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AWGSMD13 Analysing Whole-Genome Shotgun Metagenomic Data | Facebook

AWGSMD13 Analysing Whole-Genome Shotgun Metagenomic Data | Facebook | Bioinformatics Training | Scoop.it
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Open for  applications till June 21st

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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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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.

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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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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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Duke Researchers Use Polio Virus for Cancer Treatment

Duke Researchers Use Polio Virus for Cancer Treatment | Bioinformatics Training | Scoop.it
The cure to cancer could come from researchers at the Duke University Hospital Cancer Center.

Via Ed Rybicki, Chris Upton + helpers
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Serious games for bioinformatics education. ISMB 2014 education work…

This presentation surveys the current state of games in bioinformatics education.

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BioCoder

BioCoder | Bioinformatics Training | Scoop.it
BioCoder is a quarterly newsletter for DIYbio, synthetic bio, and anything related.
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"Bioinformatics for Aspiring Synthetic Biologists", pages 5-16

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Breaking the Human Genome Code - Opening Pandora's Box - YouTube

Recent technology advances have resulted in the ability to sequence anyone’s genome cheaply and quickly, but we are only just beginning the journey to discov...
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Interesting talk about the present and predictable future  impact of genomics in human health. Win Hide's  inaugural lecture in Sheffield.

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Baliga Lab: A Global Map To Fight Tuberculosis

Baliga Lab: A Global Map To Fight Tuberculosis | Bioinformatics Training | Scoop.it
3 Bullets:
The disease progression of tuberculosis is extremely complex and it’s poorly understood.
ISB and Seattle BioMed researchers have made an important step by developing a comprehensive map of gene regulation in tuberculosis.
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Global migration of influenza A viruses in swine : Nature

The complex and unresolved evolutionary origins of the 2009 H1N1 influenza pandemic exposed major gaps in our knowledge of the global spatial ecology and evolution of influenza A viruses in swine (swIAVs). Here we undertake an expansive phylogenetic analysis of swIAV sequence data and demonstrate that the global live swine trade strongly predicts the spatial dissemination of swIAVs, with Europe and North America acting as sources of viruses in Asian countries. In contrast, China has the world’s largest swine population but is not a major exporter of live swine, and is not an important source of swIAVs in neighbouring Asian countries or globally. A meta-population simulation model incorporating trade data predicts that the global ecology of swIAVs is more complex than previously thought, and the United States and China’s large swine populations are unlikely to be representative of swIAV diversity in their respective geographic regions, requiring independent surveillance efforts throughout Latin America and Asia.


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Emerging Viral Diseases: The One Health Connection: Workshop Summary

Emerging Viral Diseases: The One Health Connection: Workshop Summary | Bioinformatics Training | Scoop.it
In the past half century, deadly disease outbreaks caused by novel viruses of animal origin - Nipah virus in Malaysia, Hendra virus in Australia, Hantavirus in the United States, Ebola virus in Africa, along with HIV (human immunodeficiency virus),...

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burkesquires's curator insight, March 27, 12:17 PM

Download a FREE PDF of the book!

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Ebola’s fast evolution questioned

Ebola’s fast evolution questioned | Bioinformatics Training | Scoop.it
Genome-sequencing study finds the virus evolving more slowly than thought, but others say the focus should be on monitoring the effects of new mutations.

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ISB Launches 3-Year Wilke Lyme Disease Project with $2.13M Funding

ISB Launches 3-Year Wilke Lyme Disease Project with $2.13M Funding | Bioinformatics Training | Scoop.it
Study Utilizes Systems Approaches to Develop Diagnostics and Deeper Understanding of Chronic Lyme PRESS RELEASE, SEATTLE, March 26, 2015 – Institute for Systems Biology (ISB) has received $2.13 million in transformational gifts from Jeff and Liesl...
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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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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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OpenHelix for bioinformatics software training

Knowing which tools are available, and learning to use them, can be challenging in genomics. The OpenHelix site connects you to information and software training about bioinformatics resources....
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Video Tip of The Week: Jalview for multiple sequence alignment editing and visualization | The OpenHelix Blog

Video Tip of The Week: Jalview for multiple sequence alignment editing and visualization | The OpenHelix Blog | Bioinformatics Training | Scoop.it
The multiple sequence alignment editing question recently on our What's the Answer? feature was popular. We have covered MSA editors in the past, and we include

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Adaptive Evolution and Environmental Durability Jointly Structure Phylodynamic Patterns in Avian Influenza Viruses

Adaptive Evolution and Environmental Durability Jointly Structure Phylodynamic Patterns in Avian Influenza Viruses | Bioinformatics Training | Scoop.it
Avian influenza viruses show high genetic diversity, but give rise to pandemic human influenza strains which are much less diverse; we show that these contrasting degrees of viral diversity can be explained by both host (demography) and viral...

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Utilizing genomics for proteomics data analysis, David Fenyo, NYU Medical School December 3, 2014

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NIH-Led Effort – Including ISB – Launches Big Data Portal for Alzheimer’s Drug Discovery

NIH-Led Effort – Including ISB – Launches Big Data Portal for Alzheimer’s Drug Discovery | Bioinformatics Training | Scoop.it
The National Institutes of Health announced the launch of a new Alzheimer’s Big Data portal, which includes the first wave of data for use by the research community.
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bionode

Bionode provides pipeable UNIX command line tools and JavaScript APIs for bioinformatic analysis workflows.


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PLOS Pathogens: Catch Me If You Can: The Link between Autophagy and Viruses

PLOS Pathogens: Catch Me If You Can: The Link between Autophagy and Viruses | Bioinformatics Training | Scoop.it

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A Novel Host-Proteome Signature for Distinguishing between Acute Bacterial and Viral Infections

A Novel Host-Proteome Signature for Distinguishing between Acute Bacterial and Viral Infections | Bioinformatics Training | Scoop.it
Bacterial and viral infections are often clinically indistinguishable, leading to inappropriate patient management and antibiotic misuse.

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This 17-Year-Old Has Discovered DNA Mutations That Could Combat HIV And Meningitis

This 17-Year-Old Has Discovered DNA Mutations That Could Combat HIV And Meningitis | Bioinformatics Training | Scoop.it
High schooler Andrew Jin is answering previously unasked questions in biology.

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