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Ensembl Genomes 39 has been released!

written 2 days ago by Ensembl Blog

We are pleased to announce the latest release of Ensembl Genomes (EG!39). Highlights include new genomes (Stalk-eyed fly and Waterflea) and a polyploid view for Wheat. Read on to find out more about new data and features: Metazoa New genomes: Stalk-eyed fly (Teleopsis dalmanni) and Waterflea (Daphnia magna) Updated protein domains using InterProScan (with InterPro version […]

Mission Bio Launches Custom Panels

written 6 days ago by Omics! Omics! by Keith Robinson

Back in October I covered the launch of Mission Bio's single cell platform, Tapestri. Tapestri is a microfluidic platform which encapsulates cells and sets of barcoded primers into droplets, lyses the cells within the droplets and executes PCR on the released DNA. Mission initially targeted hematologic cells, since they do not require disaggregation, and offered a standard panel of primes. Around the time of AGBT, Mission launched a custom panel option and took the time to sit down with me. Now with AACR, Mission has announced placing Tapestri at multiple major cancer centers: the NCI, Mt. Sinai, MD Anderson, Memorial Sloan Kettering, St. Jude's, UCSF, U Penn and Washington University.Read more »

A Small Rampage Over STAT's Movie Piece

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

A movie opened this weekend which, by all prior evidence and new reviews, is unbelievably silly but destined to rake in the bucks. Rampage is very loosely - as if it could be another way - based on a video arcade game. The original game’s backstory had a mysterious ray transforming people into monsters, but the movie has changed that to CRISPR. So STAT had a piece which, to my great disappointment, gave the movie’s science a near pass in a piece featuring two writers chatting . . (Note: this post has mild spoilers, though if you've seen the trailers they give almost all of this away).Read more »

Getting to know us: Mag from Core

written 9 days ago by Ensembl Blog

This month we’re getting to know Mag, who is the Ensembl Core Senior Project Leader. Read on to find out more about her career path and what she gets up to in her day-to-day role! What is your job in Ensembl? I am the Ensembl Core senior project leader. The Core team is responsible […]

Do you use transcripts for your work?

written 12 days ago by Ensembl Blog

Ensembl and NCBI have been working to align the GENCODE and RefSeq reference transcripts. As part of that effort, we are also developing plans to define a primary transcript for every gene as well as a minimal set of clinically relevant transcripts. To guide that effort, we have developed a small survey to get input on how […]

The Power of Sequencing Data Re-analysis

written 16 days ago by KidsGenomics

The clinical genetics group at our hospital holds a weekly conference to discuss patients recently seen by the clinicians and/or genetic counselors. I began attending this “post-clinic conference” when I moved here a year and a half ago. It’s been very educational for me, both in learning about some of the rare conditions affecting our […] The post The Power of Sequencing Data Re-analysis appeared first on KidsGenomics.

Ensembl 92 has been released!

written 17 days ago by Ensembl Blog

We have been busy over Easter and Ensembl 92 is now live! Read on to check out the highlights of this release and join us for our release webinar on Monday 9th April 2018 at 16:00 GMT to learn more about the new data and features. New species: Goat (Capra hircus) The eagerly-awaited highlight of […]

Moving from RPubs to Github documents

written 18 days ago by What You're Doing Is Rather Desperate by Neil Saunders

If you still follow my Twitter feed – I pity you, as it’s been rather boring of late. Consisting largely of Github commit messages, many including the words “knit to github document”. Here’s why. RPubs, an early offering from RStudio, has been a great platform for easy and free publishing of HTML documents generated from … Continue reading Moving from RPubs to Github documents

Three gotchas when using R for Genomic data analysis

written 28 days ago by Diving into Genetics and Genomics

2018 – a year of conferences

written 4 weeks ago by Ensembl Blog

We think conferences are great opportunities to use talks and posters to tell people about all the cool stuff we’re developing, provide training with workshops and learn more about what’s going on in our fields of interest. Ensembl team members attend many conferences a year and 2018 is no exception, we’re planning to attend nineteen (so […]

Pydoit, snakemake, and workflows-as-applications

written 4 weeks ago by Living in an Ivory Basement by Titus Brown

Writing applications around workflow systems

A Most Unfortunate Sequencing Error

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

If you are in the sequencing business, you'd like to get things right. But sequencing is a form of measurement and measurement has error. No matter how diligent and committed you are, sometimes the data doesn't break your way. Mick Watson has a set of posts and a preprint illustrating quality issues in many deposited bacterial genomes. Some of those are bad luck and some of those are from complacency. Some errors radically affect biological interpretation and some don't. I'm going to detail here one of the worst cases of bad luck I've seen, where relatively small errors sat undetected for over a decade and triggered some published head scratching over their erroneous implications. So let's look at the rap sheet of this error.Read more »

FTP and mirrors down for maintenance, 22nd March

written 4 weeks ago by Ensembl Blog

The FTP site and the worldwide mirrors (useast.ensembl.org, uswest.ensembl.org and asia.ensembl.org) will be down for maintenance 10.30-14.30 GMT on Thursday 22nd March 2018. The mirror sites should automatically redirect back to the main site at www.ensembl.org, so browser users should be unaffected. However, you will not able to download files from the FTP site in […]

JD: Sr. Software DevOps Engineer at Guardant Health

written 4 weeks ago by Kevin's GATTACA World

https://jobs.smartrecruiters.com/GuardantHealth/743999667525776-sr-software-devops-engineerGotta love this line “We wanted flying cars and instead we got 140 characters” is a much-repeated complaint about Silicon Valley. But with all due respect to flying cars, we believe that our mission is even more critical. notable skills in the JD to pursue Ansible / ChefDockerThis paragraph sounds exactly like what I face on a daily basisYour troubleshooting skills are excellent, and you enjoy a good daily challenge in supporting rapid growth and a diverse set of end user needs. You have the ability to maintain day to day support while running various key projects that move the business forward by automating and creating new tools that facilitate management of the environment.

