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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 […]
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 »
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 »
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 […]
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 […]
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.
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 […]
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
written 28 days ago by Diving into Genetics and Genomics
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 […]
written 4 weeks ago by Living in an Ivory Basement by Titus Brown
Writing applications around workflow systems
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 »
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 […]
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.
written 5 weeks ago by Living in an Ivory Basement by Titus Brown
How do you grow community? Slowly and carefully.
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 […]
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
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 […]
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.
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 […]
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 »
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 ...
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.
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 […]
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.
News about the Ensembl Project and its genome browser
155 posts, last updated 2 days ago
A computational biologist's personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery
237 posts, last updated 6 days ago
KidsGenomics focuses on genetic diseases that affect children, including rare inherited disorders and pediatric cancers.
4 posts, last updated 16 days ago
Notes from the life of a computational biologist
98 posts, last updated 18 days ago
A wet lab biologist' bioinformatic notes. Mostly is about Linux, R, python, reproducible research, open science and NGS. I am into data science! I am working on glioblastoma (a terrible brain cancer) genomics at MD Anderson cancer center. Disclaimer: For posts that I copied from other places, credits go to the original authors.
50 posts, last updated 28 days ago
bioinformatics education, metagenomics assembly, python programming
228 posts, last updated 4 weeks ago
Weblog on Bioinformatics, Genome Science and Next Generation Sequencing
69 posts, last updated 4 weeks ago
bioinformatics, genomes, biology etc. "I don't mean to sound angry and cynical, but I am, so that's how it comes across"
44 posts, last updated 5 weeks ago
News and commentary from the UniProt developers
33 posts, last updated 7 weeks ago
Medical genomics in the post-genome era
71 posts, last updated 7 weeks ago
Reviews and commentary on computational biology
84 posts, last updated 9 weeks ago
My name is Guillaume Filion. I am a scientist who loves biology and mathematics. As of late I also got into computers and the Internet. I intend my blog to be recreational, and not academic nor educational. I wish you will find some of the posts inspiring for your own reflection.
28 posts, last updated 10 weeks ago
Assistant professor of computer science at University of Iceland.
9 posts, last updated 11 weeks ago
Making Sense of Next-Gen Sequencing Data
87 posts, last updated 3 months ago
Biology, sequencing, bioinformatics and more
32 posts, last updated 4 months ago
Tips && tricks from a cluster of bioinformaticians
15 posts, last updated 5 months ago
A news portal with postings about genomics resources, genomics news and research, science and more.
391 posts, last updated 7 months ago
This blog is written by Giovanni M. Dall’Olio, a research associate at the Cancer Evolutionary Genomics‘s group of Francesca Ciccarelli at the King’s College of London. My primary interests are in the system biology of cancer and in identifying new potential drug targets for this disease.
13 posts, last updated 9 months ago
My worklog on bioinformatics, science and research. Small tasks and cute tricks included :)
34 posts, last updated 11 months ago
Getting Things Done in Genetics & Bioinformatics Research
60 posts, last updated 14 months ago
virology, bioinformatics, genetics, science, java
65 posts, last updated 15 months ago
Thoughts and opinions from the associate director of the EMBL-European Bioinformatics Institute
57 posts, last updated 16 months ago
Bioinformatics tips, tricks, tools and commentary - all with a microbiological NGS bent. Authored by Dr Torsten Seemann from Melbourne, Australia.
29 posts, last updated 19 months ago
Bioinformatics tips, tricks, tools and commentary with a microbial genomics bent. Written by Torsten Seemann from Melbourne, Australia.
25 posts, last updated 19 months ago
Frontier in Bioinformatics
185 posts, last updated 23 months ago
bioinformatics, biopython, genomic analysis
38 posts, last updated 2.0 years ago
bioinformatics, genomes, biology etc. "I don't mean to sound angry and cynical, but I am, so that's how it comes across"
78 posts, last updated 2.2 years ago
21 posts, last updated 3.4 years ago
A group blog providing expert, independent commentary on the personal genomics industry.
34 posts, last updated 3.5 years ago
The Knight Lab at Yale University » BlogThe Knight Lab at Yale University » Bioinformatics and Genetics
Bioinformatics and Genetics
3 posts, last updated 3.7 years ago
miRBase news and views
14 posts, last updated 3.7 years ago
25 posts, last updated 4.4 years ago
Mostly bioinformatics, NGS, and cat litter box reviews
25 posts, last updated 4.6 years ago
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