nesting commands in xargs

cat links.txt | xargs -I {} sh -c "wget {} | tar czvf {}.tar.gz {}"

or write a for loop

or write xargs command in a separate script

cat links.txt | xargs -I {} myscript.sh {}

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

http://www.andyd.net/2009/escaping-a-pipe-inside-xargs/


---getAndZip.sh----
URL=$1
FN=`basename $1`

echo URL = $1
echo FN = $FN

wget $URL
tar cvzf $FN.tar.gz $FN
rm $FN

Android Dev - Silence camera click (needs a rooted phone)

1) Turn On USB Debugging
settings > applications > development

2) Install ADB Tools
http://developer.android.com/guide/developing/tools/adb.html

android-sdk-linux/tools$ ./android

Select 'Android SDK Platform-tools'

adb kill-server
sudo adb start-server
adb devices

http://groups.google.com/group/android-discuss/browse_thread/thread/f85a795644e65b59?pli=1

3) Remove the camera_click.ogg file from your phone.

http://androidforums.com/motorola-droid/30759-turn-off-camera-shutter-sound.html

You must be rooted to do this but you can do this using ADB Shell or Terminal Emulator. Make sure to change /system to RW first.
ADB shell
SU # this requires a rooted phone, else permission denied
mount -o remount,rw /dev/block/mtdblock4 /system
mv /system/media/audio/ui/camera_click.ogg /system/media/audio/ui/camera_click.ogg.old

Done!!! No more Clicking sound

There are a few programs on the market that allow you access the file on root as well through a GUI if your not comfortable using command lines.

My Brain Notes

http://mybrainnotes.com/memory-brain-stress.html

The amygdala, stress, OCD, and PTSD:

Kindling and stress—how experience affects the brain:

The hippocampus, memory, and depression:

The term hippocampus is derived from the Greek word meaning "sea-horse," which might somehow describe the shape of each hippocampal nucleus,

Wilcoxon rank sum test

> wilcox.test(rnorm(10), rnorm(10, 2), conf.int = TRUE)

Wilcoxon rank sum test

data: rnorm(10) and rnorm(10, 2)
W = 7, p-value = 0.0004871
alternative hypothesis: true location shift is not equal to 0
95 percent confidence interval:
-2.9488832 -0.8543696
sample estimates:
difference in location
-2.002531

Dot Net Nuke CMS

Dot Net Nuke
http://www.dotnetnuke.com/
DotNetNuke Content Management System (CMS) for ASP.NET

R group-by aggregate()

squishes down (by rows)

> x
x gene
Scarb1[2551] -0.005680804 LHX6
Slc41a3[73512484] -0.014839480 SLC41A3
Lhx6[635] -0.001436172 LHX6
Traf7[2527] -0.013320662 TRAF7
Pcyt1b[74641319] -0.027368717 PCYT1B
E330014M11Rik*[77280559] -0.016545674 E330014M11RIK*

> aggregate(x$x, list(x$gene), mean)
Group.1 x
1 E330014M11RIK* -0.016545674
2 LHX6 -0.003558488
3 PCYT1B -0.027368717
4 SLC41A3 -0.014839480
5 TRAF7 -0.013320662

Change and acceptance

"The first step toward change is awareness. The second step is acceptance."
--Nathaniel Branden

Courage

"A timid person is frightened before a danger, a coward during the time, and a courageous person afterward."
--Jean Paul Richter

Walking beside

"Don't walk in front of me, I may not follow; don't walk behind me, I may not lead; walk beside me, and just be my friend."
--Albert Camus

ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression

ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression

Summary: We introduce ProfileChaser, a web server that allows for querying the Gene Expression Omnibus based on genome-wide patterns of differential expression. Using a novel, content-based approach, ProfileChaser retrieves expression profiles that match the differentially regulated transcriptional programs in a user-supplied experiment. This analysis identifies statistical links to similar expression experiments from the vast array of publicly available data on diseases, drugs, phenotypes and other experimental conditions.

