Microbial community profiling workshop in UK

Mike Head left a comment about a workshop which looks interesting. Would loved to be there.

http://idrn.org/events/upcoming/microbial.php

AIM
The aim of such an event would be to bring together researchers interested in profiling whole bacterial communities using techniques such as metagenomics, (16s rDNA sequencing and whole bacterial DNA sequencing), T-RFLP, and other commercial applications.

OBJECTIVES
To allow interested researchers and clinicians to better understand the potential of such techniques and to identify the best method of profiling their bacterial community of choice. To provide researchers who wish to use such methods with an overview of the theory of these methods such that experimental design is possible. Use of methods will be illustrated with examples of their use in infection research

IMPORTANCE Such techniques are used in environmental microbiology and are now being used in projects such as the human microbiome projects to investigate the diversity human pathogens and commensals and to characterise the microbial profile of various niches and relate this to conditions such as GI and respiratory disease.

CONFIRMED SPEAKERS
Alan Walker (Sanger, UK)
Geraint Rogers (Kings, UK)
Mike Cox (Imperial, UK)
Bill Cookson (Imperial, UK)
Nick Loman / Mark Pallen (Bham, UK)
Chris Quince (Glasgow, UK)
Luanne Hall-Stoodley (Southampton, UK)
Bill Keevil (Southampton, UK)
Nick Jakubovics (Newcastle, UK)

Omics! Omics!: Has Ion Torrent Taken A 318-Sized Lead over MiSeq?...

Omics! Omics!: Has Ion Torrent Taken A 318-Sized Lead over MiSeq?...: "About a week ago, Ion Torrent's President Greg Fergus and Head of Marketing Manesh Jain were kind enough to engage me in a nearly an hour of..."

Kevin: Excellent lengthy discussion of the merits of Ion Torrent and compares the sample prep time to the MiSeq in a virtual scenario.

Guide/tutorial for the analysis of RNA-seq data

link in seqanswers

Excellent starting point for those confused about the RNA-seq data analysis procedure.

Hello,

I've written a guide to the analysis of RNA-seq data, for the purpose of differential expression analysis. It currently lives on our internal wiki that can't be viewed outside of our division, although printouts have been used at workshops. It is by no means perfect and very much a work in progress, but a number of people have found it helpful, so I thought it would useful to have it somewhere more publicly accessible.

I've attached a pdf version of the guide, although really what I was hoping was that someone here could suggest somewhere where it could be publicly hosted as a wiki. This area is so multifaceted and fast-moving that the only way such a guide can remain useful is if it can be constantly extended and updated.

If anyone has any suggestions about potential hosting, they can contact me at myoung @wehi.edu.au

Cheers

Matt

Update: I've put a few extra things on our local Wiki and seeing as people here seem to be finding this useful I thought I'd post an updated version. I'm also an author on a review paper on Differential Expression using RNA-seq which people who find the guide useful, might also find relevant...

RNA-seq Review

Softgenetics Nextgene has Ion Torrent analysis webinar

NextGENe 2nd generation sequence analysis

Update: links are javascripted popups (hate those, tried inserting the header if it still doesn't work , you need to go via
http://www.softgenetics.com/analysisCorner2.html

Thanks for the headsup!

NextGENe Software Basics for Biologists
http://www.softgenetics.com/webinarC.html

Target Capture Analysis with NextGENe (part 1)
http://www.softgenetics.com/webinarA.html

Target Capture Analysis with NextGENe (part 2)
http://www.softgenetics.com/webinarB.html

Ion Torrent
http://www.softgenetics.com/webinar/sg_iontorrent.html

Public Survey on data privacy while using data analysis workflows

We are researchers at Carnegie Mellon University who are conducting a survey of users who compose web services in their workflows to build applications. One of the goals of this survey is to better understand the privacy concerns of web service users (or lack thereof), and how well users are able to resolve these concerns. Even if you have no data privacy and security problems while using web services, we would still appreciate your feedback because that would give us a better perspective of the problem scenario.

Please take time to fill the following questionnaire:
https://www.surveymonkey.com/s/RCC7XWT

The survey consists of maximum 17 questions and can be completed in about 10 minutes. There are no correct or incorrect responses. This survey is approved by CMU Institutional Review Board (IRB), and would follow the appropriate safety protocols set by the IRB (Protocol Number: HS11-091). All responses would be treated confidentially and will not be traceable to individual respondents.

