Thursday, 28 March 2013

Fancy new interactive visualization of coverage depth for exome sequencing.

Fancy new interactive visualization of coverage depth for exome sequencing.

This has to appeal to the biologists ...

Nature Special:"The Future of Publishing"

The fact that NPG has published a special on "The Future of Publishing" shows that change is underway. The special gives a balanced view including M. Eisen's views (as reported by Van Noorden The True Cost of Science Publishing ) but naturally the message that they wish to convey is in the last (concluding) article in the series.

“As a young investigator you have to do what's economically viable,” says Stephen Macknik, a neuroscientist at the Barrow Neurological Institute in Phoenix, Arizona. Paying an article-processing charge for a reputable open-access journal may be a good middle ground for young researchers, he says.
But scientists shouldn't sacrifice funding that was meant for research. “To maximize their competitiveness it is vital that young researchers maintain a productive profile of high-quality research, and this means using research funds to do as much high-quality research as possible,” says Chambers. “It falls to the more senior scientists to change the system.”


  • Disciplinary action

    How scientists share and reuse information is driven by technology but shaped by discipline.
    Nature (  )


  • Sham journals scam authors

    Con artists are stealing the identities of real journals to cheat scientists out of publishing fees.
    Nature (  )


  • The library reboot

    As scientific publishing moves to embrace open data, libraries and researchers are trying to keep up.
    Nature (  )
  • The dark side of publishing

    The explosion in open-access publishing has fuelled the rise of questionable operators.
    Nature (  )


  • Beyond the paper

    The journal and article are being superseded by algorithms that filter, rate and disseminate scholarship as it happens, argues Jason Priem.
    Nature (  )
  • A fool's errand

    Objections to the Creative Commons attribution licence are straw men raised by parties who want open access to be as closed as possible, warns John Wilbanks.
    Nature (  )
  • How to hasten open access

    Three advocates for a universally free scholarly literature give their prescriptions for the movement’s next push, from findability to translations.
    Nature (  )


  • Q&A: Knowledge liberator

    Robert Darnton heads the world's largest collection of academic publications, the Harvard University Library system. He is also a driver behind the new Digital Public Library of America. Ahead of its launch in April, he talks about Google, science journals and the open-access debate.
    Nature (  )


  • Open to possibilities

    Opting for open access means considering costs, journal prestige and career implications.
    Nature (  )

Monday, 25 March 2013

Affymetrix, Inc. (NASDAQ: AFFX) today announced that it has signed a contract with UK Biobank to genotype 500,000 DNA samples donated by UK residents

Affymetrix, Inc. (NASDAQ: AFFX) today announced that it has signed a contract with UK Biobank to genotype 500,000 DNA samples donated by UK residents as part of a prospective epidemiological study of complex diseases that are of great relevance to public health. Affymetrix' Axiom® Genotyping Solution will be used to generate billions of high-quality genotypes which will provide UK Biobank and the research community with valuable insight to genetic factors underlying human diseases for improved prevention, diagnosis, and treatment of conditions such as heart disease, cancer, and diabetes.

Sent from myPhone

Friday, 22 March 2013

Adventures with my WD My Book Live (A PowerPC Debian Linux Server with 2 TB HDD)

I shoulda known to googled before probing at the CLI with stuff and I would have found out what I needed to know. but oh well damage done. What I needed to know was that it's a debian Linux (quite up to date!) with the standard perl/python/sqlite installed. CPU and RAM ain't super impressive but if you are just looping through text files I doubt that it matters a lot. Heck it's roughly equivalent to a older gen of Raspberry Pi with 256 Mb ram

The My Book Live is based upon the APM82181, a 800 MHz PowerPC 464 based platform (PDF). It has a host of features which are not utilized by the MyBook Live. For example, the PCI-E ports as well as the USB 2.0 OTG ports are fully disabled. The SATA port and GbE MAC are the only active components. The unit also has 256 MB of DRAM.(Source

It's such a shame that the PCI-E ports and USB ports are disabled but at the least the root account isn't disabled which opens up possibilities to install and hack the system into a low power device with a 2 TB HDD to do a bit of bioinformatics eh?

Imagine shipping someone's genomic data in one of these babies that allows you to slice and dice the fastq file to extract pertinent info! After all it already is a web server, won't be too much of a strain to make web apps or just simple web interface as a wrapper for scripts to generate graphical reports (*Dreams of putting galaxy webserver on the WD mybooklive*)
or perhaps use HTSeq or Erange to do something that doesn't strain the 256 Mb of DRAM

Post in Comments what you might do with a 800 Mhz CPU and 256 Mb Ram with Debian under it's hood.

