Bioinformatics Training
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Bioinformatics Training
Bioinformatics, blended with education and health sciences subjects
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Forget your fancy data science, try overkill analytics

Forget your fancy data science, try overkill analytics | Bioinformatics Training | Scoop.it

Meet Carter S. He used to be a lawyer, but now he writes predictive models for an insurance company. Admittedly green in certain new or advanced modeling methods, he prefers to use simple algorithms and throw as much computing power as possible problems. He calls the technique “overkill analytics,” and it just won him his first contest on Kaggle, defeating more than 80 other competitors


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In This Issue - ACS Synthetic Biology (ACS Publications)

In This Issue - ACS Synthetic Biology (ACS Publications) | Bioinformatics Training | Scoop.it

*ACS Synthetic Biology*
September 21st

*Compartment Size and Multimeric Protein Synthesis*
All chemical reactions in the cell take place inside a compartment, whose volume is typically in the range of a micro- to femtoliter. While the volume of the compartment is a fundamental physical parameter in such reactions and can affect intracompartmental reaction kinetics, there have been few studies to elucidate the effects of changes in volume.

*Test Tube Synthesis of the Bacteriophage T7*
The bottom-up synthesis of living systems in the laboratory is a standing challenge to biology, chemistry, and physics. Although many experimental approaches to synthesize complex biological systems in vitro have been proposed, there has been no demonstration to date of natural genome-sized DNA programs being entirely replicated and expressed in vitro into a self-assembled functioning whole.

*Evolutionary Stability of a Refactored Phage Genome*
When engineering a genetic system, only those genetic elements whose functional properties are entirely known are used. This enables elements from diverse genetic backgrounds to be put together to create new pathways and functions.

*Unsaturated Lipidoids for Efficient Intracellular Gene Delivery*
Intracellular gene delivery or gene therapy has long been viewed as a method of treatment for genetic disease. However, there is a lack of safe and efficient gene delivery vehicles.

*Engineering Functional DNA Translocation*
The “portal connector” of bacteriophage viruses is a pore-like structure that allows for DNA translocation. The high specificity of this connector along with its well-defined structure makes it attractive for use as a DNA-nanopore in synthetic tools.

*Synthetic Biology to Explain Cellular Information Processing*
Appropriate responses to environmental signals are essential for the survival of all cells and organisms. These responses are regulated by cellular networks that process these environmental cues.

http://bit.ly/Unxym5


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Motivation and #Games: Motivational Theories for Instructional Games | Kapp Notes

Motivation and #Games: Motivational Theories for Instructional Games | Kapp Notes | Bioinformatics Training | Scoop.it

These techniques can be used for Instructor-Led Training or eLearning modules. These ideas originated in work done by Mark Lepper, a researcher from Stanford University and Thomas Malone also a researcher from Stanford who’s work includes extensive investigations into why games are fun and motivational.

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Friday SNPpets | The OpenHelix Blog

Friday SNPpets | The OpenHelix Blog | Bioinformatics Training | Scoop.it
Latest Tweet. Testify RT @BioMickWatson: Bioinformatics training is essential, but always unfundable. Everyone wants it, noone wants to pay for it.Monday, 09.17.12 18:14 ...
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Human Prehistory 101: Prologue

Award winning video introduces human prehistory starting over 200000 years ago. Who were our first human ancestors? Where did they live?
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GenoCon2 Basic Science for Challenge A – Eukaryotic promoter structure

GenoCon2 Basic Science for Challenge A – Eukaryotic promoter structure | Bioinformatics Training | Scoop.it

In eukaryotes (including humans, animals and plants), transcription is initiated by the following steps. 

1. Proteins termed transcription factor bind the specific regulatory DNA sequence located near or within the gene region

2. RNA polymerase binds DNA

 

A Eukaryote has 3 types of RNA polymerase, each of which is involved in the transcription of genes, as follows. 
・RNA polymerase I: is involved in the transcriptions of the genes encoding ribosomal RNA (18S, 5.8S, 28S rRNA). 
・RNA polymerase II: is involved in the transcriptions of the all genes encoding proteins and of a part of genes encoding snRNA. 
・RNA polumerase III: is involved in the transcription of ribosomal RNA (5S rRNA), transfer RNA (tRNA), and small nuclear RNA(7SL RNA, snRNA).

