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Exome Sequencing of Volunteers Sheds Insight into How NGS Could be Rolled ... - GenomeWeb

Exome Sequencing of Volunteers Sheds Insight into How NGS Could be Rolled ... - GenomeWeb | Bioinformatics Training | Scoop.it
Exome Sequencing of Volunteers Sheds Insight into How NGS Could be Rolled ...
GenomeWeb
An exome sequencing study of 81 volunteers has shed light into how the technology could be rolled out as an adult disease risk screening test.
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Bioinformatics Training
Bioinformatics, blended with education and health sciences subjects
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GTPB: ARANGS15 Automated and reproducible analysis of NGS data - Home

GTPB: ARANGS15 Automated and reproducible analysis of NGS data - Home | Bioinformatics Training | Scoop.it
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with Rutger Vos and Darin LondonMay 11th - May 15th 2015Course DescriptionIntroduction

Next generation sequencing (NGS) technologies for DNA have resulted in a yet bigger deluge of data. Researchers are learning that analyzing the data efficiently requires the creation of sophisticated pipelines, typically using commandline tools in a Linux or other Opensource Unix variant compute environment. Many researchers have created these pipelines to successfully analyze their data. Now they are faced with the challenge of making these pipelines available to their colleagues. The issue of reproducibility has emerged as a major issue (TODO REF), as researchers, peer reviewers, and even pharmaceutical companies discover that the software and data used to produce a particular research finding are either not available, poorly documented, or targetted to specific compute infrastructures that are not available to the wider research community. To remedy this, funding agencies and journals are creating policies to promote software reproducibility. In this brief workshop we will establish several best practices of reproducibility in the (comparative) analysis of data obtained by NGS. In doing so we will encounter the commonly used technologies that enable these best practices by working through use casesthat illustrate the underlying principles. Building on the basis of an existing pipeline of commandline utilities, we will illustrate how the entire compute environment used to run the pipeline can be packaged into a unit that can be shared with other researchers such that they can make full use of the environment on their own machines, or on standard cloud compute environments such as amazon or google.

Best practicesCommandline scripting of analysis stepsProvisioning systems to standardize software environment requirementsPackaging of compute environment into static, portable unitsSharing of compute environment packagesTechnologiesNext generation sequencing platformsCommand-line executables, command line scripting and batchingProvisioning Systems: Puppet, DockerfileVirtualization with Virtualbox and VagrantContainerization with DockerTarget audience

This course is aimed at researchers who've developed pipelines to analyze NGS data and now, faced with new reproducibility requirements, would like to learn how to package their analysis pipeline into in a reproducible (and shareable) way. This course will start with a very basic NGS pipeline that runs in a Linux commandline environment, and develop this pipeline into two packages that can be shared with, and used by other researchers. The ideal attendee is a scientist who is already comfortable developing scripted pipelines on the commandline, or who is not afraid to get his/her hands dirty to acquire the computer-literacy skills for dealing with the informatics side of data analysis.

Pre-requisites

The course assumes that attendees are not intimidated by the prospect of gaining experience working on UNIX-like operating systems (including the shell, and shell scripting). Attendees should understand some of the science behind high-throughput DNA sequencing and sequence analysis, as we will not go deeply into underlying theory (or the mechanics of given algorithms, for example) as such. What will be taught are technical solutions for automating and sharing such analyses in shareable, reusable compute environments, which will include (but is not limited to) beginner-level programming, and basic Linux provisioning. General computer literacy, (e.g. editing plain text data files, navigating the command line) will be assumed.

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Genome Biology | Abstract | Temporal and technical variability of human gut metagenomes

Metagenomics has become a prominent approach for exploring the role of the gut microbiota in human health.

Via Mel Melendrez-Vallard
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Introgression Browser: High throughput whole-genome SNP visualization

Introgression Browser: High throughput whole-genome SNP visualization | Bioinformatics Training | Scoop.it
Introgression Browser: High throughput whole-genome SNP visualization Saulo Alves Aflitos, Gabino Sanchez-Perez, Dick de Ridder, Paul Fransz, Eric Schranz, Hans de Jong, Sander Peters (Submitted on...

