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What’s coming in Ensembl 96 / Ensembl Genomes 43

written 6 weeks ago by Ensembl Blog

We are planning to release Ensembl 96 and Ensembl Genomes 43 in late March or beginning of April 2019. The Ensembl 96 release includes the first pass full annotation of the mouse genome, with the GENCODE M21 gene set. The Ensembl Genomes 43 release will bring changes to our REST API and FTP server that […]

An absolute beginner’s guide to creating data frames for a Stack Overflow [r] question

written 6 weeks ago by What You're Doing Is Rather Desperate by Neil Saunders

For better or worse I spend some time each day at Stack Overflow [r], reading and answering questions. If you do the same, you probably notice certain features in questions that recur frequently. It’s as though everyone is copying from one source – perhaps the one at the top of the search results. And it … Continue reading An absolute beginner’s guide to creating data frames for a Stack Overflow [r] question

Update: Temporarily reduced Ensembl functionality- all services now restored

written 6 weeks ago by Ensembl Blog

Due to a major loss of cooling incident at one of the EMBL-EBI data centres, there was reduced Ensembl functionality between Saturday 2nd February and Wednesday 6th February. However, as of Wednesday 6th February, all Ensembl and Ensembl Genomes services have now been restored and are working as normal. If you encounter any further issues, […]

Temporarily reduced Ensembl functionality

written 6 weeks ago by Ensembl Blog

Due to a major loss of cooling incident at one of the EMBL-EBI data centres, some Ensembl functionality is down as of Saturday 2 February 2019 and is unlikely to return until at least Monday 4 February. Currently off line are the web versions of most Ensembl tools (VEP, BLAST, and others described on the […]

Covaris Grabs A Spot on the Liquid Handler Deck

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

For as long as I can remember, Covaris has been the standard in DNA shearing for high throughput short read sequencing. Their benchtop units had their quirks -- custom tubes being the foremost -- but they were what everyone else compared to. In 2013 when the American Society for Human Genetics was in town, the PacBio folks did me a great favor and loaned me an exhibit hall pass. Multiple companies were offering DNA shearing instruments -- and every one compared themselves against Covaris. Now they have a new offering, moving the instrument onto a liquid handling robot deck so that it is available for high-throughput workflows. Covaris invited me down to their Woburn, Massachusetts facility to get a look at the instrument before its formal launch at the SLAS conferenceRead more »

Patent Dive: Genapsys

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

Here's a dangerous statement for me: I actually enjoyed reading some patents recently. Now, before you get any ideas in your head about suggesting more patents for me to read, let me be clear that these were unusual patents -- they're written to be read! -- and were read under strict conditions. The patents in question are from Genapsys -- found via my good friend Justia.Read more »

Price’s Protein Puzzle: 2019 update

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

Chains of amino acids strung together make up proteins and since each amino acid has a 1-letter abbreviation, we can find words (English and otherwise) in protein sequences. I imagine this pursuit began as soon as proteins were first sequenced, but the first reference to protein word-finding as a sport is, to my knowledge, “Price’s … Continue reading Price’s Protein Puzzle: 2019 update

Technologies of narcissism

written 7 weeks ago by Bits of DNA by Lior Pachter

The title of this blog post is a phrase coined by Paul Wouters and Rodrigo Costas in their 2012 publication Users, Narcissism and Control—Tracking the Impact of Scholarly Publications in the 21st Century. By “technologies of narcissism”, Wouters and Costas mean tools that allow individuals to rapidly assess the impact, usage and influence of their publications […]

Metabolic Whac-a-Mole

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

Derek Lowe summarized a really cool paper back in October. I've been meaning to grab a copy, but discovered recently that the MIT library no longer has an easy way for outsiders to slip in an use their subscriptions. So I'm working off his summary, but since this is mostly an excuse for flights of genetic fantasy actually reading the paper would probably just hinder me!Read more »

Cool stuff the Ensembl VEP can do: highlighting likely causal GWAS variants with PostGAP

written 7 weeks ago by Ensembl Blog

Identifying the causal variants from a GWAS generally involves identifying the haplotype blocks that contain your variant of interest, rather than the variant and the gene it is affecting itself. To find the actual genes involved, you need to consider all variants in LD with your identified associations. Ensembl Post-GWAS analysis pipeline (PostGAP) can provide […]

2019 Tech Speculations: Oxford Nanopore

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

As promised in the last post, I'm segregating out Oxford Nanopore. Admittedly I tend to cover them relatively closely -- though I never seem to quite finish writing up their conferences -- but at the moment ONT is the only major player in the U.S. research sequencing market not being run out of (or about to be run out of) Illumina HQ. And I'll be very to the point: ONT has a lot of balls in the air and irons in the fire, but from my point-of-view what matters most is rapid and regular progress on the accuracy front.Read more »

Uncovering the mysteries of marine mammals with UniProtKB

written 8 weeks ago by Inside UniProt

Over millions of years of evolution, distantly related species such as dolphins, seals and manatees made the move from terrestrial environments to water, in the process undergoing extraordinary changes in physiology and physical abilities. These mammals acquired limbs adapted to swimming, an enhanced capacity to store and transport oxygen to enable underwater foraging and decreased bone density - changes that occurred independently in each species through convergent evolution. Dolphin by Ed Dunens is licensed under CC BY 2.0Characterizing the underlying molecular landscape of these evolutionary adaptations could now become simpler thanks to the proteomes of twelve new marine mammal species available in the latest UniProt release. This diverse group includes cetaceans, the most aquatically adapted set comprising whales and dolphins, sirenians, the herbivorous sea cows, pinnipeds, the carnivorous seals and walruses as well as partially marine species such as the polar bear and sea otter. Some of these species, Weddell seals in particular, are known to dive deep and remain underwater for extended periods depriving vital organs of oxygen without causing organ damage, a feat impossible for most land-based animals. This phenomenon is not unlike the hypoxia experienced by humans during a heart attack or stroke that when followed by reoxygenation, often leads to permanent organ damage or even death. Ongoing studies focused on a number of different marine and non-marine species have the potential to identify therapeutic targets to alleviate injury sustained during heart attacks and strokes (Ref 1). Dr. Benjamin Neely, at the Marine Biochemical Sciences group at ...

