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weeSAM version 1.5.

written 9 weeks ago by Bioinformatics I/O

What is weeSAM? weeSAM is a python script which produces coverage statistics and coverage plots from an input SAM or BAM file. Figures and stats are written up in HTML so users can easily view the coverage for their reference assembly. weeSAM is simple to run and the steps below give an illustration. What’s new […]

Using leaflet, just because

written 9 weeks ago by What You're Doing Is Rather Desperate by Neil Saunders

I love it when researchers take the time to share their knowledge of the computational tools that they use. So first, let me point you at Environmental Computing, a site run by environmental scientists at the University of New South Wales, which has a good selection of R programming tutorials. One of these is Making … Continue reading Using leaflet, just because

Ensembl Genomes 40 has been released!

written 9 weeks ago by Ensembl Blog

We’ve been tending the Ensembl Plants garden with great care, have cultivated several new species and updated a number of genome assemblies, including a new chromosome-level wheat genome from IWGSC. The protist team have also been busy and are proud to announce an updated assembly for Leishmania major. Read on to find out more about […]

Ensembl 93 has been released!

written 9 weeks ago by Ensembl Blog

Are you feline excited for our new pawsome release?! Ensembl 93 has been released, bringing with it two new big cat genomes for tiger and leopard, and an update to the domestic cat assembly. If cats aren’t your thing, we also have a huge new dbSNP import for human and a brand new regulatory build […]

Twitter coverage of the useR! 2018 conference

written 9 weeks ago by What You're Doing Is Rather Desperate by Neil Saunders

In summary: useR! the conference for users of R was held in Brisbane earlier this month it sounded like a lot of fun and here’s an analysis of tweets that used the #useR2018 hashtag during the week The code that generated the report (which I’ve used heavily and written about before) is at Github too. … Continue reading Twitter coverage of the useR! 2018 conference

Front-End Web Developer

written 10 weeks ago by Ensembl Blog

We’re looking for a web developer to work on visual representation of genomic data. We’re looking for masters in computer science or bioinformatics with experience developing web interfaces working with Javascript, React and a scripting language. Closes 19th August. Location: EMBL-EBI Hinxton near Cambridge, UK Staff Category: Staff Member Contract Duration: 3 years initially (renewable) Grading: 5 (monthly […]

The Open Source Anti-Sisyphean League

written 10 weeks ago by Living in an Ivory Basement by Titus Brown

We need an Open Source Anti-Sisyphean League!

New guidelines to help with protein naming

written 11 weeks ago by Inside UniProt

Why is consistent protein naming important?For many proteins, a variety of different names are used across the scientific literature and public biological databases which makes effective organization and exchange of biological information a difficult task. Consistent protein nomenclature is indispensable for communication, literature searching and retrieval of database records.New protein nomenclature guidelinesTo address this issue and provide some help in protein naming, a set of protein nomenclature guidelines have been produced jointly by the European Bioinformatics Institute (EMBL-EBI), the National Center for Biotechnology Information (NCBI), the Protein Information Resource (PIR) and the Swiss Institute for Bioinformatics (SIB). UniProt has been heavily involved in this work along with other groups from the four institutes. These efforts have built on existing guidelines which were already in use by groups such as UniProt and RefSeq, expanding and consolidating them into a single shared document which provides a comprehensive set of recommendations.What makes a good protein name?A good protein name is one which is unique, unambiguous, can be attributed to orthologs from other species and follows official gene nomenclature where applicable. The guidelines help to achieve this goal by covering all aspects of protein naming from advice on expert sources of protein names and how to name novel proteins of unknown function to more detailed advice such as terms to avoid in a protein name and acceptable abbreviations.Who are the guidelines intended for?The guidelines are intended for use by anyone who wants to name a protein. Groups who will find these guidelines helpful include:Biocurators ...

On stuck records and indel errors; or “stop publishing bad genomes”

written 11 weeks ago by Opinionomics by Mick Watson

I’m in real danger of sounding like a stuck record, but readers of the blog will know I have a bee in my bonnet about researchers who (unwittingly I’m sure) publish long-read assemblies with uncorrected indel errors in them. If you are knew to the blog, please read about my simple method for detecting indels, […]

A framework for thinking about Open Source Sustainability?

written 11 weeks ago by Living in an Ivory Basement by Titus Brown

Can we apply Common Pool Resource work to open online projects?