Via Mel Melendrez-Vallard
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Genomics, Big Data, and Medicine Seminar Series – George Church

George Church, Professor, Genetics at Harvard Medical School and Director, PersonalGenomes.org, speaks on "Why Big Data Is Easier than Little Data.
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ISB Q&A: High School Science Teachers

ISB Q&A: High School Science Teachers | Bioinformatics Training | Scoop.it
From left to right: High school teachers Tami Caraballo and Jennifer Duncan-Taylor work with ISB’s Claudia Ludwig, Baliga Lab Education Program Manager, to learn about ocean acidification, cancer cells, and biofuel.
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Artificial Intelligence helps mold future of genomics

J. Craig Venter Institute CEO J. Craig Venter discusses human longevity and where science is taking us. Watch Maria Bartiromo talk about Strategy on Opening ...
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Retroviral influence on human embryonic development

Retroviral influence on human embryonic development | Bioinformatics Training | Scoop.it
Some of the thousands of human endogenous retroviral genomes are activated during human embryogenesis, suggesting that they may play a role in development.

Via Kenzibit
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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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The Non-parametric Bootstrap as a Bayesian Model

The Non-parametric Bootstrap as a Bayesian Model | Bioinformatics Training | Scoop.it
The non-parametric bootstrap was my first love. I was lost in a muddy swamp of zs, ts and ps when I first saw her. Conceptually beautiful, simple to implement, easy to understand (I thought back then, at least).

Via Mel Melendrez-Vallard
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edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test

edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test | Bioinformatics Training | Scoop.it
edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an uncondit... http://t.co/zl8zthB67b

Via Mel Melendrez-Vallard
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Traning programe on31st march 2015

Traning programe on31st march 2015 | Bioinformatics Training | Scoop.it
BIOINFORMATICS IN MICROBIAL VESICULAR ARBUSCULAR MYCORRHIZA (VAM) RESEARCH.
Link: http://t.co/fx7lh37vPy

Via Jean-Michel Ané
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Cambrian Genomics has found a way to radically reduce the cost of making DNA, enabling

Cambrian Genomics has found a way to radically reduce the cost of making DNA, enabling anyone to design an organism. I've seen this movie before. We all ...
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Translational Genomics

Taking the hocus pocus out of Translational Genomics: A new approach to optimize the utility of gene and SNP array outputs in pre-clinical and clinical trials ...
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Rescooped by Pedro Fernandes from Virology and Bioinformatics from Virology.ca
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Sensitive SNP Sifting With Statistics

Sensitive SNP Sifting With Statistics | Bioinformatics Training | Scoop.it
Requiring neither genotyping nor whole-genome sequencing, the G-SCI method has been used to link genetic variations to autoimmune disease.

Via idtdna, Chris Upton + helpers
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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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Fast principal components analysis reveals independent evolution of ADH1B gene in Europe and East Asia

Fast principal components analysis reveals independent evolution of ADH1B gene in Europe and East Asia | Bioinformatics Training | Scoop.it
Fast principal components analysis reveals independent evolution of ADH1B gene in Europe and East Asia Kevin J Galinsky , Gaurav Bhatia , Po-Ru Loh , Stoyan Georgiev , Sayan Mukherjee , Nick J Patt...

Via Mel Melendrez-Vallard
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Procrustes Analyses in R

Procrustes Analyses in R | Bioinformatics Training | Scoop.it
Procrustes transformations (i.e. a form of multidimensional scaling that allows the comparison of two data sets) have been used extensively in recent literature to assess the similarity of geograph...

Via Mel Melendrez-Vallard
Pedro Fernandes's insight:

See aso: http://www.molecularecologist.com/2012/09/genes-in-space/

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Rescooped by Pedro Fernandes from Virology and Bioinformatics from Virology.ca
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Frontiers | A review on computational systems biology of pathogen–host interactions | Infectious Diseases

Pathogens manipulate the cellular mechanisms of host organisms via Pathogen-Host Interactions (PHIs) in order to take advantage of the capabilities of host cells, leading to infections.