Availability: http://profilechaser.stanford.edu

Contact: abutte@stanford.edu

Run over

"Even if you are on the right track, you will get run over if you just sit there."
--Will Rogers

BioLayout Express 3D

BioLayout Express 3D

Network visualizer in 3D

Believe you Can!

"When you believe you can...you can!"
--Maxwell Matlz

NIH Videocasts

NIH Videocasts
http://videocast.nih.gov/PastEvents.asp?c=16

Wintergreen winter green Gaultheria procumbens

Mitchella repens (Partridge Berry) vs Gaultheria procumbens (winter green)

Mitchella repens , or Partridge Berry,[1][2][3][4] or Squaw Vine, is the best known plant in the genus Mitchella. It is a creeping prostrate herbaceous woody shrub, occurring in North America and Japan, and belonging to the madder family (Rubiaceae).

Prefers well-drained shaded areas.

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

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

I don't think I would start them indoors. I would start stratifying the seeds in the refregerator, so that mice won't eat tehm. Them I would put them in the ground before the end of winter, and let the seeds decide when to sprout. Wintergreen is native to your climate and it knows exactly when to sprout. The roots will grow exactly the right way for your soil.

http://answers.yahoo.com/question/index?qid=20090920165907AAaUhoa

www.nsl.fs.fed.us/wpsm/Gaultheria.pdf

http://www.herbs2000.com/herbs/herbs_wintergreen.htm

UCLA Multimodal Connectivity Database

UCLA Multimodal Connectivity Database
Web-based brain network analysis and data sharing

http://jessebrown.webfactional.com/metrics

Brainbow

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

Brainbow is a term used to describe the process by which individual neurons in the brain can be distinguished from neighboring neurons using fluorescent proteins. By randomly expressing different ratios of red, green, and blue derivatives of green fluorescent protein in individual neurons, it is possible to flag each neuron with a distinctive color. This process has been a major contribution to the field of connectomics, or the study of neural connections in the brain.

Principal Component Analysis and Gene Ontology reviews

http://bib.oxfordjournals.org/content/12/6/714.abstract?etoc

Principal component analysis based methods in bioinformatics studies

http://bib.oxfordjournals.org/content/12/6/723.abstract?etoc

The what, where, how and why of gene ontology—a primer for bioinformaticians

Never give in

"Never give in - never, never, never, never, in nothing great or small, large or petty, never give in except to convictions of honour and good sense. Never yield to force; never yield to the apparently overwhelming might of the enemy."
--Winston Churchill

http://en.wikipedia.org/wiki/Winston_Churchill
Sir Winston Leonard Spencer-Churchill, KG, OM, CH, TD, PC, DL, FRS, Hon. RA (30 November 1874 – 24 January 1965) was a predominantly Conservative British politician and statesman known for his leadership of the United Kingdom during the Second World War. He is widely regarded as one of the greatest wartime leaders of the century and served as Prime Minister twice (1940–45 and 1951–55). A noted statesman and orator, Churchill was also an officer in the British Army, a historian, a writer, and an artist. He is the only British prime minister to have received the Nobel Prize in Literature, and was the first person to be made an Honorary Citizen of the United States.

HTML5 = HTML + CSS + JavaScript

HTML5 = HTML + CSS + JavaScript

http://html5center.sourceforge.net/building-apps-in-html5

teach and discover

"You cannot teach a man anything; you can only help him discover it in himself."
--Galileo

Gene expression: The dynamics of the brain transcriptome revealed

Gene expression: The dynamics of the brain transcriptome revealed

The tight regulation of gene expression in space and time is key to understanding how the complexity and variation within and between organisms can arise from a relatively simple DNA blueprint. Until now, few studies had been able to characterize the temporal dynamics of gene transcription in the human brain with the depth reported in two recent papers published in Nature.

http://www.nature.com.proxy.lib.sfu.ca/nrn/journal/v12/n12/full/nrn3145.html?WT.ec_id=NRN-201112

