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CoolMPS Revealed

written 1 day ago by Omics! Omics! by Keith Robinson

Having summarized MGI's announcement they are launching into the U.S. market this spring and started digging into the performance characteristics of MGI's instrument lineup, let us now turn to their BioRxiv pre-print on the CoolMPS chemistry, as it has many useful technical details.Read more »

MGI Dual Drop of CoolMPS News Ahead of AGBT

written 2 days ago by Omics! Omics! by Keith Robinson

Friday morning I got excited because a preprint showed up at BioRxiv detailing the CoolMPS sequencing technology from MGI (aka BGI aka Complete Genomics). First announced in Fall 2018, this approach sounded, well, cool. Using fluorescently labeled antibodies specific to each reversible terminator seemed like a crazy pipe dream. So getting a good look at it in a manuscript is an event! But then Friday afternoon MGI had a second big pre-AGBT reveal: launch of their sequencing systems in the U.S. later this year. Below is a quick run-down of the sequencer announcement; the pre-print has many details I'm still parsing.Read more »

A Lazy Look at The Field of Sequencing Startups

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

AGBT looms ahead of me next week which serves as impetus to let fly an idea I've had simmering for a while: to look at sequencing startups by a particular type of information they choose to reveal. I'm not expecting any big announcements at AGBT from this space, though would be thrilled to be surprised. But there is the risk of getting contaminated with some on-the-sly scuttlebutt, so better to get this done now. By the way, in the full disclosure category, I have consulted for a few companies here and have NDAs either on my own or via employers; everything here is based on public information.Read more »

Skimming Seq

written 5 days ago by Omics! Omics! by Keith Robinson

My last post discussed BioJulia in the face of a challenge from the new Seq programming language. Tonight I'm going to take a bit more of a look at Seq itself and touch on both why I'm tempted to try it and why I remain reticent to do so. I hope if any of the Seq team sees this they will regard it as some parts constructive criticism and some parts market feedback.Read more »

Reduced functionality: 16th-25th March 2020

written 6 days ago by Ensembl Blog

During March (16th-25th) the EMBL-EBI data centre will be migrating to a new physical location resulting in a period of reduction in availability and functionality in a number of Ensembl services. This blog post will be updated with new information concerning the migration. What will be affected? There will be a temporary loss of all […]

Two talks at JGI in May: sourmash, spacegraphcats, and disease associations in the human microbiome.

written 8 days ago by Living in an Ivory Basement by Titus Brown

Using k-mers and taxonomy to find contamination in metagenomes

A Short Master Class in Benchmarking

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

There's a blog post on BioJulia.net that is well worth reading, even if you don't use Julia or I'd argue if you don't actually program. It looks at an issue of performance that was raised with BioJulia and with fierce but respectful passion examines the critique and explores just why BioJulia didn't perform well in the comparison. In the end, this triggers a code review and a huge speed increase in the problematic areas -- which will widely benefit BioJulia users.Read more »

Sampling Current &amp; Future Directions in PCR Diagnostics

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

My qPCR explainer seems to have done relatively well, though it took some refinement after readers caught a number of errors. The most embarrassing of those is that I got my PCR ramp units upside down, so instead of 4 seconds or so per degree C it's degrees C per second so my times were off by a factor of 16! Ouch! Despite that miscue, I'm here going to explore some of the variants on PCR that are out there, including some that are being employed searching for the newly renamed COVID-19 virus. Included here are some of my own speculations and musings, so as always remember I'm someone who thinks about these things and sometimes talks other people into running them, but I haven't set up a PCR in 8 years. Also, the field of PCR variations for diagnostics is enormous and I don't claim to have anything near complete knowledge of it, so this should be seen as a sampler and not a comprehensive review. Also, the usual reminder I am a paid consultant for a diagnostics company but they are neither aiming at viruses nor using PCR, so I won't discuss them -- but if you feel that shifts your priors on how I treat other companies you have the information to do so.Read more »

Wuhan 2019-2020 Coronavirus - UniProtKB acts to serve community need

written 17 days ago by Inside UniProt

The 2019–20 Wuhan coronavirus outbreak is a viral epidemic which started in mainland China but has since spread to several other countries and territories. The virus was first identified in Wuhan, the capital of China's Hubei province. Wuhan 2020 Coronavirus (nCoV) is an enveloped single-stranded RNA virus. The particles are decorated with petal-shaped surface projections which are reminiscent of the solar corona. These viruses are found in many vertebrate species and cause respiratory diseases, such as the common cold or SARS. The more recent Wuhan 2020 coronavirus has emerged from a still unknown animal reservoir and can be transmitted from human to human. Coronaviruses possess the largest genomes among all known RNA viruses. The 30 kilobase genome of the Wuhan seafood market strain has been sequenced (MN908947, NC_045512), this genome encodes a total of 13-14 proteins. In order to fast-track scientific research, these proteins have been manually annotated by UniProt biocurators and the entries made available as a pre-release dataset. This file provides pre-release access to the 2019-nCoV Wuhan Coronavirus protein sequences in UniProt from the current public health emergency. The data will become part of a future UniProt release and may be subject to further changes. A high-resolution crystal structure of 2019-nCoV coronavirus 3CL hydrolase (6lu7) has been determined by Zihe Rao and Haitao Yang's research team at ShanghaiTech University and is cross-referenced from P0DTD1. Two copies of the 3C-like hydrolase (P0DTD1 -PRO_0000449623)in a catalytically active assembly In common with other public domain resources, UniProt has moved rapidly to ...