Via burkesquires
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An evaluation of the accuracy and speed of metagenome analysis tools

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Via Mel Melendrez-Vallard
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SYSTEMS BIOLOGY 101: On Being Interdisciplinary

SYSTEMS BIOLOGY 101: On Being Interdisciplinary | Bioinformatics Training | Scoop.it
In describing systems biology and the distinguishing characteristics of ISB’s approach, we always emphasize how our lab groups are intentionally and necessarily interdisciplinary.
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On publishing software

On publishing software | Bioinformatics Training | Scoop.it
This post is a response to Titus and Daniel's blog posts on whether published software should be re-useable, and covers some elements of an argument I had with Aylwyn on Twitter. What is the purpos...

Via Chris Upton + helpers
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Rescooped by Pedro Fernandes from Virology and Bioinformatics from Virology.ca
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Friendly Viruses Protect Us Against Bacteria

Friendly Viruses Protect Us Against Bacteria | Bioinformatics Training | Scoop.it
Viruses in mucus may be important line of defense against disease

Via Kenzibit
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Rescooped by Pedro Fernandes from Bioinformatics Software: Sequence Analysis
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Mapping KEGG pathway names to IDs using KEGG.db package

Mapping KEGG pathway names to IDs using KEGG.db package | Bioinformatics Training | Scoop.it
#bioinformatics Mapping KEGG pathway names to IDs using KEGG.db package http://t.co/y8ZVv2Icfx

Via Mel Melendrez-Vallard
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CoMeta: Classification of Metagenomes Using k -mers

CoMeta: Classification of Metagenomes Using  k -mers | Bioinformatics Training | Scoop.it
Nowadays, the study of environmental samples has been developing rapidly. Characterization of the environment composition broadens the knowledge about the relationship between species composition and environmental conditions.

Via Mel Melendrez-Vallard
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ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching « Homolog.us – Bioinformatics

ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching « Homolog.us – Bioinformatics | Bioinformatics Training | Scoop.it
A new scaffolding paper is published in Bioinformatics.
MOTIVATION:
Next-generation high-throughput sequencing (HTS) has become a state-of-the-art technique in genome assembly. Scaffolding is one of the main stages of the assembly pipeline.

Via Mel Melendrez-Vallard
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Rescooped by Pedro Fernandes from Virology and Bioinformatics from Virology.ca
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To prevent the next Ebola, scientists try to catch new viruses before they break out

To prevent the next Ebola, scientists try to catch new viruses before they break out | Bioinformatics Training | Scoop.it
With the Ebola outbreak not yet behind us, global health workers are already scrambling to prevent what could be the next big outbreak of an emerging disease caused by a virus that jumped from animals into humans.

Via Kenzibit
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Malaria genomics: tracking a diverse and evolving parasite population

Malaria genomics: tracking a diverse and evolving parasite population Professor Dominic Kwiatkowski, University of Oxford and Wellcome Trust Sanger Institute ...
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Rescooped by Pedro Fernandes from Virology and Bioinformatics from Virology.ca
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Targeted diversity generation by intraterrestrial archaea and archaeal viruses : Nature Communications : Nature Publishing Group

Targeted diversity generation by intraterrestrial archaea and archaeal viruses : Nature Communications : Nature Publishing Group | Bioinformatics Training | Scoop.it

In the evolutionary arms race between microbes, their parasites, and their neighbours, the capacity for rapid protein diversification is a potent weapon. Diversity-generating retroelements (DGRs) use mutagenic reverse transcription and retrohoming to generate myriad variants of a target gene. Originally discovered in pathogens, these retroelements have been identified in bacteria and their viruses, but never in archaea. Here we report the discovery of intact DGRs in two distinct intraterrestrial archaeal systems: a novel virus that appears to infect archaea in the marine subsurface, and, separately, two uncultivated nanoarchaea from the terrestrial subsurface. The viral DGR system targets putative tail fibre ligand-binding domains, potentially generating >1018 protein variants. The two single-cell nanoarchaeal genomes each possess ≥4 distinct DGRs. Against an expected background of low genome-wide mutation rates, these results demonstrate a previously unsuspected potential for rapid, targeted sequence diversification in intraterrestrial archaea and their viruses.

  

Via Ed Rybicki
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