1. Kang, H. J. et al. Spatio–temporal transcriptome of the human brain. Nature 478, 483–489 (2011)
   • Article
2. Colantuoni, C. et al. Temporal dynamics and genetic control of transcription in the human prefrontal cortex. Nature 478, 519–524 (2011).
   • Article

gmail notify in ubuntu (gm-notify)

http://www.addictivetips.com/ubuntu-linux-tips/gm-notify-displays-gmail-notifications-in-ubuntu-with-bubble-messages/

$ sudo add-apt-repository ppa:gm-notify-maintainers/ppa
$ sudo apt-get update ; sudo apt-get install gm-notify
$ gm-notify.py

Ubuntu screenlets

$ sudo apt-get install screenlets

Applications > Accessories > Screenlets

$ sudo add-apt-repository ppa:screenlets-dev/ppa
$ sudo apt-get update

googlecalendar-screenlet
http://gnome-look.org/content/show.php?content=125346

Adjust par margins par('mar') to that axis labels fit inside the window

Adjust par margins to that axis labels fit inside the window

http://ww2.coastal.edu/kingw/statistics/R-tutorials/graphs.html

We could make the font smaller, but I'm stubborn. I don't wanna! The data labels are printed in the margins of the plotting area, and we can see what those are by querying the "mar" settings...

> par("mar")
[1] 5.1 4.1 4.1 2.1

I don't know the units (and the help page does not give up this info--apparently, it is top secret), but these are respectively the bottom, left, top, and right margin sizes. What we need to do is shift the graph up in the plotting window to make room for the data labels on the x-axis...

> par(mar=c(6.4,4.1,2.7,2.1))
> barplot(data.table, beside=T, axis.lty=1, las=2)
> title(main="Passengers by Class:Titanic")
> title(ylab="Number of Passengers")

-----
data(cars)
heatmap.2(as.matrix(cars), cexCol=1, margins=c(5,5))

Popup menu gets stuck on screen in ubuntu

menu boxes stuck on screen

http://ubuntuforums.org/showthread.php?t=1602120
System > Preferences > Appearance > Visual Effects > Normal

x11() in R opens a new R Graphics Device window

x11() in R opens a new R Graphics Device window

Animated desktop wallpaper

http://tech.shantanugoel.com/projects/linux/shantz-xwinwrap

http://www.ubuntu-unleashed.com/2008/04/howto-loop-movie-or-video-as-desktop.html

Shantz xwinrap

$ nice -n 15 xwinwrap -ni -o 0.20 -fs -s -sp -st -b -nf -- /usr/lib/xscreensaver/glmatrix -root -window-id WID

$ nice -n 15 xwinwrap -ni -o 0.20 -fs -s -sp -st -b -nf -- /usr/lib/xscreensaver/glslideshow -root -window-id WID

$ xwinwrap -ni -fs -s -st -sp -b -nf -- mplayer -wid WID -nosound "Steal This Film II.Xvid.avi" -loop 0

