OTT: Stephen Wolfram Blog : A Moment for Particle Physics: The End of a 40-Year Story?

Out of Topic but I do wonder if there are > 40 year old mysteries in biology that might invite so much interest and well money to find out .... 

The announcement early yesterday morning of experimental evidence for what's presumably the Higgs particle brings a certain closure to a story I've watched (and sometimes been a part of) for nearly 40 years. In some ways I felt like a teenager again. Hearing about a new particle being discovered. And asking the same questions I would have asked at age 15. "What's its mass?" "What decay channel?" "What total width?" "How many sigma?" "How many events?"
http://blog.stephenwolfram.com/2012/07/a-moment-for-particle-physics-the-end-of-a-40-year-story/

 (Display the citation in PubMed)

1.	Bioinformatics. 2012 Jul 3. [Epub ahead of print] OmegaPlus: A Scalable Tool for Rapid Detection of Selective Sweeps in Whole-Genome Datasets. Alachiotis N, Stamatakis A, Pavlidis P. Source The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies. Abstract MOTIVATION: Recent advances in sequencing technologies have led to the rapid accumulation of molecular sequence data. Analyzing whole-genome data (as obtained from next-generation sequencers) from intra-species samples allows to detect signatures of positive selection along the genome and therefore identify potentially advantageous genes in the course of the evolution of a population.We introduce OmegaPlus, an open-source tool for rapid detection of selective sweeps in whole-genome data based on linkage dis-equilibrium. The tool is up to two orders of magnitude faster than existing programs for this purpose and also exhibits up to two orders of magnitude smaller memory requirements. AVAILABILITY: OmegaPlus is available under GNU GPL at http://www.exelixis-lab.org/software.html. CONTACT: pavlos.pavlidis@h-its.org SUPPLEMENTARY INFORMATION: Available at Bioinformatics online. Free Article
	PMID: 22760304 [PubMed - as supplied by publisher]
	http://bioinformatics.oxfordjournals.org/content/early/2012/07/03/bioinformatics.bts419.long

JoVE: Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

The video tutorial along with the main text does make it easier for non-bioinfo ppl to follow the workflow, (perhaps even convince a few to buy a Mac to work as a bioinformatics console lol ) the wet lab portion looks quite pointless though the graphical explainations are useful. I wonder if this might become a trend, Galaxy styled tutorial videos for papers. Hmmm


JoVE: Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Cite this Article

Vallania, F., Ramos, E., Cresci, S., Mitra, R. D., Druley, T. E. Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER. J. Vis. Exp. (64), e3943, DOI: 10.3791/3943 (2012).

Abstract

As DNA sequencing technology has markedly advanced in recent years², it has become increasingly evident that the amount of genetic variation between any two individuals is greater than previously thought³. In contrast, array-based genotyping has failed to identify a significant contribution of common sequence variants to the phenotypic variability of common disease^4,5. Taken together, these observations have led to the evolution of the Common Disease / Rare Variant hypothesis suggesting that the majority of the "missing heritability" in common and complex phenotypes is instead due to an individual's personal profile of rare or private DNA variants^6-8. However, characterizing how rare variation impacts complex phenotypes requires the analysis of many affected individuals at many genomic loci, and is ideally compared to a similar survey in an unaffected cohort. Despite the sequencing power offered by today's platforms, a population-based survey of many genomic loci and the subsequent computational analysis required remains prohibitive for many investigators.

To address this need, we have developed a pooled sequencing approach^1,9 and a novel software package¹for highly accurate rare variant detection from the resulting data. The ability to pool genomes from entire populations of affected individuals and survey the degree of genetic variation at multiple targeted regions in a single sequencing library provides excellent cost and time savings to traditional single-sample sequencing methodology. With a mean sequencing coverage per allele of 25-fold, our custom algorithm, SPLINTER, uses an internal variant calling control strategy to call insertions, deletions and substitutions up to four base pairs in length with high sensitivity and specificity from pools of up to 1 mutant allele in 500 individuals. Here we describe the method for preparing the pooled sequencing library followed by step-by-step instructions on how to use the SPLINTER package for pooled sequencing analysis (http://www.ibridgenetwork.org/wustl/splinter). We show a comparison between pooled sequencing of 947 individuals, all of whom also underwent genome-wide array, at over 20kb of sequencing per person. Concordance between genotyping of tagged and novel variants called in the pooled sample were excellent. This method can be easily scaled up to any number of genomic loci and any number of individuals. By incorporating the internal positive and negative amplicon controls at ratios that mimic the population under study, the algorithm can be calibrated for optimal performance. This strategy can also be modified for use with hybridization capture or individual-specific barcodes and can be applied to the sequencing of naturally heterogeneous samples, such as tumor DNA.

