http://www.biomart.org/faqs.html
http://llama.mshri.on.ca/synergizer/doc/
http://david.abcc.ncifcrf.gov/conversion.jsp
Friday, October 7, 2011
You can't fool God!
"God knows what you've been doing, everything you've been doing. You may fool me, but you can't fool God!"
--Great Gatsby
--Great Gatsby
Thursday, October 6, 2011
Computational and statistical approaches to analyzing variants identified by exome sequencing
Computational and statistical approaches to analyzing variants identified by exome sequencing
Nathan O Stitziel1,2†, Adam Kiezun2,3† and Shamil Sunyaev2,3*
http://genomebiology.com/2011/12/9/227
New sequencing technology has enabled the identification of thousands of single nucleotide polymorphisms in the exome, and many computational and statistical approaches to identify disease-association signals have emerged.
Here we review the computational and statistical approaches that have emerged for managing these data in this rapidly exploding field. First, we briefly review the process for identifying variants in next-generation sequencing (NGS) studies and then discuss strategies for identifying the causal variant in Mendelian disorders among the total number of variants identified. We also discuss strategies for identifying the causal gene(s) in complex diseases among all genes in the genome, before outlining some challenges facing current exome sequencing studies.
Nathan O Stitziel1,2†, Adam Kiezun2,3† and Shamil Sunyaev2,3*
http://genomebiology.com/2011/12/9/227
New sequencing technology has enabled the identification of thousands of single nucleotide polymorphisms in the exome, and many computational and statistical approaches to identify disease-association signals have emerged.
Here we review the computational and statistical approaches that have emerged for managing these data in this rapidly exploding field. First, we briefly review the process for identifying variants in next-generation sequencing (NGS) studies and then discuss strategies for identifying the causal variant in Mendelian disorders among the total number of variants identified. We also discuss strategies for identifying the causal gene(s) in complex diseases among all genes in the genome, before outlining some challenges facing current exome sequencing studies.
Waltz through hippocampal neuropil
http://www.youtube.com/watch?v=FZT6c0V8fW4
Reconstruction of a block of hippocampus from a rat approximately 5 micrometers
on a side from serial section transmission electron microscopy in the lab
of Kristen Harris at the University of Texas at Austin in collaboration with
Terry Sejnowski at the Salk Institute and Mary Kennedy at Caltech. Josef Spacek,
Daniel Keller, Varun Chaturvedi, Chandrajit Bajaj, Justin Kinney and Tom Bartol
made major contributions to the reconstruction and the video.
For more reconstructions:
http://www.cell.com/neuron/abstract/S0896-6273(10)00624-0
Links to laboratories:
http://cnl.salk.edu/
http://synapses.clm.utexas.edu/lab/lab.stm
http://www.its.caltech.edu/~mbklab/mary.html
http://www.cs.utexas.edu/~bajaj/
http://synapses.clm.utexas.edu/lab/spacek/josef.html
... (more info)
(less info)
Reconstruction of a block of hippocampus from a rat approximately 5 micrometers
on a side from serial section transmission electron microscopy in the lab
of Kristen Harris at the University of Texas at Austin in collaboration with
Terry Sejnowski at the Salk Institute and Mary Kennedy at Caltech. Josef Spacek,
Daniel Keller, Varun Chaturvedi, Chandrajit Bajaj, Justin Kinney and Tom Bartol
made major contributions to the reconstruction and the video.
For more reconstructions:
http://www.cell.com/neuron/abstract/S0896-6273(10)00624-0
Links to laboratories:
http://cnl.salk.edu/
http://synapses.clm.utexas.edu/lab/lab.stm
http://www.its.caltech.edu/~mbklab/mary.html
http://www.cs.utexas.edu/~bajaj/
http://synapses.clm.utexas.edu/lab/spacek/josef.html
... (more info)
(less info)
rss TIOBE Programming Community Index for September 2011
http://www.tiobe.com/index.php/content/paperinfo/tpci/index.html
Position
Sep 2011-Position Sep 2010-Position Delta in Position Programming Language Ratings
Sep 2011 Delta-Sep 2010 Status
1 1 Java 18.761% +0.85% A
2 2 C 18.002% +0.86% A
3 3 C++ 8.849% -0.96% A
4 6 C# 6.819% +1.80% A
5 4 PHP 6.596% -1.77% A
6 8 Objective-C 6.158% +2.79% A
7 5 (Visual) Basic 4.420% -1.38% A
8 7 Python 4.000% -0.58% A
9 9 Perl 2.472% +0.03% A
10 11 JavaScript 1.469% -0.20% A
11 10 Ruby 1.434% -0.47% A
Position
Sep 2011-Position Sep 2010-Position Delta in Position Programming Language Ratings
Sep 2011 Delta-Sep 2010 Status
1 1 Java 18.761% +0.85% A
2 2 C 18.002% +0.86% A
3 3 C++ 8.849% -0.96% A
4 6 C# 6.819% +1.80% A
5 4 PHP 6.596% -1.77% A
6 8 Objective-C 6.158% +2.79% A
7 5 (Visual) Basic 4.420% -1.38% A
8 7 Python 4.000% -0.58% A
9 9 Perl 2.472% +0.03% A
10 11 JavaScript 1.469% -0.20% A
11 10 Ruby 1.434% -0.47% A
Brain disorders cost Europe 800 billion euros a year: study
http://www.pharmatimes.com/Article/11-10-05/Brain_disorders_cost_Europe_800_billion_euros_a_year_study.aspx
The cost of brain disorders in Europe soared to 798 billion euros last year, double the figure for 2005 and equating to 1,550 euros per capita, says a new report.