 

A Promoter, which is composed of several short sequences, takes an important role in initializing gene transcription. The promoter that is involved in the transcription by RNA polymerase II is divided into the following parts...... http://genocon.org/assignment-2012/assignment-a/basic-science-a-eukaryotic-promoter/


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Hans Rosling's shortest TED talk

This talk 'happened' during a spontaneous interview with Hans Rosling, the famous TED speaker. Hans joined us at the TEDxSummit 2012 in Doha, April 15 -- 20,...
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Instructional Games: A Framework

Instructional Games: A Framework | Bioinformatics Training | Scoop.it
Abstract In the last few years, there has been a lot of excitement about games in E-Learning. While everyone understands the concept of games (didn’t we all grow up playing games?), we see differen...
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MGH Plans to Convert SNaPshot Genotyping Assay to NGS as First Step in ... - GenomeWeb

MGH Plans to Convert SNaPshot Genotyping Assay to NGS as First Step in ... - GenomeWeb | Bioinformatics Training | Scoop.it
MGH Plans to Convert SNaPshot Genotyping Assay to NGS as First Step in ...GenomeWebMassachusetts General Hospital's Diagnostic Molecular Pathology Laboratory and Translational Research Laboratory are planning to implement next-generation sequencing...
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Facebook photo tagging: A crowdsourced success story | Socialbrite

Facebook photo tagging: A crowdsourced success story | Socialbrite | Bioinformatics Training | Scoop.it
Tweet This work is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported.
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23andWe Research Findings - 23andMe

23andWe Research Findings - 23andMe | Bioinformatics Training | Scoop.it

A summary of research findings made possible, directly or indirectly by the results that 23andMe has captures.

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Turning a new phage

by

Lauren Gravitz

"The idea of using bacteria-fighting viruses as a weapon against hard-to-treat infections is making a surprising comeback, but with a twist on how it has been attempted for nearly a century. Researchers and companies are now tweaking and deconstructing these bacteria killers in an effort to develop a new arsenal against antibiotic-resistant superbugs—one with more potency and a better likelihood of regulatory approval....."

http://bit.ly/QgJ5Co


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Illumina announces five NGS content sets - Equities.com

Illumina announces five NGS content sets - Equities.com | Bioinformatics Training | Scoop.it
Illumina announces five NGS content setsEquities.comSep 16, 2012 (Datamonitor via COMTEX) -- Illumina, Inc., a developer and manufacturer of life science tools and integrated systems, has announced five initial TruSight content sets for use in...
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The changing privacy landscape in the era of big data

The changing privacy landscape in the era of big data | Bioinformatics Training | Scoop.it

by

Eric E Schadt

"Thirty years ago, it was relatively easy to protect one's privacy and remain anonymous. Few computerized systems existed to store our personal information, the internet was so primitive that most were not even aware it existed, and only a few thousand individuals were privileged enough to own a handheld cellular phone. Fast forward to our current day and life—everything has changed. Rapid electronic transactions among individuals and between individuals and entire communities occur on an unprecedented scale, our life stream is continuously digitized and archived—GPS positioning information, cell phone calls, text messages, credit card purchases, e-mails, online social network chatter and even our electronic medical records (Figure 1). In fact, today the marketing department of your neighborhood Target can know before you that your own daughter is pregnant, given changes in purchase patterns (Duhigg, 2012). Long gone are the days of anonymity and privacy."

http://bit.ly/SQ5KFy


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Organ engineering - combining stem cells, biomaterials, and bioreactors to produce bioengineered organs for transplantation

 

by
Murphy SV, Atala A.