Retirement of Ensembl archive 74

written 8 weeks ago by Ensembl Blog

The archive website for Ensembl release 74 will be retired along with our release of Ensembl 95. This is inline with our rolling retirement policy, where archives are retired after five years, unless they contain the last instance of an important dataset for a key species. The database will still be available for direct queries […]

RECOMB 2019 Accepted Papers List

written 8 weeks ago by Next Gen Seek

RECOMB 2019, one of the long standing computational biology conferences has announced the list of accepted papers for this year’s RECOMB. RECOMB 2019 is going be held in The George Washington University in the first week of May from 5th-8th. As usual, the main RECOMB 2019 will be preceded by a number of satellite workshops; RECOMB Genetics, RECOMB-CCB, […]

Job: Ensembl Compara Project Leader

written 8 weeks ago by Ensembl Blog

We’re looking for a bioinformatician to manage our comparative genomics team, running homology and alignment pipelines on Ensembl genes. We’re looking for PhDs in Molecular Biology or Bioinformatics with experience in comparative genomics, relational databases, HPC clusters and programming. Closes 1st March. Location: EMBL-EBI, Hinxton near Cambridge, UK Staff Category: Staff Member Contract Duration: 3 years […]

Open sourcing bioinstruments

written 8 weeks ago by Bits of DNA by Lior Pachter

The long-standing practice of data sharing in genomics can be traced to the Bermuda principles, which were formulated during the human genome project (Contreras, 2010). While the Bermuda principles focused on open sharing of DNA sequence data, they heralded the adoption of other open source standards in the genomics community. For example, unlike many other […]

2019 Sequencing Tech Speculations: Will We Actually See New Entrants?

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

An astute reader caught a sentence fragment about MGI in last night's Illumina JPM roundup -- the unfortunate evidence of a a mental battle over whether to put any further comments on MGI in an Illumina-centric post. So now I'll sweep that bit into a general post about not-Illumina (and not-Oxford, that will go in yet another).Read more »

Illumina JPM Talk

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

Illumina CEO Francis deSouza delivered his J.P. Morgan Healthcare Conference talk (webcast audio, slides &amp; Q&amp;A audio) a week ago. I can claim that some of my speculations came true -- just the most boring and obvious ones. Overall, the presentation was the talk of a confident market leader. Read more »

Job: WormBase Project Leader

written 9 weeks ago by Ensembl Blog

We’re looking for a manager to lead EMBL-EBI’s contribution to WormBase, a genomics resource for C. elegans. We’re looking for PhDs in Molecular Biology or Bioinformatics, with experience in model organism genomics, using databases for modelling biological data and a programming language. Closes 26th February. Location: EMBL-EBI, Hinxton near Cambridge, UK Staff Category: Staff Member Contract Duration: […]

Revisiting authorship, and JOSS software publications

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

The question du jour: how should authorship on software papers be decided?

Regulatory build update for Ensembl 95

written 9 weeks ago by Ensembl Blog

A brand new regulatory build for the human GRCh38 and GRCh37 assemblies was released in Ensembl 95 earlier this week. The new regulatory build incorporates data for 55 new and 38 updated epigenomes from the ENCODE project. So what are the differences from the previous regulatory build? The Ensembl regulatory build The Ensembl regulatory build uses experimental data to […]

Job: Ensembl Metazoa Bioinformatician

written 9 weeks ago by Ensembl Blog

We’re looking for a bioinformatician to work on genomes of non-vertebrate metazoa. We’re looking for Masters in computing or related scientific discipline, with experience in bioinformatics and proficiency in Perl, Python, SQL and Unix. Location: EMBL-EBI, Hinxton near Cambridge, UK Staff Category: Staff Member Contract Duration: 3 years Grading: 5 or 6 (monthly salary starting […]

Voice is dead, will email be far behind?

written 10 weeks ago by Opinionomics by Mick Watson

I have a not-so-secret secret – I never answer the phone. With landlines, it is 100% of the time, because I can’t see who is calling me. Despite the fact my work landline has a messages facility, I don’t listen to those either. Not in 8 years since I moved to Edinburgh. I must have […]

Ensembl and friends at PAG XXVII

written 10 weeks ago by Ensembl Blog

Excited for PAG? So are we! You can find several representatives of Ensembl at the conference, if not during our talks, workshops and posters then at the EBI booth 309 where we can chat with you about your data and how to use Ensembl. A full schedule of talks, posters and demonstrations from researchers and staff […]

Ensembl Genomes 42 is out!

written 10 weeks ago by Ensembl Blog

We’ve just released Ensembl Genomes 42, with new and updated plant species, including soya and tomato, as well as three new species for Ensembl Metazoa. New assemblies and gene annotation We have now included the genome assembly and annotation for Arabidopsis halleri. Arabidopsis halleri is a close relative of the model plant Arabidopsis thaliana. It […]
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