Same videos
http://www.youtube.com/watch?v=s34d6GIqXxQ&feature=related

http://www.youtube.com/watch?v=kJGjueu-s0U&feature=related

Ubuntu themes

LaGaDesk 102 Suite 1.0.0

https://www.ultimateeditionoz.com/forum/viewtopic.php?t=1342&p=9855

Epigenetic Regulation of Motor Neuron Cell Death through DNA Methylation

Epigenetic Regulation of Motor Neuron Cell Death through DNA Methylation

DNA methylation is an epigenetic mechanism for gene silencing engaged by DNA methyltransferase (Dnmt)-catalyzed methyl group transfer to cytosine residues in gene-regulatory regions. It is unknown whether aberrant DNA methylation can cause neurodegeneration. We tested the hypothesis that Dnmts can mediate neuronal cell death. Enforced expression of Dnmt3a induced degeneration of cultured NSC34 cells. During apoptosis of NSC34 cells induced by camptothecin, levels of Dnmt1 and Dnmt3a increased fivefold and twofold, respectively, and 5-methylcytosine accumulated in nuclei. Truncation mutation of the Dnmt3a catalytic domain and Dnmt3a RNAi blocked apoptosis of cultured neurons. Inhibition of Dnmt catalytic activity with RG108 and procainamide protected cultured neurons from excessive DNA methylation and apoptosis. In vivo, Dnmt1 and Dnmt3a are expressed differentially during mouse brain and spinal cord maturation and in adulthood when Dnmt3a is abundant in synapses and mitochondria. Dnmt1 and Dnmt3a are expressed in motor neurons of adult mouse spinal cord, and, during their apoptosis induced by sciatic nerve avulsion, nuclear and cytoplasmic 5-methylcytosine immunoreactivity, Dnmt3a protein levels and Dnmt enzyme activity increased preapoptotically. Inhibition of Dnmts with RG108 blocked completely the increase in 5-methycytosine and the apoptosis of motor neurons in mice. In human amyotrophic lateral sclerosis (ALS), motor neurons showed changes in Dnmt1, Dnmt3a, and 5-methylcytosine similar to experimental models. Thus, motor neurons can engage epigenetic mechanisms to drive apoptosis, involving Dnmt upregulation and increased DNA methylation. These cellular mechanisms could be relevant to human ALS pathobiology and disease treatment.

Sensitive Heart

"God's heart is the most sensitive and tender of all. No act goes unnoticed, no matter how insignificant or small."
--Richard J Foster

The road to fraud starts with a single step

http://www.nature.com/news/the-road-to-fraud-starts-with-a-single-step-1.9321?WT.ec_id=NEWS-20111115

Diederik Stapel, a social psychologist and author of many published papers, has resigned his position at Tilburg University in the Netherlands after admitting to fabricating data in his research (see Nature 479, 15; 2011).

Such cases of outright fraud in science are distressing for many reasons. For example, they damage the careers of students and collaborators, and raise doubts about all papers by the same author. Most importantly, they damage public trust in science and in scientists. In this case, trust in social psychologists, and the work we do, has been undermined.

To understand fraud in science, the useful lesson is the significance of that first tiny step. Every minor transgression — dropping an inconvenient data point, or failing to give credit where it is due — creates a threat to self-image. The perpetrators are forced to ask themselves: am I really that sort of person? Then, to avoid the discomfort of this threat, they rationalize and justify their way out, until their behaviour feels comfortable and right. This makes the next transgression seem not only easier, but even morally correct.

Music and words

"Music expresses that which cannot be put into words and that which cannot remain silent."
--Victor Hugo

In France, Hugo's literary fame comes first from his poetry but also rests upon his novels and his dramatic achievements. Among many volumes of poetry, Les Contemplations and La Légende des siècles stand particularly high in critical esteem, and Hugo is sometimes identified as the greatest French poet. Outside France, his best-known works are the novels Les Misérables and Notre-Dame de Paris (also known in English as The Hunchback of Notre-Dame).
http://en.wikipedia.org/wiki/Victor_Hugo

‘Computational pathologist’ (C-Path) diagnoses different grades of breast cancer

named C-Path, for computational pathologist — developed a new list of features that best predicted patient outcome. Instead of focusing on the tumour cells themselves, C-Path determined that the most predictive features were found in the cells surrounding the tumour, in a region called the stroma. The results were published today in Science Translational Medicine (Beck, A. H. et al. Science Trans. Med. 3, 108ra113 (2011)).

http://www.nature.com/news/the-computer-will-see-you-now-1.9324?WT.ec_id=NEWS-20111115

Serotype - cell surface antigens

Serotype or serovar refers to distinct variations within a subspecies of bacteria or viruses. These microorganisms, viruses, or cells are classified together based on their cell surface antigens. Determining serotypes, the process of serotyping, can be based on a variety of factors, including virulence, lipopolysaccharides (LPS) in Gram-negative bacteria, presence of an exotoxin (such as pertussis toxin in Bordetella pertussis), plasmids, phages, genetic profile (such as determined by polymerase chain reaction), or other characteristics which differentiate two members of the same species,[1][2] allowing the epidemiologic classification of organisms to the sub-species level.[1][3] A group of serovars with common antigens is called a serogroup.