UPDATE: Unfortunately I have managed to brick my WD Mybooklive by being overzealous in installing stuff that required the HTTP webserver as well. DOING that to a headless server with NO terminal/keyboard access is a BAD BAD idea especially if it breaks the SSH login if it hangs at boot up :(

Sigh hope to fix it soon and will be more careful in trying to test packages on my Ubuntu box before trying it on the mybooklive

MyBookLive:~# cat /proc/cpuinfo
processor       : 0
cpu             : APM82181
clock           : 800.000008MHz
revision        : 28.130 (pvr 12c4 1c82)
bogomips        : 1600.00
timebase        : 800000008
platform        : PowerPC 44x Platform
model           : amcc,apollo3g
Memory          : 256 MB

MyBookLive:~# apt-get update
Get:1 squeeze Release.gpg [1672B]
Get:2 wheezy Release.gpg [836B]
Get:3 squeeze Release [99.8kB]
Ign squeeze Release
Get:4 wheezy Release [223kB]
Ign wheezy Release
Get:5 squeeze/main Packages [6493kB]
Get:6 wheezy/main Packages [5754kB]
Fetched 12.6MB in 1min17s (163kB/s)
Reading package lists... Done

MyBookLive:~# perl -v

This is perl, v5.10.1 (*) built for powerpc-linux-gnu-thread-multi
(with 51 registered patches, see perl -V for more detail)

Copyright 1987-2009, Larry Wall

Perl may be copied only under the terms of either the Artistic License or the
GNU General Public License, which may be found in the Perl 5 source kit.

Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl".  If you have access to the
Internet, point your browser at, the Perl Home Page.

MyBookLive:~# python
Python 2.5.2 (r252:60911, Jan 24 2010, 18:51:01)
[GCC 4.3.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.

MyBookLive:~# sqlite3
SQLite version 3.7.3
Enter ".help" for instructions
Enter SQL statements terminated with a ";"

MyBookLive:~# free
             total       used       free     shared    buffers     cached
Mem:        253632     250112       3520          0      53568      52352
-/+ buffers/cache:     144192     109440
Swap:       500608     146048     354560

Ok if you are interested below is the exact model of WD MyBookLive that I own right now.

Related Links
Hacking WD My Book Live

Tuesday, 19 March 2013

SSH access on my Western Digital mybooklive

I didn't realise that the little black box holds so much wonders! I had assumed that SSH access would have been locked down or not installed at all. Now I am deeply curious about the OS and the other things that might be insde my 2 TB WD mybooklive :)

I hope rsync is one of them!

essentially if you haven't changed the hostname of ur mybooklive
you only need to login to the UI
then enter this link to enable SSH access to the drive


Found this out when I was googling for a faster way to move files within the little NAS (silly enough, it seems to route the data back to the PC then back to the new folder location within the same shared drive )

other neat things I discovered not of so much bioinfomatics relevance was that the twonky server has a HTTP frontend that can be accessed via a browser on your mobile devices! :)


Sunday, 17 March 2013

A call for params used for bwa mem for variant calling applications

---------- Forwarded message ----------
From: Sean Davis
Date: Sunday, 17 March 2013
Subject: [Bio-bwa-help] bwa mem for variant calling applications
To: BWA Help List <>

Hi, all.

We are playing with bwa mem as a potential replacement for bwa aln in variant calling applications for 70-150bp pe reads because of increased speed, increased sensitivity, and for the potential for being more sensitive in finding some unusual variants, particularly 10-50bp indels.  However, we are finding that the default parameters result in soft clipping to an extent that many true variants are simply soft-clipped out.  I know other folks are probably experimenting the same way and wondered what tuning people are trying.

I'll say that I personally hate "what parameters should I use questions", but I thought at this early stage in bwa mem experimentation, we could benefit from each others' experiences.  


Saturday, 9 March 2013

Linux CLI gems

Was alerted to this 'shell script' on github that contains several lines of linux commandline gems. That's how I store my code snippets too so that I can see them in contextual colors when you open in VIM or some other editor that is aware of the content (see example below)

# remove spaces from filenames in current directory
rename -n 's/[\s]/''/g' *

another good resource for picking up new CLI magic is at


Datanami, Woe be me