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The three technologies bioinformaticians need to be using right now

written 9 weeks ago by Opinionomics by Mick Watson

I’m old. Sometimes I feel really old. I’m old enough to remember when you had to install things manually, and that’s if you were allowed to; worse would be that you depend on an IT department to install software for you. I am old enough to remember when changing servers meant reinstalling everything again from […]

Getting to know us: Astrid from Outreach

written 9 weeks ago by Ensembl Blog

Ever wondered what an Outreach Officer does? Meet Astrid who talks about her job and how she got here. What is your job in Ensembl? I am an Outreach Officer in a small team that forms the public face of Ensembl. A major part of my job is organising and delivering training both in person […]

Job: Project Leader – Model Organism Genomics

written 9 weeks ago by Ensembl Blog

We’re looking for a bioinformatics manager to lead annotation and integration of genomic data for model organisms including C. elegans. We’re looking for PhDs in molecular biology, bioinformatics or a related field, with experience in model organism genomics and programming. Closes 10th September. Location: EMBL-EBI, Hinxton near Cambridge, UK Staff Category: Staff Member Contract Duration: 3 years […]

Massive scale assembly of genomes from metagenomes in ruminants

written 9 weeks ago by Opinionomics by Mick Watson

Hopefully some of you will have seen our recent paper published in Nature Biotech: Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery Robert D. Stewart, Marc D. Auffret, Amanda Warr, Alan W. Walker, Rainer Roehe &amp; Mick Watson Nature Biotechnology volume 37, pages 953–961 (2019) In this paper we analyse […]

Epilepsy Exomes Harbor Ultra-Rare Variants

written 10 weeks ago by KidsGenomics

Epilepsy is a broad term used to describe brain disorders that cause seizures. About 1.2% of the population has active epilepsy; in the United States this includes more than 3 million adults and 470,000 children. According to the CDC, about 1 in 10 people will have a seizure in their lifetime. (Side note: this means […] The post Epilepsy Exomes Harbor Ultra-Rare Variants appeared first on KidsGenomics.

Cool stuff the Ensembl VEP can do: parse protein HGVS

written 11 weeks ago by Ensembl Blog

HGVS notation is an excellent way to describe variants in proteins, and VEP can interpret variants described this way to see if they are already known or if they affect other genomic features, so long as there is enough information to find a unique genomic location. If there isn’t, the Variant Recoder can help you […]

UK CMA &amp; ILMN/PACB: The Inconvenience of Being Earnest.

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

As part two of a yet-to-be-determined number of pieces on the UK's CMA preliminary analysis of the proposed Pacific Biosciences acquisition by Illumina, I'd like to briefly explore the surprising authority of this agency to plumb internal documents at the two companies.Read more »

UK CMA's Write-up of PacBio Acquisition by Illumina Makes for XXX Reading; Clearly They Believe XXX and XXX

written 12 weeks ago by Omics! Omics! by Keith Robinson

After writing my two recent pieces on the business side of the long read industry I planned, after a recent extended family vacation, to try to get back to science. Particularly after my chagrin when various correspondents pointed out a fact from each I should have found and didn't: in my ONT piece I failed to discover that ONT has two share classes and the Woodford fund's shares cannot be used to gain control of the company and in the PacBio piece that there is a $100M breakup fee due PacBio if for any reason the deal doesn't go thru. I'm particularly red faced on that one, as a breakup fee would play importantly into PacBio's financial health should the deal go south; $100M would buy perhaps two quarters time.But then a bunch of people threw my way the UK Competition and Mergers Authority (CMA) report on the merger and I foolishly opened the document. It makes for interesting reading, but that is hampered by the fact it is highly redacted -- like my title. Reserving the right to comment on the contents substance at a future date (or never), I'd just like to give a tour around some of the redactions.Read more »

Comparing two genome binnings quickly with sourmash

written 12 weeks ago by Living in an Ivory Basement by Titus Brown

Comparing two sets of MAGs, for fun and profit!

