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How many doubly manlocked scientists are there?

written 2 days ago by Bits of DNA by Lior Pachter

Algorithmic bias is a term used to describe situations where an algorithm systematically produces outcomes that are less favorable to individuals within a particular group, despite there being no relevant properties of individuals in that group that should lead to distinct outcomes from other groups . As “big data” approaches become increasingly popular for optimizing complex […]

Changes in BioMart species support

written 6 days ago by Ensembl Blog

As Ensembl continues to rapidly grow in terms of the number of supported species, we continually assess our provided resources effectively match the scientific needs of the researchers using them. In order to maintain our BioMart service at its current performance level, we will be making changes to data availability in BioMart starting with the […]

Update: Simplifying our GRCh37 Services

written 7 days ago by Ensembl Blog

Following our consultation on simplifying our GRCh37 services, we have decided to remove all support for non-human data from our dedicated GRCh37 database from release 100 onwards in early 2020. This will impact the website at grch37.ensembl.org, the REST server at rest.grch37.ensembl.org and the database at ensembldb.ensembl.org:3337. Non-human data will still be supported on the e75.ensembl.org […]

Ensembl is part of the first Google Season of Docs!

written 12 days ago by Ensembl Blog

Google Season of Docs (GSoD) provides a framework for technical writers and open source projects to work together remotely towards the common goal of improving an open source project’s documentation. This exciting new programme ran for the first time from September to November 2019! During the programme technical writers spend a few months working closely […]

An outrage at UC Davis

written 14 days ago by Bits of DNA by Lior Pachter

Yesterday I found out via a comment on this blog that Yuval Peres, a person who has been accused by numerous students, trainees, and colleagues of sexual harassment, will be delivering a lecture today in the UC Davis Mathematical Physics and Probability Seminar. The facts I am aware of at least 11 allegations by women of […]

Job: Bioinformatics Developer

written 22 days ago by Ensembl Blog

We’re looking for a bioinformatician to work on integrating model organism genomic data, including variation, gene and comparative genomics data. We’re looking for degrees in biological or computer science, with experience in programming, databases and genome analysis. Closes 8th December. Location: EMBL-EBI, Hinxton near Cambridge, UK Staff Category: Staff Member Contract Duration: 3 years Grading: […]

Job: Genomics Project Leader

written 23 days ago by Ensembl Blog

We’re looking for a bioinformatics manager to lead development of pipelines for and curation of gene annotation resources for model organisms. We’re looking for PhDs in bioinformatics or a related field and experience in genome annotation and large-scale databases. Closes 8th December. Location: EMBL-EBI, Hinxton near Cambridge, UK Staff Category: Staff Member Contract Duration: 3 years […]

CMA Drops the (Preliminary) Hammer on ILMN-PacBio

written 26 days ago by Omics! Omics! by Keith Robinson

Today the United Kingdom's Competition and Merger Authority (CMA) issued their preliminary report on the proposed acquisition of Pacific Biosciences by Illumina. The report has no dry British phrasing: they clearly state that the merger is anticompetitive and that the only legal remedy is to block the transaction. Interestingly, today was also the scheduled Illumina Q3 earnings call, but the subject wasn't even broached there.Read more »

Cool stuff the Ensembl VEP can do: transcript selection

written 26 days ago by Ensembl Blog

By default VEP will tell you the consequences for every transcript affected by a variant. You may wish to prioritise your analysis to only the most important or well supported transcripts for each gene, and VEP provides information to help you do that. A number of flags are added to human transcripts in Ensembl to […]

OpenHelix to exhibit at TRICON

written 28 days ago by The OpenHelix Blog

Also, for the developer types: they offer a way for you to interact with the Aquaria software to add your own features of interest with their API. Maybe you have new mutations you have found in some sequence you’ve obtained in your lab, for example. They are offering guidance on that here: http://bit.ly/aquaria-features. They touch on this […] The post OpenHelix to exhibit at TRICON appeared first on Open Helix.

WHAT’S THE ANSWER? (BEGINNER PROJECTS TO PICK UP)

written 28 days ago by The OpenHelix Blog

This week’s highlighted discussion tackles the topic of small projects for folks who are just beginning their training in bioinformatics, or possibly a career transition into a new area. It’s an issue that has come up a number of times, and this new idea for connecting students and projects is a good one, I think. […] The post WHAT’S THE ANSWER? (BEGINNER PROJECTS TO PICK UP) appeared first on Open Helix.

VIDEO TIP OF THE WEEK: DESIGNING PROTEINS, USING ROSETTA

written 28 days ago by The OpenHelix Blog

As often happens, last week’s tip on visualizing structures led me to some more reading and thinking about creating protein structures. And although it’s important for biologists to be able to use more of the information about protein structures and variations in their work from tools like Aquaria or PDB, it’s also important for some researchers to be on the […] The post VIDEO TIP OF THE WEEK: DESIGNING PROTEINS, USING ROSETTA appeared first on Open Helix.

VIDEO TIP OF THE WEEK: PROTEIN STRUCTURE INFORMATION FOR PUBLIC OUTREACH. REALLY.

written 28 days ago by The OpenHelix Blog

This week’s tip isn’t about a specific tool–but a really interesting look at how a tool was used in the context of some general public outreach messaging. Recently I posted about Aquaria, a new tool available to let biologists explore protein structures, mutations, and domains in user-friendly ways. But an interesting example of how the information about protein […] The post VIDEO TIP OF THE WEEK: PROTEIN STRUCTURE INFORMATION FOR PUBLIC OUTREACH. REALLY. appeared first on Open Helix.

