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written 1 day 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 »
written 4 days 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 ...
written 8 days 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!
written 19 days 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 […]
written 20 days 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 […]
written 20 days 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 […]
written 22 days 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 […]
written 22 days 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 »
written 25 days 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 […]
written 26 days 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, […]
written 27 days 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?
written 28 days 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: […]
written 28 days 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
written 29 days 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 […]
written 4 weeks ago by Living in an Ivory Basement by Titus Brown
Participation is good!
written 4 weeks 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
written 4 weeks 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?
This post is the second 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 […]
This post is the first 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 […]
This post is the third 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 […]
written 4 weeks ago by Omics! Omics! by Keith Robinson
There's an unfortunate chain of events that may end up causing a headache for Oxford Nanopore, and it's completely outside their control. One of the their key investors has just had his luck - or perhaps more critically his reputation -- at stock picking disintegrate. Because of some unusual choices, that has potential repercussions for ONT.Read more »
written 5 weeks ago by Ensembl Blog
Work continues on our exciting new website, which is available as a pre-alpha release. We’ve been consulting with some of you in various ways, such as interviews and meetings, because we want to make sure that the new Ensembl serves your needs. We’re now asking for your help with a short survey, which will just […]
I noted in my roundup of Oxford Nanopore technical announcements that I loved the Plongle concept. This is really both a new application-specific integrated circuit (ASIC) and using it to build a 96-well sequencer. Let me expand on what there is to love.Read more »
In the coverage of ONT's announcements at London Calling, I specifically left out one of Clive's Skunk Works projects. This would be a device to use nanopores to write digital information. I'll give him points for creativity, but the reason I held this for here is I truly and sincerely hate the concept and didn't want my vitriol to distract within the other piece. But here I will let loose.Read more »
The annual big Clive Brown London Calling talk had a twist this year Brown introduced a set of senior lieutenants at Oxford Nanopore and then tacked on a few "and one more thing" moments at the end. If you're looking for the TL;DR version from me, it is that there were a lot of sensible but non-Earth shattering updates from the team followed by Clive updating on one prior crazy idea and throwing out two more -- one of which I love and the other I believe should be thrown out posthaste.Read more »
A computational biologist's personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery
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The Knight Lab at Yale University » BlogThe Knight Lab at Yale University » Bioinformatics and Genetics
Bioinformatics and Genetics
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