"Often the only treatment available for patients suffering from diseased and injured organs is whole organ transplant. However, there is a severe shortage of donor organs for transplantation. The goal of organ engineering is to construct biological substitutes that will restore and maintain normal function in diseased and injured tissues. Recent progress in stem cell biology, biomaterials, and processes such as organ decellularization and electrospinning has resulted in the generation of bioengineered blood vessels, heart valves, livers, kidneys, bladders, and airways. Future advances that may have a significant impact for the field include safe methods to reprogram a patient's own cells to directly differentiate into functional replacement cell types. The subsequent combination of these cells with natural, synthetic and/or decellularized organ materials to generate functional tissue substitutes is a real possibility. This essay reviews the current progress, developments, and challenges facing researchers in their goal to create replacement tissues and organs for patients."
http://1.usa.gov/UqW5uP


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Work 2.0 - FT.com

Work 2.0 - FT.com | Bioinformatics Training | Scoop.it
Last time “Work”, Ford Madox Brown’s vibrant, populous street scene of navvies laying water pipes in Hampstead, was shown at London’s Tate gallery, it was 1984. Margaret Thatcher, not known as a connoisseur of fine art, attended the opening.
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Genetics 101 Part 1: What are genes?

Find out about the basics of cells, chromosomes, and the genes contained in your DNA.
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The Story of You: ENCODE and the human genome

Ever since a monk called Mendel started breeding pea plants we've been learning about our genomes. In 1953, Watson, Crick and Franklin described the structure of the molecule that makes up our genomes: the DNA double helix.
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Speeding Up Genome Analysis: MIT Algorithms for Direct Computation on Compressed Genomic Datasets

Speeding Up Genome Analysis: MIT Algorithms for Direct Computation on Compressed Genomic Datasets | Bioinformatics Training | Scoop.it
Reporter: Aviva Lev-Ari, PhD, RN A New Approach Uses Compression to Speed Up Genome Analysis Public-Domain Computing Resources Structural Bioinformatics  Genomics  Systems Biology  Other Structural...
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PHG Foundation | US court upholds human gene patents

PHG Foundation | US court upholds human gene patents | Bioinformatics Training | Scoop.it

The US Court of Appeals for the Federal Circuit has upheld the validity of the human gene patents held by the company Myriad Genetics.

The three judge panel ruled in a 2-1 decision that “each of the claimed molecules represents a non-naturally occurring composition of matter”. The court also upheld Myriad’s patent on a technique for identifying potential cancer therapies by monitoring effects on cell growth, but denied their claim on assessing cancer risk by comparing DNA sequences because the method is based on “abstract, mental steps” of logic that are not “transformative”.

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Illumina Granted FDA Contract For NGS Tech To Identify Foodborne Pathogens - RTT News

Illumina Granted FDA Contract For NGS Tech To Identify Foodborne Pathogens - RTT News | Bioinformatics Training | Scoop.it
Illumina Granted FDA Contract For NGS Tech To Identify Foodborne PathogensRTT NewsIllumina Granted FDA Contract For NGS Tech To Identify Foodborne Pathogens. E-MAIL · SHARE. FONT-SIZE. 9/18/2012 12:56 PM ET (RTTNews) - Illumina Inc.
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New platform for online courses stresses team-based, experiential learning | School of Engineering

New platform for online courses stresses team-based, experiential learning | School of Engineering | Bioinformatics Training | Scoop.it

A new online course on a new online platform at Stanford succeeds not only in joining people from dozens of countries but enabling them to directly collaborate on group projects: A group of women in Iran put together a tourism project; three men in India devised a way of connecting Indian musicians, audiences and venues; a pair of men in Trinidad and Tobago figured out how to ease road transportation; a team with members in Germany, the United Kingdom and Russia developed a mobile app for buying and selling locally designed products; and four Americans and a Pakistani created a search engine to find online classes.

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Infosecurity - Quantum Key Distribution takes to the air

An aircraft in flight has successfully transmitted quantum encryption keys to a ground station, bringing closer the time when satellites can be used to provide a theoretically (allegedly) secure communications network.
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NGS in Clinical Research "Results and Lessons Learned"

Dr. Andreas Kremer from ERASMUS Medical Center, discusses the next generation sequencing data analysis tool and how Genome Trax is able to transform the NGS ...
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