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

WGCNA: an R package for weighted correlation network analysis

WGCNA: an R package for weighted correlation network analysis

http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/

Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray samples. Weighted correlation network analysis (WGCNA) can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures. Correlation networks facilitate network based gene screening methods that can be used to identify candidate biomarkers or therapeutic targets. These methods have been successfully applied in various biological contexts, e.g. cancer, mouse genetics, yeast genetics, and analysis of brain imaging data. While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial.

The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis. The package includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software. Along with the R package we also present R software tutorials. While the methods development was motivated by gene expression data, the underlying data mining approach can be applied to a variety of different settings.

Ideas and spontaneous

Quote from Steve Jobs: There is a temptation in our networked age to think that ideas can be developed by email and iChat. That is crazy. Creativity comes from spontaneous meetings, from random discussions. You run into someone, you ask what they are doing, you say Wow and soon you are cooking up all sorts of ideas. Unquote

Life sciences: Biomarkers on the brain * Alla Katsnelson

Life sciences: Biomarkers on the brain
* Alla Katsnelson
Nature

http://www.nature.com/naturejobs/2011/111103/full/nj7371-139a.html?WT.ec_id=NATUREjobs-20111103

joint clinical and research residency in neurochemistry at Sahlgrenska University Hospital at the University of Gothenburg in Sweden

“Biomarkers are really in vivo measurements of the pathology of the disease, so it's an opportunity to investigate the disease mechanisms on a patient level,”

protein biomarkers in the cerebrospinal fluid (CSF)

In the past few years, interest in the discovery and validation of biomarkers for Alzheimer's disease has grown rapidly in both academia and industry. The surge is driven by a growing awareness that disease pathology takes root a decade or more before symptoms of cognitive decline become apparent. The most effective therapies will have to be administered early on, before symptoms are evident — and well validated biological measures will be needed for both diagnosis and prognosis.

Alzheimer's Disease Neuroimaging Initiative (ADNI), is a public–private partnership with researchers at almost 60 institutions in the United States and Canada.

Data-analysis skills are in high demand across biomarker research. Increasingly, researchers are investigating panels of biomarkers rather than single proteins, and studies can involve hundreds or thousands of subjects, each with samples taken at several points over many years.

“Bioinformatics, biostatistics, database handling — those are the most critical skills.”

From lab to therapy

One area of the industry that is hiring, notes Soares, is translational medicine, in which biomarkers are commonly used to help gauge the effectiveness and specificity of a drug candidate as it moves from bench to bedside. Vacancies exist at most pharmaceutical companies, and are generally open to people with MDs, PhDs and pharmacology doctorates, says Soares. Rather than generating biomarker data, these jobs are “more about strategy — how you use the biomarkers to make decisions”.

Mind and rust

"Iron rusts from disuse, stagnant water loses its purity, and in cold weather becomes frozen, even so does inaction sap the vigor of the mind."

--Leonardo da Vinci

Co-expression vs coregulation

From co-expression to co-regulation: how many microarray experiments do we need?

www.ncbi.nlm.nih.gov/pubmed/15239833

The primary thrust of this paper is to provide guidance to
researchers who wish to use cluster analysis of gene expres-
sion data to identify co-regulated genes.

We define co-
expressed genes as genes that share similar expression pat-
terns as discovered by cluster analysis, and we define co-reg-
ulated genes as genes that are regulated by at least one
common known transcription factor.

Canadian Association for Neuroscience

http://www.can-acn.org/graduate-student-positions

The Association welcomes Canada's investment of up to 100 million dollars in the Canada Brain Research Fund

The purpose of the Canadian Association for Neuroscience shall be:

1- To promote communication among neuroscientists throughout Canada.