Become a contributor of literature and knowledge in UniProt

written 12 weeks ago by Inside UniProt

The UniProt Knowledgebase (UniProtKB) contains a vast amount of protein sequence and function information. Expert curation in UniProtKB includes a critical review of experimental data from the literature as well as predicted data from sequence analysis tools. A representative set of publications is selected as evidence for the data. Thus, many literature articles with potentially relevant content may not be associated with a protein entry.We have developed a prototype for literature submission where you will be able to add publications that you deem relevant to a protein entry, along with performing several optional tasks, such as classifying the article and adding annotations. Contribute in a few simple steps: Find your UniProt protein entry of interestSign in with your ORCID ID (you can create one during the submission process if you do not already have one)Fill in the submission form (retrieve publication and add annotation)SubmitBibliography submission prototype: https://uuw.dbi.udel.edu/bbsub/bbsub.htmlThe publication and annotations will be included in the publication section of the UniProt entry in a future UniProt release. ORCIDs are used to validate and credit your contribution. The publications section currently provides all expert-curated literature as well as an additional set of computationally mapped literature. Why should you contribute?You are the expertIt will help scale up curationIt will provide a comprehensive set of articles related to a given protein entryBenefits to youYou will be credited for the papers and annotations contributedYour contribution will be citable and can be used to broaden the impact of your researchYou can play a role in improving ...

Twitter coverage of the useR! 2019 conference

written 3 months ago by What You're Doing Is Rather Desperate by Neil Saunders

Very briefly: Last week was useR! conference time again, coming to you this time from Toulouse, France I’ve retrieved 8 318 tweets that mention #user2019 and run them through my report generator And here are the results Take-home message this year: the R Ladies rock!

Job: Ensembl Web Back-end Project Leader

written 3 months ago by Ensembl Blog

We’re looking for a web development manager to work on the Ensembl back-end. We’re looking for masters or PhDs in biology, bioinformatics, software engineering with experience developing web applications. Closes 14th August. Location: EMBL-EBI, Hinxton near Cambridge, UK Staff Category: Staff Member Contract Duration: 3 years Grading: 7 (monthly salary starting at £3,351.44 after tax) Closing […]

Job: Ensembl Regulation Developer

written 3 months ago by Ensembl Blog

We’re looking for a developer to work on annotating epigenomic elements and regulatory features on the genome. We’re looking for PhDs or MScs in molecular biology, bioinformatics or computer science, with experience in software development, genomics, object oriented programming, Git and SQL. Closes 13th August Location: EMBL-EBI, Hinxton near Cambridge, UK Staff Category: Staff Member […]

Ensembl 97 and Ensembl Genomes 44 have been released!

written 3 months ago by Ensembl Blog

Ensembl 97 and Ensembl Genomes 44 have been released! In this release you’ll find many new species, including some hybrid livestock, as well as important changes to gene sets for human and mouse and a new update to the human Regulatory Build. Read on to explore the full details. GENCODE updates and lncRNA biotype changes […]

High velocity RNA velocity

written 3 months ago by Bits of DNA by Lior Pachter

This post is the fifth in a series of five posts related to the paper “Melsted, Booeshaghi et al., Modular and efficient pre-processing of single-cell RNA-seq, bioRxiv, 2019“. The posts are: Near-optimal pre-processing of single-cell RNA-seq Single-cell RNA-seq for dummies How to solve an NP-complete problem in linear time Rotating the knee (plot) and related […]

Will Regulators Scotch PacBio Acquisition?