STAT-Seq: Rapid WGS on the HiSeq 2500 - Implications for a Neonatal Intensive Care Unit recorded webinar

www.illumina.com STAT-Seq: Rapid WGS on the HiSeq 2500: Implications for a Neonatal Intensive Care Unit Thank you for registering for our recent webinar with Dr. Stephen Kingsmore, Director, Center for Pediatric Genomic Medicine at Children's Mercy Hospital, Kansas City, MO. Due to unforeseen travel delays Dr. Kingsmore was unable to make the live event, however a recording is now available for viewing. We appreciate your interest in the Illumina Webinar Series and hope you will join us for future events. To have an Illumina representative contact you about our products and services, please complete our request form and someone will be in contact with you shortly. Sent by Illumina 1.800.809.4566 toll-free (U.S.)  |  +1.858.202.4566 tel

Sort::Rank - search.cpan.org

I have a problem where I needed the non unique rank of SNP id based on a score. I thought that this seemed a terribly popular thing to do but so far most of the options that turned out are Excel and this was the only Perl module that seems to be able to do it.

Sort::Rank - Sort arrays by some score and organise into ranks. http://search.cpan.org/~andya/Sort-Rank-v0.0.2/lib/Sort/Rank.pm

If I needed a unique rank then I could have done it this way

sort -n -k 3 snp_score.csv | nl > ranksorted-snp-score.csv

I could conceivably parse the file again and edit the ranking based on uniqueness of the score value ...

Anyone has a better / faster way to sort 2 million records?

inputfile looks like this

rs  bla 0.8200E+02
rs  bla 1.9200E+02
rs  bla 1.7200E+02
rs  bla 1.8200E+02   
rs  bla 1.8200E+02

I want to get something like

 1  rs  bla 0.8200E+02
 2  rs  bla 1.7200E+02
 3  rs  bla 1.8200E+02
 3  rs  bla 1.8200E+02
 4  rs  bla 1.9200E+02

CIMB Regional Scholarship in two areas: Genetics and Nutrition studies. CIMB Group - Corporate Social Responsibility -

http://www.cimb.com/index.php?ch=g2_csr&pg=g2_csr_content&ac=2&tpt=cimb_group.

CIMB REGIONAL SCHOLARSHIP

In line with our vision to be The Leading ASEAN Franchise, CIMB Group is committed towards building the region's intellectual properties and capabilities. With this in mind, CIMB Group has established the CIMB Regional Scholarship, which aims to provide outstanding individuals from all ASEAN countries a chance to pursue full-time postgraduate degree programmes at top graduate schools throughout the world. For this purpose, CIMB Group seeks highly talented individuals who have attained an impressive track record of academic and personal achievements and can see themselves playing a significant role in the development of the ASEAN region. This year, we are seeking to award five scholarships to deserving individuals in two areas: Genetics and Nutrition studies. Genetics DNA is the hereditary molecule that is found in all living cells. It is the simplest building block of life that is responsible for the observable diversity across and between all species. Ever since the double helix was discovered by Watson and Crick, research into genetics has increased exponentially. The implications of genetic research have been paramount to advances in many fields such as medicine and agriculture. If your passion lies in the following areas, we would like to support you in the quest for another breakthrough in the area of genetic research. Genomics Ecological Genetics / Conservation Genetics Behavioural Genetics / Psychiatric Genetics Genetic Engineering Genetic Medicine / Clinical Genetics Nutrition In terms of nutritional science, studies on the responses of the human body to diet and nutrients are essential for the continued well-being of ASEAN communities. This is particularly important in combating malnutrition, obesity and other health issues. In addition, given the significance of agriculture to the region's economy and food self-sufficiency, plant nutrition and animal nutrition in relation to livestock are also key areas of research. If you are passionate about making a difference through the following areas of nutrition, we would like to bring you a step closer towards realising your dreams: Human Nutrition Animal Nutrition Plant Nutrition

mapping your data .. SYTYCD — where are these terrific dancers come from? | (R news & tutorials)

Tony plotted the origins of about 20 finalists from the 9th season of So You Think You Can Dance. and then overlayed the numbers on US map. 

http://www.r-bloggers.com/sytycd-where-are-these-terrific-dancers-come-from/

(This article was first published on Tony's bubble universe » R, and kindly contributed to R-bloggers)

The resulting interactive map is definitely something I see useful .. 

shall investigate googlevis soon!

http://code.google.com/p/google-motion-charts-with-r/