Archive for February, 2016

Helpful Guidance from the IRS

Thursday, February 25th, 2016

Useful :

NYTimes: A New Breed of Trader on Wall Street: Coders With a Ph.D.

Wednesday, February 24th, 2016

In the world of exchange-traded funds, a $2.8 trillion industry, Jane Street takes the marriage of high tech and high intellect to a new level.

A Group of American Teens Are Excelling at Advanced Math – The Atlantic

Monday, February 22nd, 2016

IBM Launches New Mainframe With Focus On Security And Hybrid Cloud | TechCrunch

Sunday, February 21st, 2016

Hillary Owes Americans the Truth About the Cause of Her Concussion. Trust Is Earned. | RedState

Sunday, February 21st, 2016

Truth About the Cause of [Clinton’s] Concussion Wild post on a #conspiracy theory that’ll make a great movie plot


A Deadly Deployment, a Navy SEAL’s Despair – The New York Times

TIGRA: a targeted iterative graph routing assembler for breakpoint assembly. – PubMed – NCBI

Sunday, February 21st, 2016

TIGRA: Targeted Iterative Graph Routing Assembler for breakpoint[s ] key steps: read extraction & de Bruijn #assembly

This presents a breakpoint assembler used for many projects including 1000 Genomes. It uses a targeted iterative graph routing approach. The program consists of two steps: read extraction and then assembly. The assembly step uses a de Bruin graph-based approach to create contigs from the selected reads. A shortcoming of TIGRA is it depends on the success of the first step of the program, selection of reads that span breakpoints. Thus TIGRA is sensitive to the breakpoint annotation accuracy input. Breakpoints determined from discordant paired-end or split-end alignments and by predictors like breakdancer, delly, genomestrip are excellent for TIGRA, but those determined only by read-depth such as CNVnator and RDX are poor performers.

As input TIGRA requires putative breakpoints annotation/prediction (preferably at nucleotide level or at least within 100bp resolution) and BAM files (sequence reads aligned to reference genome).
In the read extraction TIGRA tries to select all the reads that are likely associated with the breakpoint as long ass they have at least one ned or subsegment that is confidently mapped. For known SV types, TIGRA extract reads selectively to reduce the over representation of the reference allele. The assembly step uses the a de Bruin graph-based approach to create contigs from the selected reads. For this TIGRA first uses an iterative procedure to explore multiple k-mers and thus increases the chance of assembling of low coverage reads. Next it records alternative path in the contain graph

Steven Girvin, Robert Schoelkopf, and Nikhil Padmanabhan among the most influential scientific minds of 2015 | Department of Physics

Sunday, February 21st, 2016

MG mentioned on Thomson Reuter’s
in 2 categories: Biochem & Genetics

Apple-FBI Phone Fight Gets Technical – WSJ

Sunday, February 21st, 2016

To Keep America Safe, Embrace Drone Warfare – The New York Times

Sunday, February 21st, 2016

Visualizing matrix multiplication as a linear combination – Eli Bendersky’s website

Saturday, February 20th, 2016