Thank you in advance for your assistance and time !!

Best Regards,

Vishal Dwivedi and Kun Niu
Carnegie Mellon University,
Pittsburgh, USA.

Email: vdwivedi @cs.cmu.edu & kunn @andrew.cmu.edu

p.s.
The survey results would be made public once we are done processing the raw data. At this point I am trying to collect data from different communities, and would appreciate responses from Galaxy users even if they don't have privacy concerns for the kind of tasks they do, as this would help us to get a better understanding of the domain.

The survey respondents can choose to leave their email address (on a 'separate form' linked to the survey) and we would make sure that the survey results are mailed to them once we finish the analysis of the survey. I can also make it public via my homepage.

Papers on Comparison of microRNA profiling platforms

Systematic Evaluation of Three microRNA Profiling Platforms: Microarray, Beads Array, and Quantitative Real-Time PCR Array

Background

A number of gene-profiling methodologies have been applied to microRNA research. The diversity of the platforms and analytical methods makes the comparison and integration of cross-platform microRNA profiling data challenging. In this study, we systematically analyze three representative microRNA profiling platforms: Locked Nucleic Acid (LNA) microarray, beads array, and TaqMan quantitative real-time PCR Low Density Array (TLDA).

Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression

Abstract
RNA abundance and DNA copy number are routinely measured in high-throughput using microarray and next-generation sequencing (NGS) technologies, and the attributes of different platforms have been extensively analyzed. Recently, the application of both microarrays and NGS has expanded to include microRNAs (miRNAs), but the relative performance of these methods has not been rigorously characterized. We analyzed three biological samples across six miRNA microarray platforms and compared their hybridization performance. We examined the utility of these platforms, as well as NGS, for the detection of differentially expressed miRNAs. We then validated the results for 89 miRNAs by real-time RT-PCR and challenged the use of this assay as a “gold standard.” Finally, we implemented a novel method to evaluate false-positive and false-negative rates for all methods in the absence of a reference method.

NCBI To Discontinue Sequence Read Archive and Peptidome

About SRA

Due to budget constraints, NCBI will be discontinuing its Sequence Read Archive (SRA) and Trace Archive repositories for high-throughput sequence data. Closure of the databases will occur in phases. SRA and Trace will stop accepting some types of submissions in the coming weeks, and all submissions within the next 12 months. Over the next several months, NCBI will be working with staff from NIH Institutes that fund large-scale sequencing efforts to develop an approach for future access to and storage of the existing data. NCBI will continue to support and develop information resources for biological data derived from next-generation sequencing such as genotypes, common variations, rare variations, sequence assemblies and gene expression data. We therefore encourage the research community to continue submissions of these data to the applicable databases, including:

• RNA-Seq and epigenomic data to GEO
• Variants, genotypes, phased haplotypes, and polymorphisms to dbVar, dbGaP and dbSNP
• Genomic assemblies to GenBank/WGS
• Transcript assemblies to GenBank/TSA
• 16S ribosomal RNA and other targeted locus survey assemblies to GenBank

NCBI expects new applications will continue to emerge for next generation technology. We are excited to work with the community to develop strategies for archiving other summary experimental measures that are informative, efficient, and valuable to the biomedical research community.
For further information about submissions, contact NCBI's Help Desk.

About Peptidome

Due to budgetary constraints NCBI will be discontinuing the Peptidome Repository. Over the next few weeks, we will phase out the online browser, query, and display interfaces.
All existing data and metadata files will continue to be made available from our ftp server (ftp://ftp.ncbi.nih.gov/pub/peptidome/) indefinitely. Those files are named according to their Peptidome accession numbers, allowing cited data to still be identified and downloaded. Furthermore, we will endeavor to deposit all Peptidome data in a different public mass spectrometry repository; information about this effort will follow soon.
For those datasets that have been accessioned, but have not yet been made public, submitters have the option of withdrawing the data now and moving it to another repository. If we retain the data, it will move to the Peptidome FTP site on the date at which it is currently designated to go public.
If you have any specific questions, please feel free to contact us at peptidome@ncbi.nlm.nih.gov.