Thursday, February 28, 2013
Wednesday, February 27, 2013
On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE
http://gbe.oxfordjournals.org/content/early/2013/02/20/gbe.evt028
A recent slew of ENCODE Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is under 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 − 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these “functional” regions, or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly (1) by employing the seldom used “causal role” definition of biological function and then applying it inconsistently to different biochemical properties, (2) by committing a logical fallacy known as “affirming the consequent,” (3) by failing to appreciate the crucial difference between “junk DNA” and “garbage DNA,” (4) by using analytical methods that yield biased errors and inflate estimates of functionality, (5) by favoring statistical sensitivity over specificity, and (6) by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.
A recent slew of ENCODE Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is under 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 − 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these “functional” regions, or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly (1) by employing the seldom used “causal role” definition of biological function and then applying it inconsistently to different biochemical properties, (2) by committing a logical fallacy known as “affirming the consequent,” (3) by failing to appreciate the crucial difference between “junk DNA” and “garbage DNA,” (4) by using analytical methods that yield biased errors and inflate estimates of functionality, (5) by favoring statistical sensitivity over specificity, and (6) by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.
Wednesday, February 20, 2013
Monday, February 18, 2013
Making Electronic Health Records More Efficient
http://www.forbes.com/fdc/welcome_mjx.shtml
Six years ago, radiologist Michael Zalis found himself spending a lot of time logging in and out of separate electronic health records at Massachusetts General Hospital to gather lab data, clinical notes, and other non-imaging information scattered in multiple databases. “Clinicians face this every day,” says Zalis, who quantified the frequency of EHR use to interpret CT scans and MRIs, and published his findings in the American Journal of Roentgenology. “It takes hours to manually pull together information, and clinicians are under pressure to get the information they need.”
Zalis co-founded and wrote the code for QPID, which stands for Queriable Patient Inference Dossier, a natural language search tool that extracts relevant clinical information from an EHR. Since its inception in Mass General’s radiology department, QPID has grown by word of mouth, and is now deployed across Boston-based Partners HealthCare, which includes Brigham and Women’s Hospital. It is used by 5,000 clinicians in 15 departments, such as gastroenterology, anesthesia, and surgery. QPID registers an average 5 million search requests a month. “We struck a nerve,” says Zalis.
Six years ago, radiologist Michael Zalis found himself spending a lot of time logging in and out of separate electronic health records at Massachusetts General Hospital to gather lab data, clinical notes, and other non-imaging information scattered in multiple databases. “Clinicians face this every day,” says Zalis, who quantified the frequency of EHR use to interpret CT scans and MRIs, and published his findings in the American Journal of Roentgenology. “It takes hours to manually pull together information, and clinicians are under pressure to get the information they need.”
Zalis co-founded and wrote the code for QPID, which stands for Queriable Patient Inference Dossier, a natural language search tool that extracts relevant clinical information from an EHR. Since its inception in Mass General’s radiology department, QPID has grown by word of mouth, and is now deployed across Boston-based Partners HealthCare, which includes Brigham and Women’s Hospital. It is used by 5,000 clinicians in 15 departments, such as gastroenterology, anesthesia, and surgery. QPID registers an average 5 million search requests a month. “We struck a nerve,” says Zalis.
Friday, February 15, 2013
The genetics of autism: key issues, recent findings, and clinical implications.
http://www.ncbi.nlm.nih.gov/pubmed/20159341
Psychiatr Clin North Am. 2010 Mar;33(1):83-105. doi: 10.1016/j.psc.2009.12.002.
Autism spectrum disorders (ASDs) are highly heritable. Gene discovery promises to help illuminate the pathophysiology of these syndromes, yielding opportunities for the development of novel treatments and understanding of their natural history. Although the underlying genetic architecture of ASDs is not yet known, the literature demonstrates that it is not a monogenic disorder with mendelian inheritance, rather a group of complex genetic syndromes with risk deriving from genetic variations in multiple genes. This article reviews the origins of the common versus rare variant debate, highlights recent findings in the field, and addresses the clinical implications of common and rare variant discoveries.
Psychiatr Clin North Am. 2010 Mar;33(1):83-105. doi: 10.1016/j.psc.2009.12.002.
Autism spectrum disorders (ASDs) are highly heritable. Gene discovery promises to help illuminate the pathophysiology of these syndromes, yielding opportunities for the development of novel treatments and understanding of their natural history. Although the underlying genetic architecture of ASDs is not yet known, the literature demonstrates that it is not a monogenic disorder with mendelian inheritance, rather a group of complex genetic syndromes with risk deriving from genetic variations in multiple genes. This article reviews the origins of the common versus rare variant debate, highlights recent findings in the field, and addresses the clinical implications of common and rare variant discoveries.