My approach to community building and coordination

written 5 weeks ago by Living in an Ivory Basement by Titus Brown

How do you grow community? Slowly and carefully.

With great power comes great responsibility

written 5 weeks ago by Opinionomics by Mick Watson

Recently I published a blog post about a fairly simple test to find out whether you have “short” protein predictions in your bacterial genomes, and predicted that some of these short peptides may be the result of unresolved errors in long-read, single molecule assemblies. Perhaps not surprisingly, there was a reaction from the PacBio community […]

Farewell then, PubMed Commons

written 5 weeks ago by What You're Doing Is Rather Desperate by Neil Saunders

PubMed Commons, the NCBI’s experiment in comments for PubMed articles, has been discontinued. Thoroughly too, with all traces of it expunged from the NCBI website. Last time I wrote about the service, I concluded “all it needs now is more active users, more comments per user and a real API.” None of those things happened. … Continue reading Farewell then, PubMed Commons

Getting to know us: Jon from HAVANA

written 6 weeks ago by Ensembl Blog

This month we are meeting Jonathan Mudge who is the Annotation Project Leader in the HAVANA group. What is your job in Ensembl? I’m a Team Leader in the HAVANA group. We focus on manual gene annotation of the human and mouse genomes, which forms the core of the genesets produced for these species […]

The genomic landscape of pediatric cancers

written 6 weeks ago by KidsGenomics

Although pediatric cancer is rare, it’s the leading cause of disease-related death among children who survive past infancy (in the Western world). Around 1 in 500 children will be diagnosed with cancer by age 15. Like most rare diseases, childhood cancer is difficult to study because so few patients are available. Even for the most […] The post The genomic landscape of pediatric cancers appeared first on KidsGenomics.

A simple test for uncorrected insertions and deletions (indels) in bacterial genomes

written 6 weeks ago by Opinionomics by Mick Watson

A friend and a colleague of mine once said about me “he’s a details man”, and it was after we had discussed the fact some of my papers consist solely in pointing out the errors other people ignore – in RNA-Seq for example, or in genome assemblies (I have another under review!). By now, those […]

A Morning Visit to SeqLL

written 6 weeks ago by Omics! Omics! by Keith Robinson

I've written in the past about SeqLL, the company which purchased all of the hard assets from Helicos after the latter's demise. At the end of last year, CEO Elizabeth Reczek invited me to stop by for a visit and so I spent a morning having a frank discussion with Dr. Reczek and Director of Sales Lee Dalton and also was treated to a tour of their facilities.Read more »

Would you like to annotate function with UniProt's annotation systems?

written 7 weeks ago by Inside UniProt

Register your interest here: https://goo.gl/forms/IFo28dAOa5HEwfSk1One of the core activities at UniProt is to develop computational methods for the functional annotation of protein sequences. UniProt has developed two prediction systems, UniRule and the Statistical Automatic Annotation System (SAAS) to automatically annotate the unreviewed records in UniProtKB/TrEMBL with high coverage and a high degree of accuracy.These prediction systems can annotate protein properties such as protein names, function, catalytic activity, pathway membership, and subcellular location, along with sequence-specific information, such as the positions of post-translational modifications and active sites.As a result of discussions with researchers and genome sequencing centres interested in functional annotation, we plan to make our annotation rules publicly available for download. We would like to engage with users in the development of a standardised format for sharing these annotation rules, to help you use the rules for functional annotation of your own data.Apply the UniProt rules on your own proteinsWe also plan to provide a standalone tool to execute the UniProt annotation rules and enrich your own data with high-quality annotations. We invite user feedback towards the provision of such a tool for functional annotation of coding sequences.By providing input data such as the protein sequences, taxonomy data and InterProScan signatures, along with the rules, a rule engine will be able to reason on the rules to infer new protein annotations.Get involvedWould you like to try out the UniProt rules to annotate your own data? Would you like an early peek at the systems, formats and functionality we plan to ...

Ensembl sites down

written 7 weeks ago by Ensembl Blog

The main Ensembl site at ensembl.org and the GRCh37 site at grch37.ensembl.org are both down at the moment. The mirror sites at useast.ensembl.org, uswest.ensembl.org and asia.ensembl.org are all available. We are sorry about any inconvenience, and are working on rectifying this.

MassGenomics is Closed, but KidsGenomics is Open

written 7 weeks ago by MassGenomics by Dan Koboldt

Thank you to everyone who sent kind messages after I announced the end of MassGenomics earlier this month. Please rest assured that this website and all of its articles will remain online for the foreseeable future. Also, I have an important announcement. Today is Rare Disease Day, an annual event that aims to raise awareness […]

Why Rare Disease Research Matters

written 7 weeks ago by KidsGenomics

February 28th is International Rare Disease Day, an event that aims to raise awareness of rare diseases and the pressing need for more research. Rare Diseases By The Numbers Rare diseases might be rare, but the patients and families affected by them are numerous. Here are some statistics courtesy of the National Organization for Rare […] The post Why Rare Disease Research Matters appeared first on KidsGenomics.
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