QIAGEN Quashes GeneReader

written 29 days ago by Omics! Omics! by Keith Robinson

Two weeks ago QIAGEN announced they will discontinue development of their GeneReader short read instrument and move their portfolio of gene panel tests over to the Illumina MiSeq and NextSeq. Existing instrument owners will continue to be supported for an indefinite period. Thus ends QIAGEN's effort to build a fully vertically integrated sample-to-answer diagnostic sequencing system, just short of 4 years from the system's launch. What can be learned from this and how does this reshape the sequencing market?Read more »

Job: Ensembl Web Back-end Project Leader

written 4 weeks ago by Ensembl Blog

We’re looking for a web development manager to lead our back-end web-team, developing web infrastructure and APIs. We’re looking for MScs or PhDs in biology, bioinformatics, software engineering with experience working with IT infrastructure, containers, data management and Linux. Location: EMBL-EBI, Hinxton near Cambridge, UK Staff Category: Staff Member Contract Duration: 3 years Grading: 7 (monthly […]

Zero-data RNA-seq

written 4 weeks ago by Bits of DNA by Lior Pachter

The arXiv preprint server has its roots in an “e-print” email list curated by astrophysicist Joanne Cohn, who in 1989 had the idea of organizing the sharing of preprints among her physics colleagues. In her recollections of the dawn of the arXiv, she mentions that “at one point two people put out papers on the […]

What’s coming up in Ensembl release 99?

written 4 weeks ago by Ensembl Blog

What’s coming up in Ensembl release 99? Ensembl 99 (and Ensembl Genomes 46) are due out in December and we plan to include a bumper set of new and updated species. As with all releases, we cannot guarantee that anything listed here will make it into the final release. Major Data Updates: Update to […]

Where to Find Me at ASHG 2019

written 5 weeks ago by KidsGenomics

This week I’m attending the American Society of Human Genetics meeting in Houston, Texas. If you’re at this meeting, please track me down. I’d love to connect with past colleagues and long-distance collaborators as well as anyone with an interest in rare diseases and epilepsy. I’m also a new incoming member of the ASHG 2019 […] The post Where to Find Me at ASHG 2019 appeared first on KidsGenomics.

Job: Genebuild bioinformatician

written 5 weeks ago by Ensembl Blog

We’re looking for a bioinformatician to join our genebuild team, working on annotating genes onto genomes, particularly as part of the Darwin Tree of Life project. We’re looking for MScs or PhDs in Computer Science, Bioinformatics or Genetics, with experience working with complex code, genomics and alignments. Closes 20th November. Location: EMBL-EBI, Hinxton near Cambridge, UK […]

When your tools are broken, just change the data

written 6 weeks ago by What You're Doing Is Rather Desperate by Neil Saunders

It’s been 3 years since we last visited that old favourite recurring topic, data corruption by Excel. Specifically, the unwanted auto-conversion of identifiers that look like dates, e.g. SEPT1, to – well, dates. Here’s a new twist – well, a two year-old twist in fact, as I don’t keep up to date with this field … Continue reading When your tools are broken, just change the data

Is Python really faster than C++ ?

written 6 weeks ago by Bits of DNA by Lior Pachter

A few months ago, in July 2019, I wrote a series of five posts about the Melsted, Booeshaghi et al. 2019 preprint on this blog, including a post focusing on a new fast workflow for RNA velocity based on kallisto | bustools. This new workflow replaces the velocyto software published with the RNA velocity paper (La […]

Illumina Throws PacBio An Extension and a Lifeline

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

Interesting news today on the PacBio front: as reported by GenomeWeb, Illumina announced that their walkaway date for the acquisition has been extended to March 31 of next year and that Illumina will be pumping significant cash into PacBio until either the merger occurs or is terminated. In addition to publicly reinforcing Illumina's determination to get the deal done, the terms of the arrangement have interesting consequences should the deal fall throughRead more »

Where U.K.'s CMA Missed the Plot

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

I've written far more than I expected to on the PacBio merger, with it dominating my output here this summer save that recent dip in the CCS boomerangs. We still haven't heard from the U.S. FTC, which is the big hammer that could drop and the stock is still selling at a substantial discount to the price offered by Illumina. While I've hinted at it, I've never quite detailed my major objection to the form of the UK CMA's analysis of the proposed acquisition. I've missed the opportunity to lay that out during the period of public comment for the next round of the CMA. Still, worth it to write it down. Which was true about a month ago when I wrote this, then failed to actually push it to a post before I headed out for a rugged vacation in the American West. And then forgot about it after returning. And more news today to comment on -- so better finally get this out there.Read more »

Ch 3 – Biological Basis of Behavior: The Brain

written 7 weeks ago by thoughts about ...

The presentation uncovers hindbrain.Ch 3 – Biological Basis of Behavior: The Brain - ppt video online download: Ways we Study the Brain Accidents Lesions EEG CAT Scan PET Scan MRI fMRI

Debuting in a VFL/AFL Grand Final is rare

written 7 weeks ago by What You're Doing Is Rather Desperate by Neil Saunders

When Marlion Pickett runs onto the M.C.G for Richmond in the AFL Grand Final this Saturday, he’ll be only the sixth player in 124 finals to debut on the big day. The sole purpose of this blog post is to illustrate how incredibly easy it is to figure this out, thanks to the dplyr and … Continue reading Debuting in a VFL/AFL Grand Final is rare
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