Come and work with us

written 18 days ago by Opinionomics by Mick Watson

We have two amazing post-doc positions in our group: Job 1 is a two-year post-doc analysing large amounts of Illumina metagenomics data to design a chip that will be used for population profiling Job 2 is not yet live, but is for 3 years and involves writing NextFlow workflows for both long- and short- read […]

Understanding protein complexes with UniProtKB and the Complex Portal

written 20 days ago by Inside UniProt

Very few proteins are solitary biological entities which act independently. Understanding the context in which a protein carries out its function or regulates the function of other proteins is essential for a complete overview of how a protein works. UniProt and the Complex Portal provide the scientific community with the mechanistic importance and physiological contributions of individual proteins by presenting data on interactions, protein networks, and the reactions and pathways in which proteins play a role. In the recent publication entitled “Caenorhabditis elegans phosphatase complexes in UniProt and Complex Portal,” the two databases consider the phosphatome of the model organism C.elegans, and comprehensively review the way in which data characterising phosphatase-containing macromolecular complexes are presented. The databases use complementary curation approaches: UniProt is a protein-centric database and provides data on the complexes proteins may form or contribute to, whilst the Complex Portal presents data on macromolecular complexes and includes details of any specific protein functions that may be necessary for complex formation or function. This is the first study to compare and contrast the curation of phosphatase-containing complexes between the databases and portrays how collaborative efforts can answer a variety of research questions and widen investigative avenues.Phosphatases regulate intracellular signalling by catalysing the removal of phosphate groups from a diverse range of substrates. Phosphatase dis-regulation has been implicated in an increasing number of diseases, and as more than 50% of human phosphatases have a counterpart in C.elegans, this organism can complement human and mouse studies of the disease process. This ...

A qPCR (aka RT-PCR aka rRT-PCR) Explainer

written 22 days ago by Omics! Omics! by Keith Robinson

I've gotten in a number of Twitter threads and seen a lot of Quora questions about the qPCR test for the Wuhan coronavirus that I realized would really be best handled by writing an explainer. I'm intending it for financial types, reporters and anyone from the lay public interested in learning a bit more. For most regular readers of this blog, there won't be anything new to you. If you'd check me for accuracy, I'd be grateful but perhaps many will skip over this one. That also means I going to try to resist my usual urges to make lighthearted references to popular culture; they're a good way to be confusing.Read more »

Can ONT Maintain Grip on Burgeoning Flowcell Herd?

written 24 days ago by Omics! Omics! by Keith Robinson

A notion dawned on me when I was mentally planning my write-up of the Nanopore Community Meeting, but I decided to put off fleshing it out until a later date. After a bit of procrastination plus a crush of other ideas, here it is: Oxford Nanopore flowcell lineup has been a bit complicated for a while, but it's probably going to get worse. There's always been serious issues with the current level of complexity and it's hard to believe this will do anything but escalate.Read more »

Reaching under-served

written 25 days ago by Ensembl Blog

Outreach is, by its definition, tied to identifying and serving under-served populations. How does Ensembl address that? We provide services to communities who might not otherwise have access to those services through scientific outreach in low-middle income countries (LMIC) and by public engagement in groups that might lack science exposure. We provide training materials, tutorials […]

Clinical Exome Sequencing in Consanguineous Populations

written 25 days ago by KidsGenomics

Despite its proven utility for providing molecular diagnoses in patients with genetic disorders, exome sequencing is rarely the first-line diagnostic test ordered by most physicians. There are numerous valid medical and practical reasons for this. In some ways, exome sequencing is a victim of its own success: by enabling rapid discovery of many disease-causing genes, […] The post Clinical Exome Sequencing in Consanguineous Populations appeared first on KidsGenomics.