The bill will continue to rise as people live longer, and this represents "the number one economic challenge for European health care now and in the future," says the study, which was commissioned by the European Brain Council (EBC).
But without urgent action, the situation can only worsen, given the continuing rise in life expectancy in Europe, the authors warn. Because of the ageing population, degenerative disorders such as dementia, Parkinson's and stroke are particularly destined to become more common, but anxiety and mood disorders are also very prevalent in older populations, they add.
The cost of brain disorders in Europe soared to 798 billion euros last year, double the figure for 2005 and equating to 1,550 euros per capita, says a new report.
The bill will continue to rise as people live longer, and this represents "the number one economic challenge for European health care now and in the future," says the study, which was commissioned by the European Brain Council (EBC).
But without urgent action, the situation can only worsen, given the continuing rise in life expectancy in Europe, the authors warn. Because of the ageing population, degenerative disorders such as dementia, Parkinson's and stroke are particularly destined to become more common, but anxiety and mood disorders are also very prevalent in older populations, they add.
Monday, October 3, 2011
Department of Numbers
Department of Numbers
The Department of Numbers contextualizes public data so that individuals can form independent opinions on everyday social and economic matters.
http://www.deptofnumbers.com/
The Department of Numbers contextualizes public data so that individuals can form independent opinions on everyday social and economic matters.
http://www.deptofnumbers.com/
Sunday, October 2, 2011
k3b and brasero problems, can read DVD but not CD
# install cdrtools as a replacement of cdrkit
dpkg -i ./libscg1*.deb
dpkg -i ./cdda2wav*.deb
dpkg -i ./cdrecord*.deb
dpkg -i ./mkisofs*.deb
dpkg -i ./cdrtools*.deb
$ wodim --version
Cdrecord-ProDVD-ProBD-Clone 3.01a03 (x86_64-unknown-linux-gnu) Copyright (C) 1995-2010 Joerg Schilling
http://forum.ubuntuusers.de/topic/kleines-projekt-mit-paketverwaltung-die-schil/8/#post-2809761
http://www.cdrinfo.com/Sections/Reviews/Print.aspx?ArticleId=20651
Another reason why the CD/DVD drive might not read the CD properly is because it's not compatible. My drive can read Memorex type of CD-Rs (650MB) and Fujifilm (700MB), DVDs (including Maxell DVD), but not Maxell CD-Rs (700MB). Maybe it has something to do with the speed the CD was written in (16, 24, 40, 48)?
$sudo chmod +s /usr/bin/wodim
$sudo k3b
sbubba
November 7th, 2010, 04:41 AM
Hello
I had this problem with k3b 1.91.0 on ubuntu 10.04.
