’s research to reading their article on that same subject. For me, those 8-10 minutes make video option a clear winner.

    One of the envisioned uses of SciVee is to upload videos describing peer-reviewed published articles. This has two benefits for the reader: quickly getting acquainted with the essence of the article, and having that article as a complete reference for any questions not discussed in the video. For the author, this gives an additional bonus of higher visibility of his research.

    Personally, I’ve immediately found 3 videos pertinent to my topic. Of those, one was accompayning an article in PloS Biology, one was an hour-long lecture, and one was a poor quality audio recording of someone’s intended research.

    SciVee is young, and that is currently the largest drawback: not much could be found in a narrow research field. But I’m sure it will grow.


    Posted in Links, Science, Web | No Comments »

    10 simple rules for getting published

    26th June 2009

    Recently, I have come across an excellent piece of advice called Ten simple rules for getting published. The only thing I have to add is that final rule #10 should be kept in mind while checking through all the previous rules – e.g. when editing someone’s submission, make sure that you are in position to be the editor for that article, and make sure your decision will influence chief editor’s decision – otherwise there’s no use reviewing.

    PLoS Computational Biology, where the “simple rules” were published, has a Ten simple rules collection, which includes a handful of other useful advice articles, like 10 simple rules for selecting a postdoctoral position.


    Posted in Links, Misc, Science | No Comments »

    GNU make for bioinformatics presentation

    5th June 2009

    Giovanni Dall’olio has recently posted a presentation on using make.

    Although it has “bioinformatics” on the title page, this is a good and very easy to understand make intro.

    Original post is here.


    Posted in Bioinformatics, Links, Programming | 1 Comment »

    Ensembl Genomes launches Protists, Bacteria and Metazoa

    21st April 2009

    The following sites are available:

    During summer, two more sites – for Fungi and Plants – should be made available.

    Learn more about Ensembl Genomes project.


    Posted in Bioinformatics, Links, Science, Software, Web | No Comments »