Data Analysis and Graphics in R

Data Analysis and Graphics in R

install.packages('DAAG')
library('DAAG')

http://www.amazon.ca/Data-Analysis-Graphics-Using-Example-Based/dp/0521762936

http://cran.r-project.org/doc/contrib/usingR.pdf

http://www.r-project.org/doc/bib/R-books.html

http://cran.r-project.org/doc/contrib/

GridGain - In-memory Big Data

Process TBs of data on 1000s of nodes with in-memory speed anddatabase reliability using Java or Scala.

http://www.gridgain.com/
http://www.gridgain.com/blog/gridgain-hadoop-differences-synergies/

GridGain is Java-based middleware for in-memory processing of big data in a distributed environment. It is based on high performance in-memory data platform that integrates fast In-Memory MapReduce implementation with In-Memory Data Grid technology delivering easy to use and easy to scale software. Using GridGain you can process terabytes of data, on 1000s of nodes in under a second.

GridGain typically resides between business, analytics, transactional or BI applications and long term data storage such as RDBMS, ERP or Hadoop HDFS, and provides in-memory data platform for high performance, low latency data storage and processing.

Both, GridGain and Hadoop, are designed for parallel processing of distributed data. However, both products serve very different goals and in most cases are very complementary to each other. Hadoop is mostly geared towards batch-oriented offline processing of historical and analytics payloads where latencies and transactions don’t really matter, while GridGain is meant for real-time in-memory processing of both transactional and non-transactional live data with very low latencies.

 

Heteroskedasticity

http://en.wikipedia.org/wiki/Heteroscedasticity

The term means "differing variance" and comes from the Greek "hetero" ('different') and "skedasis" ('dispersion').

In statistics, a collection of random variables is heteroskedastic (often spelled heteroscedastic,^[1] and commonly pronounced with a hard k sound regardless of spelling) if there are sub-populations that have different variabilities from others. Here "variability" could be quantified by the variance or any other measure of statistical dispersion. Thus heteroscedasticity is the absence of homoscedasticity.

WHAT IT TAKES TO BE A BIOINFORMATICIAN

http://nygenome.org/blog/what-it-takes-be-bioinformatician

http://biomickwatson.wordpress.com/2013/03/18/the-alternative-what-it-takes-to-be-a-bioinformatician/

NYU Large Scale Machine Learning Class

http://cilvr.cs.nyu.edu/doku.php?id=courses:bigdata:slides:start

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.

Ten Commandments for Next-Gen Sequencing

http://massgenomics.org/2013/02/ngs-commandments.html

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.

SOCIAL MEDIA “AT A GLANCE” 2013

http://ehealth.med.ubc.ca/harnessingthesocialweb/

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.

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/
lightdm/lightdm.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

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