An Ultimately Tuftnellian Look At Oxford Nanopore R10.0 Homopolymer Performance

written 27 days ago by Omics! Omics! by Keith Robinson

Homopolymeric sequences have never been easy for any sequencing platform, but single molecule sequencers struggle the most with this. Oxford Nanopore has made remarkable strides in both raw an consensus accuracy via chemistry and software improvements, but still is challenged by systematic problems with homopolymers. The R10 series of pores is intended to significantly improve performance by having a longer narrow region to interact with more bases, and at the Nanopore Community Meeting there were several slides touting improved performance. Nanopore's slides have an X-axis that goes to 8. By happy circumstance, around that time we generated a large dataset on R10 and got results very similar to ONT's. Plus there's a dataset available from Mads Albertsen's group to support their updated pre-print on using Unique Molecular Identifiers (UMIs) to generate high quality consensus sequences. But our internal dataset is the best, as ours goes to eleven!Read more »

UST Bets on TELL-Seq

written 28 days ago by Omics! Omics! by Keith Robinson

I've made a few references recently to TELL-Seq, both in my flawed analysis of BioNano Genomics (I missed a key business development in their raising $18M in October; I stand by the science comments and fear that the fund raise buys them about a year of time) and on 10X Genomics discontinuing their genome assay kits. Now to actually dig into that technology -- a bit late given the preprint came out last fall, but better late than never. So put on your sunglasses and hoodies, conjure up the image of early television chefs and key up the theme music for The Lone Ranger, because here I go.Read more »

Can BioNano Genomics Map A Way Past Twin Perils?

written 4 weeks ago by Omics! Omics! by Keith Robinson

When playing with the structure of this piece in my mind, it occurred to me that Norman Maclean's thoughts about fly fishing apply just as well to biotechnology companiesIt is also interesting that thoughts about fishing are often carried on in dialogue form where Hope and Fear -- or, many times, two Fears -- try to outweigh each otherThe executive team at BioNano Genomics may well be gripped by this situation, as they are faced with two great perils: their finances and their markets.Read more »

Job: Genome Annotator (Regulation)

written 4 weeks ago by Ensembl Blog

We’re looking for a biologist to work on manual annotation of genes, transcripts and regulatory features onto reference genomes. We’re looking for degrees in molecular or cell Biology, genetics or genomics, with experience in gene regulation. Closes 5th March. Location: EMBL-EBI, Hinxton near Cambridge, UK Staff Category: Staff Member Contract Duration: 2 years Grading: Grade […]

Cool stuff the Ensembl VEP can do: write your own plugin

written 4 weeks ago by Ensembl Blog

Plugins can be an excellent way to extend the functionality of the VEP. They can be used to look-up information in external databases or use the Ensembl API to add to or filter your VEP output. Many plugins have already been written, both by us and external groups, but with a bit of Perl you […]

Genia: It's Alive!

written 4 weeks ago by Omics! Omics! by Keith Robinson

Once in a while I get the thrill of someone sending me a really good tip - that surge that comes with knowing that I know something that most people don't. That rush of knowing that soon I'll get to spill the beans. It's great, even if it upends my widely disseminated opinions. Even if a moment later I realize that if I had thought harder I would have unearthed the nugget on my own. All of which is the case here -- my tea leaf reading that Roche partnering with Illumina on diagnostics indicated that Genia is no more -- well, that interpretation is no more. Because I got a hot and verifiable tip that Genia is very much still an active project at Roche. And the verification is how I could I found this independently.Read more »

10X Genomics Exits Genomes

written 5 weeks ago by Omics! Omics! by Keith Robinson

10X Genomics original product was a kit for generating linked reads from genomic DNA. The idea had been kicking around for a while, partitioning long DNA into compartments and generating tagged libraries from each compartment. This enabled both genome assembly and haplotyping from very small amounts of DNA. When first reviewing 10X's slides from J.P. Morgan I had this thought "where's the genome kits" but then forgot to include it in my write-up. Now I'm even more chagrined to discover that the explanation had been posted days before the conference: 10X has told their customers that their genome library kits are in the process of being discontinued.Read more »

Diversity matters

written 5 weeks ago by Bits of DNA by Lior Pachter

The widespread establishment of statistics departments in the United States during the mid-20th century can be traced to a presentation by Harold Hotelling in the Berkeley Symposium on Mathematical Statistics and Probability in 1945. The symposium, organized by Berkeley statistician Jerzy Neyman, was the first of six such symposia that took place every five years, […]

JPM20 Loose Ends: Agilent, ThermoFisher, 10X Genomics, NanoString - plus PacBio &amp; ONT

written 5 weeks ago by Omics! Omics! by Keith Robinson

Time to close out J.P. Morgan season with a grab bag of kvetches and kibbitzing on multiple 'omics companies that presented. Much of this has been stimulated by Twitter discussions, with particular credit going to Varro Analytics and Albert Vilella. While I've never been to J.P. Morgan physically and am skeptical I'll ever go, reviewing all this is a great prep for AGBT -- which I'm happy to be returning to this year for it's last Marco Island appearance for many years (forever?).Read more »

Ensembl 99 has been released!

written 5 weeks ago by Ensembl Blog

We’re pleased to announce the release of Ensembl 99, and the corresponding release of Ensembl Genomes 46. Along with updates of human gene annotation and variation data, we have a menagerie of new and updated vertebrate species in Ensembl plus a whole set of new plants, mosquitos and flies in Ensembl Genomes. Human and Mouse […]
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