2- To represent the interests of Canadian neuroscientists at national and international levels.

3- To promote research in all disciplines contributing to the understanding of the nervous system.

4- To contribute to the advancement of education in the Neurosciences.

5- To provide for and assist in the dissemination to the general public of the results of current Neuroscience research and its significance in relation to health and disease.

6- To raise funds and to provide income for the above purposes.

(CAN-ACN By-laws, Article 6)

A role for insulator elements in the regulation of gene expression response to hypoxia

A role for insulator elements in the regulation of
gene expression response to hypoxia

http://nar.oxfordjournals.org/content/early/2011/11/07/nar.gkr842.abstract?keytype=ref&ijkey=KuQt2Hy5oAv7jK8

Maria Tiana1,2, Diego Villar1, Eva Perez-Guijarro1, Laura Gomez-Maldonado1,
Eduardo Molto , Ana Fernandez-Minan , Jose Luis Gomez-Skarmeta4,
Lluıs Montoliu and Luis del Peso *

In vertebrates, several regulatory
elements including CTCF binding motifs (36–38),
repetitive elements, [such as ALUs (39), SINE B2 (29)
and SINE B1 (30)] and scaffold/matrix-attachment
regions [S/MARs; (40,41)], have been shown to function
as insulators (25,42).

Thus, the insula-
tor activity described herein could be mediated by S/MAR
elements.


Elnitski bidirectional promoters’ prediction track

Allen Institute for Brain Science YouTube Channel

http://www.youtube.com/user/AllenInstitute#p/u

Tom Daniel
University of Washington
Sensorimotor control of movement: Even the circuits of little brains accomplish complex tasks

Michale Fee
Massachusetts Institute of Technology
Prime movers of the brain: Localizing neural circuits that drive complex motor behaviors

Itzhak Fried
University of California, Los Angeles; Tel-Aviv University, Israel
Neurons as will and representation: Recordings from the human brain

Nathaniel Heintz
The Rockefeller University; Howard Hughes Medical Institute
Genetic dissection of the mouse brain: Toward a 21st century brain pharmacology

Leah Krubitzer
University of California, Davis
How does evolution build a complex brain?

Markus Meister
Harvard University
Neural computation in the retina

Dharmendra S. Modha
IBM Research, Almaden
Cognitive computing: Neuroscience, supercomputing, nanotechnology

Sacha B. Nelson
Brandeis University
Defining the mammalian neurome

Richard Palmiter
University of Washington; Howard Hughes Medical Institute
Deciphering a neural circuit controlling anorexia in the mouse

Tomaso Poggio
Massachusetts Institute of Technology
The computational magic of the ventral stream: A theory

Sharad Ramanathan
Harvard University
Discovering circuits that control fate choices in embryonic stem cells

R. Clay Reid
Harvard Medical School
Functional and structural imaging of cortical circuits

Eric Schadt
Pacific Biosciences
A systems framework for understanding the complexity of living systems

Idan Segev
The Hebrew University, Jerusalem
Design principles for dendritic inhibition

Terry Sejnowski
Salk Institute; University of California, San Diego; Howard Hughes Medical Institute
A new view of the neuropil

Pamela Sklar
Mount Sinai School of Medicine
Genomics and psychiatry

Michael P. Stryker
University of California, San Francisco
Rewiring the cortex

Giulio Tononi
University of Wisconsin, Madison
Sleep function and synaptic homeostasis

Hongkui Zeng
Allen Institute for Brain Science
Genetic approaches for brain circuit dissection and connectivity mapping

http://www.alleninstitute.org/events/symposium/index.html

Jay Bradner: Open-source cancer research

http://www.ted.com/talks/jay_bradner_open_source_cancer_research.html

And so please consider this a work in progress, but I'd like to tell you today a story about a very rare cancer called midline carcinoma, about the protein target, the undruggable protein target that causes this cancer, called BRD4, and about a molecule developed at my lab at Dana Farber Cancer Institute called JQ1, which we affectionately named for Jun Qi, the chemist that made this molecule. Now BRD4 is an interesting protein.