Sunday, February 10, 2013
Ubuntu upgrade Stopping System V runlevel compatibility after login
Stuck on Stopping System V runlevel compatibility
http://askubuntu.com/questions/184411/stuck-on-stopping-system-v-runlevel-compatibility
See if you have lightdm and lightdm-gtk-theme.
Installing gdm package helps.
Run dpkg-reconfigure gdm.
sudo apt-get install lightdm lightdm-gtk-theme
sudo apt-get install gnome-shell
sudo dpkg-reconfigure gdm
sudo /usr/lib/lightdm/lightdm-set-defaults -g lightdm-gtk-greeter
sudo /usr/lib/lightdm/lightdm-set-defaults -d -m true -g unity-greeter
restart "sudo shutdown -r now"
http://askubuntu.com/questions/24946/how-do-i-disable-the-drum-beat-sound-on-the-login-screen
https://answers.launchpad.net/ubuntu/+source/lightdm/+question/203904
Review auth.log, syslog and /var/log/
Move (rename) ~/.Xauthority and restart lightdm.
sudo lightdm restart
http://askubuntu.com/questions/184411/stuck-on-stopping-system-v-runlevel-compatibility
See if you have lightdm and lightdm-gtk-theme.
Installing gdm package helps.
Run dpkg-reconfigure gdm.
sudo apt-get install lightdm lightdm-gtk-theme
sudo apt-get install gnome-shell
sudo dpkg-reconfigure gdm
sudo /usr/lib/lightdm/lightdm-set-defaults -g lightdm-gtk-greeter
sudo /usr/lib/lightdm/lightdm-set-defaults -d -m true -g unity-greeter
restart "sudo shutdown -r now"
http://askubuntu.com/questions/24946/how-do-i-disable-the-drum-beat-sound-on-the-login-screen
https://answers.launchpad.net/ubuntu/+source/lightdm/+question/203904
Review auth.log, syslog and /var/log/
Move (rename) ~/.Xauthority and restart lightdm.
sudo lightdm restart
How to make a stickman movie
http://www.youtube.com/watch?v=USNImOiYAck
List of animation, visualization tools for Ubuntu
http://ubuntuforums.org/showthread.php?t=293798
Synfig
http://www.youtube.com/watch?v=WUxn9jqFJrg
http://www.youtube.com/watch?v=4OTZcY2Uj1k
http://www.youtube.com/watch?v=r-FSDouTUkk
List of animation, visualization tools for Ubuntu
http://ubuntuforums.org/showthread.php?t=293798
Synfig
http://www.youtube.com/watch?v=WUxn9jqFJrg
http://www.youtube.com/watch?v=4OTZcY2Uj1k
http://www.youtube.com/watch?v=r-FSDouTUkk
Saturday, February 9, 2013
People and books
You are the same today you’ll be in five years except for two things: the people you meet and the books you read.
--Charlie Tremendous Jones
--Charlie Tremendous Jones
Friday, February 8, 2013
BGI
http://www.businessweek.com/articles/2013-02-07/bgis-young-chinese-scientists-will-map-any-genome
In agriculture, BGI is mapping genome sequences it considers proprietary and using them to engineer superior strains of rice, millet, and even fish.
The company changed its name from Beijing Genomics Institute to BGI Shenzhen and moved to the shoe factory.
In 2011, BGI reported revenue of 1.2 billion yuan. Many projects the company takes on reflect this policy of for-profit science.
BGI’s footprint is expanding. It recently received approval from the U.S. government to acquire its biggest competitor, Mountain View (Calif.)-based Complete Genomics (GNOM), which also provides commercial DNA sequencing
Complete Genomics will extend BGI’s reach, not only in terms of customers and sequencing power, but also in terms of data storage. Complete Genomics has established its own database of genetic information, complementing BGI’s efforts to build a cloud computing platform capable of holding large amounts of genomic data.
Companies that offer personalized genetic testing, such as 23andMe, typically test only for a sampling of 100 traits and diseases, or about 1/3,000th of the entire genome, Church says. For about $4,000, BGI does the whole thing.
“You’re looking for variants or parts of the genome that are hard to map,” he says. Computer programs have difficulty identifying a new variation unless a spot on the genome has already been pinpointed and entered into the computer program.
“It’s my belief that science has no limits.”
In agriculture, BGI is mapping genome sequences it considers proprietary and using them to engineer superior strains of rice, millet, and even fish.
The company changed its name from Beijing Genomics Institute to BGI Shenzhen and moved to the shoe factory.
In 2011, BGI reported revenue of 1.2 billion yuan. Many projects the company takes on reflect this policy of for-profit science.
