Meet Nephele: Harness the Power of the Cloud for Your Microbiome Data Analysis

Nephele is a project from the National Institutes of Health (NIH) that brings together microbiome data and analysis tools in a cloud computing environment. It aims to address a major challenge facing researchers today — namely, analyzing, transferring, and storing biomedical "big data" — through the use of cloud-based resources

 Why Use Nephele?

• Liberating: Nephele enables you to break free from constraints imposed on high-throughput computational analysis
• Simple: Nephele is designed to be a no-hassle, easy-to-use tool to support your research
• Sophisticated: Nephele is the most intuitive, advanced and secure microbiome analysis platform designed by our experienced computational biologists and software development team to provide exceptional capability with little effort on your part
• Fast: Nephele speeds up microbiome data analysis and paves the path to getting to your results
• Economical: Nephele's on-demand, pay-as-you-go setup offers a cost-effective alternative to using of dedicated resources for your microbiome data analysis

Ready to get started? Visit https://nephele.niaid.nih.gov/ and enter your email address. Check your inbox for a message with the subject "Your Nephele Promotional Codes."

Stay in touch! Email nephele@mail.nih.gov with your questions and feedback. You can also visit our Google+ community page to connect with other researchers in the microbiome community (https://plus.google.com/communities/107278901311674483366).

Source: https://www.biostars.org/p/204081/

Freelancing in Bioinformatics? It's happening here...uBiome FASTQ

http://www.guru.com/jobs/ubiome-raw-data-fastq-files-analysis/1210516#proposalModal

Any takers to help walk this guy through analysing ubiome raw fastq files?

p.s. I wasn't aware that ubiome gives out fastq files?

Inconsistency in Microbiome Studies due to Variable Approaches to DNA Sequencing and Data Analysis

Article Summary:

Human Longevity, Inc. and Venter Institute Scientists Publish Paper Demonstrating Inconsistency in Microbiome Studies due to Variable Approaches to DNA Sequencing and Data Analysis —SAN DIEGO, Oct. 27, 2015 /PRNewswire/ -- Human Longevity, Inc. (HLI), the genomics-based, technology-driven company, announced today that its researchers along with those from the J. Craig Venter Institute and theUniversity of California, San Diego, have published a paper in the journal, Proceedings of the National Academy of Sciences (PNAS), outlining the confusing and conflicting microbiome results generated by a variety of next generation sequencing technology. They also outline recommendations for new research community standards in the microbiome research field given these differences. The paper is being published this week in the early online edition of PNAS.

The two methods that did not require PCR resulted in lower error rates and higher-quality reads for the mock community compared with the PCR-based methods. Moreover, the four different libraries showed significant variation in the relative abundance of microbial members of the mock community and the stool samples.

What 5G mobile networks portends for the future of personal genomics

ok I saw this a while back (a month ago, yes I have been busy) http://www.engadget.com/2014/10/14/samsung-5g-network-tests-oh-god-the-speed/

I am already very impressed with 4G (LTE) speeds but with 5G you can possibly achieve 150 mb/s to 940 mb/s which is mind blowing ...

Considering that you could then possibly upload via your mobile devices, your own 100 Gb bam file in about 10 seconds (sorry I wasn't thinking how much faster a youtube video would stream). Now Google is saying that they can store your genome (actually they meant your 30x WGS bam file) for $25 a year. But with 5G speeds, why would I even bother with that?

Heck, maybe in the future with an USB OTG cable connected to Oxford Nanopore's MinION your android phone will be able to sequence and upload in realtime your DNA obtained from a buccal swab. The cloud will have the fastq reads aligned and call variants instantaneously and download the 100 Gb bam to your microsd card.

Possible applications:

1. Maybe in the future other than asking if you have a drug allergy, pharmacists will request to 'scan' your DNA for the most efficient drug. 
2. another possible application might be having your DNA be your own personal identity card, 
3. more routine sequencing of the human microbiome to monitor your health in relation to the gut microflora or other sites.

I am keen to find out what you think you can do if you could carry your whole genome sequencing with you and upload via mobile networks. Drop in your comments please!

JCVI Supports Human Mircrobiome Body Site Experts with Shotgun Data Analysis from JCVI Blog by Johannes Goll

The current survey comprises more than 700 samples from hundreds of individuals taken from up to 16 distinct body sites. Illumina sequencing has yielded more than 20 billion Illumina reads and annotation data produced from the sequences exceeds 10 terabytes. In anticipation of such data volumes, we have developed JCVI Metagenomics Reports (METAREP), an open source tool for high-performance comparative analysis, in 2010. The tool enables users to slice and dice data using a combination of taxonomic and functional/pathway signatures. To demonstrate how the tool can be used by body site experts, we picked and loaded sample data from 17 oral samples and presented a quick tutorial on how users can view, search, browse individual samples and compare multiple samples (see video). The functionality was very well received and body site experts asked JCVI to make all the 700+ samples available. As a result of the Jamboree, JCVI in agreement/collaboration with the HMP Data Analysis and Coordination Center and the rest of the HMP consortium, will soon set-up a dedicated HMP METAREP instance that will allow body-site experts and eventually other users to analyze the DAWG data in a user-friendly way via the web.