Navit for Android, the completely free and offline Navigation system for Android

Navit for Android, the completely free and offline Navigation system for Android

Navit for Android is an open source (GPL) car navigation system.
It will display your position on a map (in bird-view mode or as a 3D "visualization") from GPS sensor data, and can provide precise route calculation, touch screen functionality and supports Points of Interest (POI).

Unlike other navigation systems, Navit maps are dynamically generated in real time from vector data.
Navit is completly offline and works without an internet connection.

Features:
*) Navigate to target from google maps
*) works offline
*) spoken directions in many languages
*) uptodate OSM maps


https://market.android.com/details?id=org.navitproject.navit&hl=en

http://wiki.openstreetmap.org/wiki/Android

Curiosity and spark

"Awaken people's curiosity. It is enough to open minds, do not overload them. Put there just a spark."
--Anatole France

Google updates search engine for fresher results

Google has overhauled the way it serves up results in response to search queries.

The update is designed to work out whether a person wants up-to-date results or historical data.

The US firm estimated the alterations to its core algorithm would make a difference to about 35% of searches.

http://www.bbc.co.uk/news/technology-15590285

‘Rich club’ of 12 rule the human brain

http://www.jpost.com/Health/Article.aspx?id=244150

http://www.jneurosci.org/content/31/44/15775

“If we wanted to look for consciousness in the brain, I would bet on it turning out to be this rich club,” he said.

Best connected of all is the precuneus, an area at the back of the brain. Van den Heuvel says its function is not well understood, but thinks that it acts as an "integrator region" collating high-level information from all over the brain.

The “rich club” comprises of six pairs of identical regions, with one of each pair in each hemisphere of the brain and the best connected of all is the precuneus, an area at the back of the brain.

CPSC 310 Software Engineering: A practical introduction (2011 Winter Term 1)

http://www.ugrad.cs.ubc.ca/~cs310/


Introduction to Software Development: Specification, design, implementation and maintenance of large, multi-module software systems. Principles, techniques, methodologies and tools for computer aided software engineering (CASE); human-computer interfaces, reactive systems, hardware-software interfaces and distributed applications.

When you complete this course, you should be able to:

* Explain the technical and interpersonal challenges of software development
* Communicate technical matters with programmers, managers, and clients effectively
* Perform the activities of software development effectively, using up-to-date methodologies or tools

Nature Special issue on neuroscience: The autism enigma

Special issue on neuroscience: The autism enigma

http://www.nature.com/news/2011/111102/full/479021a.html


http://www.nature.com/nature/journal/v479/n7371/full/479033a.html

Changing perceptions: The power of autism

Scientists, too, should do more than simply study autistic deficits. By emphasizing the abilities and strengths of people with autism, deciphering how autistics learn and succeed in natural settings, and avoiding language that frames autism as a defect to be corrected, they can help shape the entire discussion.

PDF CDF

http://en.wikipedia.org/wiki/Hypergeometric_distribution
In probability theory and statistics, the hypergeometric distribution is a discrete probability distribution that describes the probability of k successes in n draws from a finite population without replacement. (cf. the binomial distribution, which describes the probability of k successes in n draws with replacement.)

Hypergeometric calculator
http://stattrek.com/tables/hypergeometric.aspx

http://www.six-sigma-material.com/Hypergeometric-Distribution.html
Assumptions
# Discrete distribution.
# Population, N, is finite and a known value.
# Two outcomes - call them SUCCESS (S) and FAILURE (F).
# Number of successes in the population is known, S.
# Used when sample size,n, is greater than or equal to 5% of N.
# Trials are done without replacement, dependent.


http://www.mathworks.com/help/toolbox/stats/hygecdf.html
hygecdf - Hypergeometric cumulative distribution function

Example
Suppose you have a lot of 100 floppy disks and you know that 20 of them are defective. What is the probability of drawing 0 through 5 defective floppy disks if you select 10 at random?