BGI’s footprint is expanding. It recently received approval from the U.S. government to acquire its biggest competitor, Mountain View (Calif.)-based Complete Genomics (GNOM), which also provides commercial DNA sequencing
Complete Genomics will extend BGI’s reach, not only in terms of customers and sequencing power, but also in terms of data storage. Complete Genomics has established its own database of genetic information, complementing BGI’s efforts to build a cloud computing platform capable of holding large amounts of genomic data.
Companies that offer personalized genetic testing, such as 23andMe, typically test only for a sampling of 100 traits and diseases, or about 1/3,000th of the entire genome, Church says. For about $4,000, BGI does the whole thing.
“You’re looking for variants or parts of the genome that are hard to map,” he says. Computer programs have difficulty identifying a new variation unless a spot on the genome has already been pinpointed and entered into the computer program.
“It’s my belief that science has no limits.”
Thursday, February 7, 2013
Community-supported agriculture
http://en.wikipedia.org/wiki/Community-supported_agriculture
Community-supported agriculture (in North America sometimes known as community-shared agriculture)(CSA) is an alternative, locally-based socio-economic model of agriculture and food distribution. A CSA also refers to a particular network or association of individuals who have pledged to support one or more local farms, with growers and consumers sharing the risks and benefits of food production. CSA members or subscribers pay at the onset of the growing season for a share of the anticipated harvest; once harvesting begins, they receive weekly shares of vegetables and fruit, in a vegetable box scheme, and also sometimes herbs, cut flowers, honey, eggs, dairy products and meat, as well. Some CSAs provide for contributions of labor in lieu of a portion of subscription costs.
An example of a week's CSA share, includingbell peppers, okra, tomatoes, beans, potatoes,garlic, eggplant, and squash.
Community-supported agriculture (in North America sometimes known as community-shared agriculture)(CSA) is an alternative, locally-based socio-economic model of agriculture and food distribution. A CSA also refers to a particular network or association of individuals who have pledged to support one or more local farms, with growers and consumers sharing the risks and benefits of food production. CSA members or subscribers pay at the onset of the growing season for a share of the anticipated harvest; once harvesting begins, they receive weekly shares of vegetables and fruit, in a vegetable box scheme, and also sometimes herbs, cut flowers, honey, eggs, dairy products and meat, as well. Some CSAs provide for contributions of labor in lieu of a portion of subscription costs.
An example of a week's CSA share, includingbell peppers, okra, tomatoes, beans, potatoes,garlic, eggplant, and squash.
Tuesday, February 5, 2013
Sparse matrix
http://en.wikipedia.org/wiki/Sparse_matrix
In the subfield of numerical analysis, a sparse matrix is a matrixpopulated primarily with zeros (Stoer & Bulirsch 2002, p. 619) as elements of the table.
In the subfield of numerical analysis, a sparse matrix is a matrixpopulated primarily with zeros (Stoer & Bulirsch 2002, p. 619) as elements of the table.
Monday, February 4, 2013
From sequence to function
http://www2.uah.es/farmamol/New_Science_Press/nsp-protein-4.pdf
Protein structure and function summary
Protein structure and function summary
Unix dash (-) symbol = stdin placeholder
(a)
~/home/user > echo '"4 plum"' | cat data/rg.txt -
ID:ga SM:hs LB:ga PL:Illumina
ID:454 SM:hs LB:454 PL:454
"4 plum"
(b)
~/home/user > echo '"4 plum"' | cat - data/rg.txt
"4 plum"
ID:ga SM:hs LB:ga PL:Illumina
ID:454 SM:hs LB:454 PL:454
So in the above examples, the (-) character puts the contents of stdin ("4 plum") before (b) or after (b) the contents of file "data/rg.txt".
cat f - g
Output f’s contents, then standard input, then g’s contents.
~/home/user > echo '"4 plum"' | cat data/rg.txt -
ID:ga SM:hs LB:ga PL:Illumina
ID:454 SM:hs LB:454 PL:454
"4 plum"
(b)
~/home/user > echo '"4 plum"' | cat - data/rg.txt
"4 plum"
ID:ga SM:hs LB:ga PL:Illumina
ID:454 SM:hs LB:454 PL:454
So in the above examples, the (-) character puts the contents of stdin ("4 plum") before (b) or after (b) the contents of file "data/rg.txt".
cat f - g
Output f’s contents, then standard input, then g’s contents.
Friday, February 1, 2013
Genotype and SNP calling from next-generation sequencing data
http://www.nature.com/nrg/journal/v12/n6/pdf/nrg2986.pdf
Abstract
Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and quantify the considerable uncertainty associated with genotype calling, and will especially benefit the growing number of studies using low- to medium-coverage data. We review these methods and provide a guide for their use in NGS studies.
Abstract
Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and quantify the considerable uncertainty associated with genotype calling, and will especially benefit the growing number of studies using low- to medium-coverage data. We review these methods and provide a guide for their use in NGS studies.
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