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Extracting data from news articles: Australian pollution by postcode

written 7 weeks ago by What You're Doing Is Rather Desperate by Neil Saunders

The recent ABC News article Australia’s pollution mapped by postcode reveals nation’s dirty truth is interesting. It contains a searchable table, which is useful if you want to look up your own suburb. However, I was left wanting more: specifically, the raw data and some nice maps. So here’s how I got them, using R. … Continue reading Extracting data from news articles: Australian pollution by postcode

A Few Things Before Nanopore Community Meeting Begins

written 7 weeks ago by Omics! Omics! by Keith Robinson

Nanopore Community Meeting begins within the hour. San Francisco is spectacular as ever -- Alcatraz Island disappearing into the fog as I fiddled with camera settings, the spectacular Bay Bridge spans are visible from the the breakfast area and I even got to see some notable locals on my walk over from the hotelIf this crowd doesn’t get a move on, they’re going to miss #nanoporeconf breakfast pic.twitter.com/rFwfGdQTit— Keith Robison (@OmicsOmicsBlog) November 28, 2018 Hans Jansen was kind enough to remind me by tweet of a couple of missed topics in my preview piece. So let's cover them!.Read more »

How Not Do Think Like A Customer: Examples from ONT and AMZN

written 8 weeks ago by Omics! Omics! by Keith Robinson

I'd planned today to use some downtime to write up a preview of the Nanopore Community Meeting which I am attending tomorrow and Thursday. I might still do that, but the same organization just engaged in the sort of customer engagement that drives me batty (yeah, twisting the lion's tail before entering their den -- smart move or what?) and it reminded me of another lousy experience I had recently with a very prominent company: Amazon.Read more »

Nanopore Community Meeting 2018 Preview

written 8 weeks ago by Omics! Omics! by Keith Robinson

Okay, now that I'm done venting -- for now -- about ONT's customer service experience (well, almost done -- they sent me the same damn letter they sent my colleague -- why were they several hours apart???) -- let's move on to the Nanopore Community Meeting. Technically it started today with the training session, but I'm not heading out until tonight. At the first one of these in NYC Oxford tried to avoid making any announcements, but they seem to now like having two major focus times a year sometimes supplemented with Clive Brown webinars in between. Here are someRead more »

Cool things the Ensembl VEP can do: regulatory feature annotation

written 8 weeks ago by Ensembl Blog

Most of the time when we talk about variant annotation, we talk about the effects of variants on genes, but did you know that the VEP can also tell you how variants affect the genomic features that regulate gene expression, such as promoter and enhancers? Regulatory features are annotated on the human and mouse genomes […]

Using OSX? Compiling an R package from source? Issues with ‘-fopenmp’? Try this.

written 9 weeks ago by What You're Doing Is Rather Desperate by Neil Saunders

You can file this one under “I may have the very specific solution if you’re having exactly the same problem.” So: if you’re running some R code and you see a warning like this: Warning message: In checkMatrixPackageVersion() : Package version inconsistency detected. TMB was built with Matrix version 1.2.14 Current Matrix version is 1.2.15 … Continue reading Using OSX? Compiling an R package from source? Issues with ‘-fopenmp’? Try this.

The story behind the spacegraphcats project and paper

written 9 weeks ago by Living in an Ivory Basement by Titus Brown

The TRUE story!

Failure: The Real Secret Sauce of Engineering

written 9 weeks ago by Omics! Omics! by Keith Robinson

I took one swing at Vijay Pande's overly rosy piece on applying engineering methods to biology and medicine and similar minded efforts were published by Ash Jogalekar at Curious Wavefunction and Derek Lowe at In The Pipeline. Perhaps I shouldn't make another go, but it is a new excuse to explore an old fascination of mine. Pande's subhead was "Billion-dollar bridges rarely fail -- whereas billion-dollar drug failures are routine". I can't argue that. Actually, it would seem from an informal search that billion dollar bridges are actually much rarer than billion dollar drug development programs. Obviously they exist -- I've traversed the new Tappan Zee Bridge which came in over $3B. On the other hand, a second crossing at perhaps the most notorious spot in bridge engineering history, the Tacoma Narrows, was built earlier in this century for only $0.8B. What I wish to explore are the failures of bridges and other structures of any cost, as it is the analysis of failures that frequently propels engineering forwards. That analysis is enabled by the relative simplicity of human engineering and the artifacts it uses and creates. Conversely, analyzing the failure of new drugs is nothing like that.Read more »

We do not wish to share

written 9 weeks ago by What You're Doing Is Rather Desperate by Neil Saunders

The article Cytotoxic T cells modulate inflammation and endogenous opioid analgesia in chronic arthritis contains a statement that I don’t recall seeing before: Availability of data and materials We do not wish to share our data at this moment. This seems odd for an open-access article, published by a “big on open-access” publisher: How is … Continue reading We do not wish to share

What’s coming in Ensembl 95 / Ensembl Genomes 42

written 10 weeks ago by Ensembl Blog

We’re planning to release the next versions of Ensembl and Ensembl Genomes in December. We’ve got some exciting new genomes, including polar bear, as well as updated genome assemblies for three important agricultural species. We’ve also got a new regulatory build for the human GRCh38 and GRCh37 assemblies and a brand new protein structure variation […]

Creating a welcoming teaching/learning environment in workshops

written 10 weeks ago by Living in an Ivory Basement by Titus Brown

It takes constant work to make a welcoming teaching/learning environment!