Ensembl Applications Project Leader

written 12 weeks ago by Ensembl Blog

We’re looking for a manager to head software development and web applications in Ensembl. We’re looking for MScs or PhDs Computational, Physical or Biological Sciences, with experience developing web applications. Closes 31st July. Location: EMBL-EBI Hinxton near Cambridge, UK Staff Category: Staff member Contract Duration: 3 years initially (renewable) Grading: 6 or 7 (monthly salary […]

Ten years of the GWAS Catalog – Past, present and future

written 12 weeks ago by Ensembl Blog

This is a guest blog from our colleagues of the GWAS Catalog who you can contact at gwas-info[at]ebi.ac.uk. This year marks a special anniversary for the GWAS Catalog, as we have reached ten years since our launch in 2008. The GWAS Catalog is a widely used publicly available resource of all published human genome wide association studies […]

DANIO-CODE is out – how can you work with it in Ensembl?

written 12 weeks ago by Ensembl Blog

Functional genomics data from DANIO-CODE has been released to the public. This international effort, similar to ENCODE in human and mouse, seeks to characterise the functional elements in the zebrafish (Danio rerio) genome. Announced on Saturday at the International Zebrafish Conference, the DANIO-CODE dataset exists as a track hub, which can be viewed in Ensembl. […]

Bioinformatician – CREST

written 12 weeks ago by Ensembl Blog

We’re looking for a bioinformatician to work on integrating clinically relevant annotation from GENCODE and RefSeq. We’re looking for MScs or PhDs in Computer Science, Bioinformatics or Genetics with experience working in eukaryotic genome annotation and object-oriented programming. Closes 5th August. Location: EMBL-EBI Hinxton near Cambridge, UK Staff Category: Staff member Contract Duration: 3 years Grading: […]

Bioinformatician – Ensembl Variation

written 12 weeks ago by Ensembl Blog

We’re looking for a bioinformatician to work on integrating variation data into our variation database and developing tools to display and work with it. We’re looking for degrees in genetics, biological or computational sciences with experience in production, genomics, Perl and Unix/Linux. Closes 5th August. Location: EMBL-EBI Hinxton near Cambridge, UK Staff Category: Staff Member Contract […]

How open is too open?

written 12 weeks ago by Living in an Ivory Basement by Titus Brown

How open is too open?

Cool stuff the VEP can do: normalisation

written 3 months ago by Ensembl Blog

One of the biggest headaches when working with insertions and deletions is how many different ways you can represent the same variant. If you’re looking to find out if there’s already known allele frequencies or phenotypes at a locus, you want to make sure that you find the right one. The VEP can take that […]

Idle thoughts lead to R internals: how to count function arguments

written 3 months ago by What You're Doing Is Rather Desperate by Neil Saunders

“Some R functions have an awful lot of arguments”, you think to yourself. “I wonder which has the most?” It’s not an original thought: the same question as applied to the R base package is an exercise in the Functions chapter of the excellent Advanced R. Much of the information in this post came from … Continue reading Idle thoughts lead to R internals: how to count function arguments

LC2018: VolTRAX

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

In my preview ahead of London Calling, I suggested that VolTRAX is a device that still hasn't found its raison d'etre. With the meeting, the device officially pre-launched and the company is now taking pre-orders for delivery in the Fall. And it still feels like a device which hasn't yet found its purpose, though Clive Brown presented a dazzling (if perhaps distant) vision of where VolTRAX might go.Read more »

GSOC with Ensembl: introducing our students

written 3 months ago by Ensembl Blog

For the third year in a row, we’re lucky to have student developers working with us as part of Google Summer of Code. We’ve got three GSOC-ers this year, working on some really exciting projects: Zeyu Tony Yang, working on primary genome analysis, Nabil Ibtehaz, working on transcript-level orthology and Somesh Chaturvedi, working on retrieving […]

LC2018: Flongle, Ubik-a-something and Metricoin

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

London Calling has been over for nearly three weeks. I originally wanted to write up at least something after the first night, but fatigue overcame me and I didn't get anything useful put together. And then travel and more fatigue set in. But beyond that and the usual temptation to procrastinate, there is the challenge of forming a coherent narrative from all the different threads at the meeting. There's all the Oxford Nanopore official announcements and then various user presentation tidbits. After several failed mental attempts to compose a big picture take on everything, I've decided to try to write a series (number yet indeterminate) of posts that will focus of various axes of the meeting. Hopefully they won't be to redundant -- or self-contradictory -- and that by following one particular thread I can actually condense some coherent thoughts. This first such thread starts with Flongle.Read more »

How long does it take to produce scientific software?

written 3 months ago by Living in an Ivory Basement by Titus Brown

How long does it take to produce scientific software?

Update to Perl and BioPerl in Ensembl

written 3 months ago by Ensembl Blog

From Ensembl 93 onwards, we plan to recommend newer versions of Perl (5.14- 5.26) and BioPerl (1.6.924) when using the Ensembl Perl API. This may affect pipelines which employ the Ensembl Perl API, since we will no longer actively support older versions of Perl and BioPerl. At Ensembl, we’ve been using Perl since the project […]

MicroRNA Gene Ontology annotations

written 3 months ago by miRBase blog

You might have noticed some additional information on the mature miRNA pages in the last few weeks. See for example: http://mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000123 http://mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069 The new section “QuickGO function” contains a set of high quality manual annotations of Gene Ontology terms for mature miRNAs, the vast majority of which come from the work of Rachel Huntley et [...]

Gene Variant Image retirement for human, e93

written 3 months ago by Ensembl Blog

As of Ensembl release 93, which is due at the end of the month, the Gene Variant Image view will be retired for human. We have elected to retire this page because we feel that the density of known genetic variation is too great for this view to be informative in its current form. The […]
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