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Geographic population structure analysis of worldwide human populations infers their biogeographical origins : Nature Communications : Nature Publishing Group

written 6.5 years ago by Kevin's GATTACA World

There's no stopping a cheesy geneticist when he puts his mind to making a research idea stick ... like coming up with acronyms like GPS to determine biogeographical origin ...

When is db=all not db=all? When you use Entrez ELink.

written 6.5 years ago by What You're Doing Is Rather Desperate

Just a brief technical note. I figured that for a given compound in PubChem, it would be interesting to know whether that compound had been used in a high-throughput experiment, which you might find in GEO. Very easy using the E-utilities, as implemented in the R package rentrez: Browsing the rentrez documentation, I note that […]

Gut check: Microbes in our stomachs may be making us miserable -

written 6.5 years ago by Kevin's GATTACA World

Seems like gut microbiome is getting more and more air time in news.;utm_medium=socialflow

Fwd: Welcome to the Google Genomics Preview

written 6.5 years ago by Kevin's GATTACA World

Sweet!!---------- Forwarded message ---------- Welcome to the Google Genomics Preview! You've been approved for early access to the API. The goal of the Genomics API is to encourage interoperability and build a foundation to store, process, search, analyze and share tens of petabytes of genomic data. We've loaded sample data from public BAM files: * The complete 1000 Genomes Project * Selections from the Personal Genome Project How to get started: * Follow the instructions in the developer documentation * Try the sample genome browser which calls the API * Try out the other open source examples -- an R script, Python MapReduce, and a Java file-based implementation * Write your own code to call the API and explore new uses This is only the beginning. Your feedback will be essential to make the API useful. Please submit feature requests, bugs and suggestions on our GitHub page. Thank you for being part of the first wave. If you'd rather join with a different email address (Gmail or Google Apps domain), please fill out the request form with that address too, and we'll grant access soon. Thank you for your interest! Sincerely, The Google Genomics team

On the road: CSS and eResearch Conference 2014

written 6.6 years ago by What You're Doing Is Rather Desperate

Next week I’ll be in Melbourne for one of my favourite meetings, the annual Computational and Simulation Sciences and eResearch Conference. The main reason for my visit is the Bioinformatics FOAM workshop. Day 1 (March 27) is not advertised since it is an internal CSIRO day, but I’ll be presenting a talk titled “SQL, noSQL […]

“Advance” access and DOIs: what’s the problem?

written 6.6 years ago by What You're Doing Is Rather Desperate

When I arrive at work, the first task for the day is “check feeds”. If I’m lucky, in the “journal TOCs” category, there will be an abstract that looks interesting, like this one on the left (click for larger version). Sometimes, the title is a direct link to the article at the journal website. Often […]

Improving reproducibility and installation of genomic analysis pipelines with Docker

written 6.6 years ago by Blue Collar Bioinformatics

Motivation bcbio-nextgen is a community developed, best-practice pipeline for genomic data processing, performing automated variant calling and RNA-seq analyses from high throughput sequencing data. It has an automated installation script that sets up the code and third party tools used during analysis, and we’ve been working on improving the process to make getting started with […]

NGS Saves A Young Life

written 6.7 years ago by Omics! Omics!

One of the most electrifying talks at AGBT this year was given by Joe DeRisi of UCSF, who gave a brief intro on the difficulty of diagnosing the root cause of encephalitis (as it can be autoimmune, viral, protozoal, bacterial and probably a few other causes) and then ran down a gripping case history which seemed straight out of House.Read more »

A Sunset for Draft Genomes?

written 6.7 years ago by Omics! Omics!

The sun set during AGBT 2014 for a final time over a week ago. The posters have long been down, and perhaps the liver enzyme levels of the attendees are now down to normal as well. This year’s conference underscored a possibility that was suggested last year: that the era of the poorly connected, low quality draft genome is headed for the sunset as wellRead more »

How will you deal with GRCh38?

written 6.7 years ago by Omics! Omics!