I've had to purge and reinstall some packages:
hal libhal1 libhal-storage1 k3b wodim
(apt-get wants to remove many packages in addition to these, you have to reinstall all of them)
k3b always says cdrecord has no permission to open device and brasero knows theres a blank disc in but says it has 0 bites free
http://ubuntuforums.org/archive/index.php/t-1291337.html
LG GSA-H55N Firmware
http://www.lg.com/us/support/product/support-product-profile.jsp?customerModelCode=GSA-H55N&matchedModelCode=NOT_MATCHED&searchEngineModelCode=GSA-H55N&initialTab=documents&targetPage=support-product-profile#
http://www.sevenforums.com/hardware-devices/99286-hl-dt-st-dvd-ram-gsa-h55n-ata-device-wont-read-dvds-but-reads-cd-2.html
dpkg -i ./libscg1*.deb
dpkg -i ./cdda2wav*.deb
dpkg -i ./cdrecord*.deb
dpkg -i ./mkisofs*.deb
dpkg -i ./cdrtools*.deb
$ wodim --version
Cdrecord-ProDVD-ProBD-Clone 3.01a03 (x86_64-unknown-linux-gnu) Copyright (C) 1995-2010 Joerg Schilling
http://forum.ubuntuusers.de/topic/kleines-projekt-mit-paketverwaltung-die-schil/8/#post-2809761
http://www.cdrinfo.com/Sections/Reviews/Print.aspx?ArticleId=20651
Another reason why the CD/DVD drive might not read the CD properly is because it's not compatible. My drive can read Memorex type of CD-Rs (650MB) and Fujifilm (700MB), DVDs (including Maxell DVD), but not Maxell CD-Rs (700MB). Maybe it has something to do with the speed the CD was written in (16, 24, 40, 48)?
$sudo chmod +s /usr/bin/wodim
$sudo k3b
sbubba
November 7th, 2010, 04:41 AM
Hello
I had this problem with k3b 1.91.0 on ubuntu 10.04.
I've had to purge and reinstall some packages:
hal libhal1 libhal-storage1 k3b wodim
(apt-get wants to remove many packages in addition to these, you have to reinstall all of them)
k3b always says cdrecord has no permission to open device and brasero knows theres a blank disc in but says it has 0 bites free
http://ubuntuforums.org/archive/index.php/t-1291337.html
LG GSA-H55N Firmware
http://www.lg.com/us/support/product/support-product-profile.jsp?customerModelCode=GSA-H55N&matchedModelCode=NOT_MATCHED&searchEngineModelCode=GSA-H55N&initialTab=documents&targetPage=support-product-profile#
http://www.sevenforums.com/hardware-devices/99286-hl-dt-st-dvd-ram-gsa-h55n-ata-device-wont-read-dvds-but-reads-cd-2.html
Saturday, October 1, 2011
Cell-Specific Mechanism-Based Gene Therapy Approach to Treat Retinitis Pigmentosa
http://www.sciencedaily.com/releases/2011/09/110930153050.htm?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+sciencedaily+%28ScienceDaily%3A+Latest+Science+News%29
Furthermore, they used a tissue-specific promoter to achieve cell-specific expression of the transduced genes, which is unusual for shRNA delivery.
Furthermore, they used a tissue-specific promoter to achieve cell-specific expression of the transduced genes, which is unusual for shRNA delivery.
ALLEN INSTITUTE FOR BRAIN SCIENCE 2011 Annual Symposium: Open Questions in Neuroscience
http://www.alleninstitute.org/events/symposium/index.html
Sacha B. Nelson, Brandeis University
http://www.bio.brandeis.edu/faculty/nelson.html
Defining the mammalian neurome
Nathaniel Heintz, Investigator, Howard Hughes Medical Institute
http://www.rockefeller.edu/research/faculty/labheads/NathanielHeintz/
Research in Dr. Heintz’s laboratory aims to identify the genes, circuits, cells, macromolecular assemblies and individual molecules that contribute to the function and dysfunction of the mammalian brain. Dr. Heintz and his colleagues have developed a suite of novel approaches based on the manipulation of bacterial artificial chromosomes (BACs) to investigate the histological and functional complexities of the mammalian brain in vivo and to understand how these mechanisms become dysfunctional in disease.
Pamela Sklar, M.D., Ph.D.
http://pngu.mgh.harvard.edu/faculty/sklar/index.php
Genomics and psychiatry
Sacha B. Nelson, Brandeis University
http://www.bio.brandeis.edu/faculty/nelson.html
Defining the mammalian neurome
Nathaniel Heintz, Investigator, Howard Hughes Medical Institute
http://www.rockefeller.edu/research/faculty/labheads/NathanielHeintz/
Research in Dr. Heintz’s laboratory aims to identify the genes, circuits, cells, macromolecular assemblies and individual molecules that contribute to the function and dysfunction of the mammalian brain. Dr. Heintz and his colleagues have developed a suite of novel approaches based on the manipulation of bacterial artificial chromosomes (BACs) to investigate the histological and functional complexities of the mammalian brain in vivo and to understand how these mechanisms become dysfunctional in disease.
Pamela Sklar, M.D., Ph.D.
http://pngu.mgh.harvard.edu/faculty/sklar/index.php
Genomics and psychiatry
Subscribe to:
Posts (Atom)