No, the Groves Fallacy Can't be Retired Yet

written 10 weeks ago by Omics! Omics! by Keith Robinson

Vijay Pande has a thought-provoking piece in Scientific American on the Groves Fallacy, though in the end I'm afraid mostly what he provokes in me is the thought that he's in most cases pretty far off base. Titled "How to Engineer Biology", he claims that the Grove Fallacy -- the idea that biology can't be tamed by engineering -- is quickly being put to rest. And Pande isn't some naive Silicon Valley type, but a professor at Stanford whose lab works in experimental biology. So he has some street cred -- but that doesn't mean he isn't mostly wrong.Read more »

Repeatability in Practice (2018 version)

written 10 weeks ago by Living in an Ivory Basement by Titus Brown

How we do repeatability in the DIB Lab

Job: Regulation Project Leader

written 11 weeks ago by Ensembl Blog

We’re looking for a developer/manager to lead our efforts to annotate the genome with features that regulate gene expression, working with data from large scale epigenomics projects. We’re looking for PhDs in molecular biology, bioinformatics or genomics with experience in gene regulation and high-performance computing. Closes 7th December. Location: EMBL-EBI, Hinxton near Cambridge, UK Staff […]

Job: Bioinformatician – comparative genomics

written 11 weeks ago by Ensembl Blog

We’re looking for a bioinformatician to join our comparative genomics team working on gene trees and homology and whole genome alignments. We’re looking for PhDs or MScs in molecular biology or bioinformaics, with experience in Perl or Python, relational databases and Unix. Closes 7th December. Location: EMBL-EBI, Hinxton near Cambridge, UK Staff Category: Staff Member […]

I was wrong (part 3)

written 11 weeks ago by Bits of DNA by Lior Pachter

Last year I wrote a blog post on being wrong. I also wrote a blog post about being wrong three years ago. It’s not fun to admit being wrong, but sometimes it’s necessary. I have to admit to being wrong again. To place the admission in context I need to start with Mordell’s finite basis […]

Illumina Buys PacBio: More Thoughts

written 11 weeks ago by Omics! Omics! by Keith Robinson

Illumina surprised pretty much everyone in the genomics community by announcing the purchase of Pacific Biosciences. I had spent Thursday deep in the weeds of a combined PacBio-ONT-Illumina dataset, so was caught completely by surprise on my commute home by an email asking for my comment. If you do want to hear hot takes on it from myself and AllSeq's Shawn Baker, Theral Timpson over at Mendelspod interviewed us that night. There has of course been much discussion of the deal and tributes. I've had the weekend to ponder things, and here are some somewhat better thought out and detailed comments -- though I don't believe I've retreated from any of the themes in the podcast. I've grouped the thoughts into a few themes.Read more »

The combinatorics of authorship in the biological sciences

written 11 weeks ago by Bits of DNA by Lior Pachter

A few years ago I wrote a post arguing that it is time to end ordered authorship. However that time has not yet arrived, and it appears that it is unlikely to arrive anytime soon. In the meantime, if one is writing a paper with 10 authors, a choice for authorship ordering and equal contribution […]

Cool stuff the VEP can do: splice site variant annotation

written 12 weeks ago by Ensembl Blog

If a variant hits a splice site, you want to know if splicing is going to occur as normal, or if you can expect a different protein isoform. We have a few cool tools with the VEP that will help you to assess that for your own variants. SpliceRegion was developed in collaboration with researchers from […]

GSoC with Ensembl: catching up with 2018’s students

written 12 weeks ago by Ensembl Blog

In this blog we catch up with Ensembl’s 2018 Google Summer of Code (GSoC) students and hear about their now completed projects, and their reflections on the experience. You may have already seen our previous blog post which we published as they were just beginning their projects. Read on to find out how they went, […]

Changes to paralogy in release 94

written 3 months ago by Ensembl Blog

We’ve heard from a number of you about missing paralogues in release 94. We have lost some paralogy relationships and we’re looking to restore them in future. We’re sorry for any problems this caused. For release 94, we launched a major change to our gene tree pipeline, which we use to infer orthologues and paralogues. […]

Get involved in community gene annotation for Zymoseptoria tritici

written 3 months ago by Ensembl Blog

If you work with Zymoseptoria tritici genes, we’re looking for your help. We need people to get involved with community annotation of genes. All questions that can be asked about the genome of a pathogen hinge on a consistent and accurate gene set. Unlike for key model organisms that may have dedicated teams doing manual gene […]

You Can Be Impatient Running MInIONs, But Not Feeding Them

written 3 months ago by Omics! Omics! by Keith Robinson

Yes, it's been way too long since I wrote here. Even longer since I did so with any regularity. There was always some list of things draining my time and energy. But I resolved this week to get back on the horse -- and that was even before today's bit of dilithium news. In particular, in one twenty-four hour span three different people remarked on the prolonged hiatus -- a professional contact, a commenter on the blog and finally some very cutting remarks from Draco (aka TNG). And what better way to get going again but to kvetch about Oxford Nanopore's supply chain model?Read more »

New Ensembl motif features

written 3 months ago by Ensembl Blog

In its latest release, Ensembl has completely reviewed its reporting of potential Transcription Factor (TF) binding sites. TF proteins are key players of gene expression regulation that bind to specific DNA regions characterised by approximate sequence patterns, or transcription factor binding motifs (TFBM). These motifs are generally represented as a Position Specific Frequency Matrix, or […]

Where to Find Me At ASHG 2018

written 3 months ago by KidsGenomics

This week, I’ll be traveling to the American Society of Human Genetics Meeting in San Diego, CA. This is a massive meeting, and while I love it, I sometimes find it hard to meet friends, colleagues, and blog readers. So here’s where to find me in San Diego this week. As usual, you can catch […] The post Where to Find Me At ASHG 2018 appeared first on KidsGenomics.
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