web development

http://x10hosting.com/forums/off-topic/148593-how-do-i-start-building-website-im-stuck-forum-site.html

http://www.slideshare.net/peterlind/google-app-engine-java-style
http://www.youtube.com/watch?v=bfgO-LXGpTM
https://developers.google.com/appengine/docs/python/gettingstarted/devenvironment

• Google App Engine (the cloud http://your_app_id.appspot.com) and Google Sites
• x10hosting 

Nicholas Sparks

http://www.imdb.com/name/nm0817023/

• 
  The Notebook (2004)

  
  The Last Song (2010)

  
  A Walk to Remember (2002)

  
  Dear John (2010)

ORNL microscopy yields first proof of ferroelectricity in simplest amino acid

http://esciencenews.com/articles/2012/04/19/ornl.microscopy.yields.first.proof.ferroelectricity.simplest.amino.acid

The boundary between electronics and biology is blurring with the first detection by researchers at Department of Energy's Oak Ridge National Laboratory of ferroelectric properties in an amino acid called glycine. A multi-institutional research team led by Andrei Kholkin of the University of Aveiro, Portugal, used a combination of experiments and modeling to identify and explain the presence of ferroelectricity, a property where materials switch their polarization when an electric field is applied, in the simplest known amino acid -- glycine.

Breast cancer study reclassifies disease into 10 new categories.

http://www.thestar.com/news/canada/article/1164311--breast-cancer-study-reclassifies-disease-into-10-new-categories?bn=1


“This is a major step forward in building the genetic encyclopedia of breast cancer and in the process we’ve learned there are many more subtypes of breast cancer than we imagined,” said Dr. Sam Aparicio, study co-lead author and professor in the department of pathology and laboratory medicine at UBC.
The 10 subtypes of breast cancer are grouped by common genetic features, which correlate with survival.

Meantime, a separate study by a team of Italian researchers has shown that the drug Herceptin, given to women who produce excess quantities of HER2 cells (human epidermal growth factor 2), reduces breast cancer mortality by one third. However, the risk of heart toxicity went up five times for women on the drug, compared with women receiving only standard therapy such as chemotherapy and radiation.

Achieving greatness

"Every study of high achieving men and women proves that greatness in life is only possible when you become outstanding at your chosen field."
--Brian Tracy


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

• "Our mind is the most valuable possession that we have. The quality of our lives is, and will be, a reflection of how well we develop, train, and utilize this precious gift."
• "Successful people tend to become more successful because they are always thinking about their successes."
• "If you consistently and persistently do the things that other successful people do, nothing in the world can stop you from being a big success also."
• "You are the architect of your own destiny; you are the master of your own fate; you are behind the steering wheel of your life. There are no limitations to what you can do, have, or be. Except the limitations you place on yourself by your own thinking.
• "Resolve in advance that you will never give up, no matter what happens."

Professional master's degree

http://www.nature.com/nbt/journal/v30/n4/full/nbt.2180.html?WT.ec_id=NATUREjobs-20120419


Many PhDs are finding out the hard way how challenging it is to obtain that first position out of the academic laboratory. The skills learned as a PhD student or postdoctoral scientist do not always translate into industry and are often not enough to impress employers. All things being equal, employers will always hire the PhD with additional business administration training.

The reality is now setting in for many PhDs that they need additional training. Professional master's degrees have a proven record of benefitting individuals trained in science, reorienting their career towards nontraditional fields. The monetary and time investment that goes into obtaining a professional master's degree, although significant, is in the end worthwhile.

How to get unique data frame rows in R

struct.uniq <- aggregate(struct, by=list(struct$structure_id), unique)

No shame

The handling of results suggesting faster-than-light neutrinos was a model of fitting behaviour.

Physicists saw plenty of reasons to doubt OPERA's extraordinary claim, and Ereditato and Auterio did not disagree. Even as they presented the result, they invited their colleagues to comment, and encouraged others to try to reproduce their results. Within months, CERN had sent a new beam of neutrinos to Italy and a second experiment found neutrinos travelling at the expected speed. After a great deal of searching, members of the OPERA group eventually traced the discrepancy to a cable that was not fully screwed in.

“The message here is that scientists are not afraid to question the big ideas.”

Ereditato and Auterio acted responsibly when speaking publicly by sticking close to their data and avoiding over-interpretation.

Some Italian journalists aside, the press responsibly reported the initial result as simultaneously incredible and very possibly wrong.

The no-confidence vote and resignations are a matter for the collaboration's internal processes, and have no bearing on the quality of the collaboration's science.

http://www.nature.com/nature/journal/v484/n7394/full/484287b.html?WT.ec_id=NATURE-20120419

School days

"It is indeed ironic that we spend our school days yearning to graduate and our remaining days waxing nostalgic about our school days." -- Isabel Waxman

Children of the 90s: Coming of age

http://www.nature.com/news/children-of-the-90s-coming-of-age-1.10396?WT.ec_id=NEWS-20120417

“It's the deepest phenotyping and biobank resource of any large birth cohort.”

Avon Longitudinal Study of Parents And Children (ALSPAC)
http://www.bristol.ac.uk/alspac/
http://en.wikipedia.org/wiki/Avon_Longitudinal_Study_of_Parents_and_Children

This library is the harvest from an unusual study of humanity. In 1990, researchers started to collect tissues and detailed information from more than 14,500 pregnant women in this western British city and its surrounding region of Avon. The women filled in more than 100 pages of questionnaires about their health, relationships, work and home. After birth, researchers tracked the children's development through surveys, clinical examinations and biological samples. They know what the kids ate, when they first talked, how often they fell sick and when a parent read to them — or deserted them. They know when the children started to hit puberty, drink alcohol, have sex and leave home. In that wealth of data — collected at a cost of some £42 million (US$67 million) so far — they are tracing how genetic and environmental factors in the children's early years affect their later ones.

One showed that eating oily fish during pregnancy was associated with better eye and cognitive development in children^{5, 6}. Another helped to cement advice that babies should be put to sleep on their backs to reduce the risk of cot death, by showing that this sleeping position did not cause any developmental delays⁷. A third showed the first association between peanut allergy — an emerging epidemic in Western countries — and peanut oil in baby lotions⁸. Manufacturers soon started identifying the ingredient on labels.

ROC curves with pROC

http://web.expasy.org/pROC/

pROC: display and analyze ROC curves in R and S+

pROC is a set of tools to visualize, smooth and compare receiver operating characteristic (ROC curves). (Partial) area under the curve (AUC) can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.

In R

http://web.expasy.org/pROC/files/pROC_1.5.3_R_manual.pdf

data(aSAH)

# Build a ROC object and compute the AUC

roc(aSAH$outcome, aSAH$s100b)

roc(outcome ~ s100b, aSAH)

Most popular websites

http://mostpopularwebsites.net/1-50/

Ab initio

http://www.ncbi.nlm.nih.gov/pubmed/22163331

Protein 3D structure computed from evolutionary sequence variation

The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing.In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy.We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues, including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7-4.8 Å C(α)-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org). This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of protein structures, new strategies in protein and drug design, and the identification of functional genetic variants in normal and disease genomes.