I was foolishly attempting to catch up with Twitter last night during Valerie Schneider's AGBT talk last night on the new human reference, GRCh38. After all, my personal answer to my title is nothing, because this isn't a field I work in. But Dr. Schneider is a very good speaker and I could not help but have my attention pulled in. While clearly not the final word on a human reference, this new edition fixes many gaps, expands the coverage of highly polymorphic regions, and even models the difficult to assemble centromeres. Better assembly, combined with emerging tools to better handle those complex regions via graph representations, means better mapping send better variant calls.So, a significant advance, but a bit unpleasant one if you are in the space. You now have several ugly options before you with regard to your prior data mapped to an earlier reference.The do nothing option must appeal to some. Forgo the advantages of the new reference and just stick to the old. Perhaps start new projects on the new one, leading to a cacophony of internal tools dealing with different versions, with an ongoing risk of mismatched results. Also, cross your fingers that none of changes might be revised if analyzed against the new reference. Perhaps this route will be rationalized as healthy procrastination until a well-vetted set of graph-aware mappers exist, but once you start putting-off it is hard to stop doing so. The other pole would be to embrace the new reference whole-heartedly ...

Parallelizing #RStats using #make

written 6.7 years ago by YOKOFAKUN

In the current post, I'll show how to use R as the main SHELL of GNU-Make instead of using a classical linux shell like 'bash'. Why would you do this ? awesomeness Make-based workflow management Make-based execution with --jobs. GNU make knows how to execute several recipes at once. Normally, make will execute only one recipe at a time, waiting for it to finish before executing the next. However

Mapping the UCSC/Web-Sequences to a world map.

written 6.7 years ago by YOKOFAKUN

People at the UCSC have recently released a new track for the GenomeBrowser We BLATted the Internet! The DNA sequences from 40 billion webpages mapped to hg19 and other species: UCSC Genome Browser (@GenomeBrowser) January 23, 2014"We're pleased to announce the release of the Web Sequences track on the UCSC Genome Browser. This track, produced in collaboration with

(video) #renabigo2013 "Make &amp; Bioinformatics:everything but #usegalaxy"

written 6.8 years ago by YOKOFAKUN

(In French): "Mon Make à moi": parallélisations, workflows et pipelines pour le NGS, tout sauf Galaxy [34:50 mn] Les workflows en Bio-Informatique Centre Inria de Rennes - IRISA 29 Novembre 2013

Updated comparison of variant detection methods: Ensemble, FreeBayes and minimal BAM preparation pipelines

written 7.0 years ago by Blue Collar Bioinformatics

Variant evaluation overview I previously discussed our approach for evaluating variant detection methods using a highly confident set of reference calls provided by NIST’s Genome in a Bottle consortium for the NA12878 human HapMap genome, In this post, I’ll update those conclusions based on recent improvements in GATK and FreeBayes. The comparisons use bcbio-nextgen, an […]

Summary from Bioinformatics Open Science Codefest 2013: Tools, infrastructure, standards and visualization

written 7.3 years ago by Blue Collar Bioinformatics

The 2013 Bioinformatics Open Source Conference (BOSC) starts tomorrow in Berlin, Germany. It’s a yearly conference devoted to community-based software development projects supporting biological research. Members of the Open Bioinformatics Foundation discuss implementations and approaches to better provide interoperable and reusable software, libraries and pipelines. For the past five years, a two day Codefest and […]
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Planet Feeds

Kevin's GATTACA World
My Weblog on Bioinformatics, Genome Science and Next Generation Sequencing
3 posts, last updated 6.5 years ago
What You're Doing Is Rather Desperate
Notes from the life of a computational biologist
3 posts, last updated 6.5 years ago
Blue Collar Bioinformatics
3 posts, last updated 6.6 years ago
Omics! Omics!
A computational biologist's personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery
3 posts, last updated 6.7 years ago
3 posts, last updated 6.7 years ago


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