In Matlab:
p = hygepdf(0:5,100,20,10)
p =
0.0951 0.2679 0.3182 0.2092 0.0841 0.0215

In R:
> library('stats')
> dhyper(0:5,20,80,10)
[1] 0.09511627 0.26793316 0.31817063 0.20920809 0.08410730 0.02153147

> phyper(0:5,20,80,10) # CDF, at most 5
[1] 0.09511627 0.36304943 0.68122006 0.89042815 0.97453545 0.99606692
> 1-phyper(5,20,80,10) # at least 6
[1] 0.003933076

http://www.youtube.com/watch?v=1xQ4r2gcW3c

Picking advisors and committee members

http://www.experience.com/alumnus/article?channel_id=advanced_degree_development&source_page=home&article_id=article_1150430925421

http://edit911.com/2011/03/choosing-your-dissertation-committee/

http://www.articlesbase.com/writing-articles/choosing-your-dissertation-committee-4366352.html

RNA-editing Exome vs Transcriptome

http://milospjanic.blogspot.com/2011/08/widespread-sequence-differences-between.html

Editing events were more common in 3ÚTR exons then in other exons.

Exome - DNA, protein-coding mutations, mendelian disease
Transcriptome - mRNA, alternative splicing, expression

Libreoffice over OpenOffice

LibreOffice is like OpenOffice. Only OpenOffice was acquired by Oracle and later released under Apache Software Foundation and lags a bit in terms of features. For example, LibreOffice has the insert table / chart / video icon in the middle, lines seem to be straighter, but it still has the same problem of missing second-level bullet points when opening .PPT ...

http://joesteiger.com/2011/03/23/install-libreoffice-ubuntu-10-10/


# NOTE: This will uninstall openoffice because libreoffice does not play with it!
sudo apt-get purge openoffice*.*

sudo add-apt-repository ppa:libreoffice/ppa

sudo apt-get update

sudo apt-get install libreoffice libreoffice-gnome language-support-en

Human brain and Complexity

“If the human brain were so simple that we could understand it, we would be so simple that we couldn't.”
—Emerson Pugh (in The Biological Origin of Human Values)

Prejudice and Humanity

"I have no color prejudices nor caste prejudices nor creed prejudices. All I care to know is that a man is a human being, and that is enough for me; he can't be any worse."
--Mark Twain

Generate Factor Levels

> gl(2, 8, labels = c("Control", "Treat"))
[1] Control Control Control Control Control Control Control Control Treat
[10] Treat Treat Treat Treat Treat Treat Treat
Levels: Control Treat
> ?gl
> gl(2, 1, 20)
[1] 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2
Levels: 1 2

Google Chart API with Gaelyk on the Google App Engine

http://ice09.wordpress.com/2009/11/04/google-chart-api-with-gaelyk-on-the-google-app-engine/

Neurons

http://psychology.about.com/od/biopsychology/f/neuron01.htm

Unlike other body cells, neurons stop reproducing shortly after birth. Because of this, some parts of the brain have more neurons at birth than later in life because neurons die but are not replaced. While neurons do not reproduce, research has shown that new connections between neurons form throughout life.

It is estimated that there are 10 to 50 times more glial cells than there are neurons in the brain.

Neurotransmitters
Acetylcholine: Associated with memory, muscle contractions, and learning. A lack of acetylcholine in the brain is associated with Alzheimer’s disease.

Endorphins: Associated with emotions and pain perception. The body releases endorphins in response to fear or trauma. These chemical messengers are similar to opiate drugs such as morphine, but are significantly stronger.

Dopamine: Associated with thought and pleasurable feelings. Parkinson’s disease is one illness associated with deficits in dopamine, while schizophrenia is strongly linked to excessive amounts of this chemical messenger.

Worries and shadows

"Worry often gives a small thing a big shadow."
--Swedish proverb