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

When Illumina announced its proposed acquisition of Pacific Biosciences last fall, an immediate question arose as to whether the deal would pass antitrust review. Illumina must have been optimistic, as they originally expected the deal to close in "mid-2019". That timetable has now been rolled back to late 2019 in the face of the UK agency with jurisdiction over mergers deciding to go for a second round of review and no word yet from the U.S.'s Federal Trade Commission.Read more »

Cool stuff the Ensembl VEP can do: where in a transcript?

written 3 months ago by Ensembl Blog

Interpreting a single variant can be a lot more involved than just finding out its consequence. Sometimes to understand a variant, you need to know exactly where it falls, which exon, which amino acid, sometimes even which base in the codon. The VEP gives you all of this by default. To really know what’s going […]

A guide to hosting an Ensembl Workshop

written 3 months ago by Ensembl Blog

Are you interested in having us come to your institute to deliver an Ensembl workshop, but are not quite sure what it involves? This blog is a guide for you. What workshops does Ensembl offer? We offer three types of workshops, which are summarised here (full details in the header links): Browser workshop (full day, […]

Can random forest provide insights into how yeast grows?

written 3 months ago by What You're Doing Is Rather Desperate by Neil Saunders

I’m not saying this is a good idea, but bear with me. A recent question on Stack Overflow [r] asked why a random forest model was not working as expected. The questioner was working with data from an experiment in which yeast was grown under conditions where (a) the growth rate could be controlled and … Continue reading Can random forest provide insights into how yeast grows?

Job: Ensembl Production Software Developer

written 3 months ago by Ensembl Blog

We’re looking for a software engineer to join our production team, responsible for creating and running software for Ensembl production releases. We’re looking for postgrad qualifications in computer science or bioinformatics, with experience in bioinformatics, Python, MySQL and data processing workflows. Closes 19th July. Location: EMBL-EBI, Hinxton near Cambridge, UK Staff Category: Staff Member Contract Duration: […]

Geelong and the curse of the bye

written 3 months ago by What You're Doing Is Rather Desperate by Neil Saunders

This week we return to Australian Rules Football, the R package fitzRoy and some statistics to ask – why can’t Geelong win after a bye? (with apologies to long-time readers who used to come for the science) Code and a report for this blog post are available at Github. First, some background. In 2011 the … Continue reading Geelong and the curse of the bye

Rotating the knee (plot) and related yoga

written 3 months ago by Bits of DNA by Lior Pachter

This post is the fourth in a series of five posts related to the paper “Melsted, Booeshaghi et al., Modular and efficient pre-processing of single-cell RNA-seq, bioRxiv, 2019“. The posts are: Near-optimal pre-processing of single-cell RNA-seq Single-cell RNA-seq for dummies How to solve an NP-complete problem in linear time Rotating the knee (plot) and related […]

How to encourage participation in teleconferences

written 3 months ago by Living in an Ivory Basement by Titus Brown

Participation is good!

Focus on: the Kullback-Leibler divergence

written 3 months ago by The Grand Locus

The story of the Kullback-Leibler divergence starts in a top secret research facility. In 1951, right after the war, Solomon Kullback and Richard Leibler were working as cryptanalysts for what would soon become the National Security Agency. Three years earlier, Claude Shannon had shaken the academic world by formulating the modern theory of information. Kullback and Leibler immediately saw how this could be useful in statistics and they came up with the concept of information for discrimination, now known as relative entropy or Kullback-Leibler divergence. The concept was introduced in an oringinal article, and later expanded by Kullback in the book Information Theory and Statistics. It has now found applications in most aspects of information technologies, and most prominently artificial neural networks. In this post, I want to give an advanced introduction on this concept, hoping to make it intuitive. Discriminating information The original motivation given by Kullback and Leibler is still the best way to expose the main idea, so let us follow their rationale. Suppose that we hesitate between two competing hypotheses $(H_1)$ and $(H_2)$. To make things more concrete, say that we have an encrypted message $(x)$ that may come from two possible... Read more on the blog: Focus on: the Kullback-Leibler divergence

Is your phone giving you horns?

written 3 months ago by What You're Doing Is Rather Desperate by Neil Saunders

No. Why would you even ask that? Well, because this. I sense problems immediately. First, the story is tagged “evolution”. The horns are not arising through inheritance of advantageous mutations, so that isn’t evolution. Second: HORNS. — Alex Holcombe (@ceptional) June 20, 2019 Yes last time I checked, horns were external and pointed upwards. The … Continue reading Is your phone giving you horns?
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