News archive 2015

December

15 Dec 2015

Ensembl Genomes 30 is out!

The latest release of Ensembl Genomes contains 30,586 genomes from 5,319 species! New features include image export and the latest cross-references to the Pathogen-Host Interaction Database. Read more
The gene view of RAT1 and its neighouring genes in F. graminearum
10 Dec 2015

Periodic table of protein complexes

'Periodic Table of Protein Complexes' makes it easier to visualise, understand and predict how proteins combine to drive biological processes. Read more
Periodic Table of Protein Complexes | EMBL-EBI
9 Dec 2015

UniProt 2015_12 release

UniProt 2015_12 release is out now with 55,820,795 UniProt proteins! This release, read headline article about SERINC3 and SERINC5 proteins reducing HIV-1 infectivity and the latest release news at http://www.uniprot.org/help/2015/12/09/release. Read more
9 Dec 2015

ENA Release 126

Release 126 of ENA's assembled/annotated sequences now available Read more
8 Dec 2015

Ensembl 83 is out!

Ensembl version 83 offers updated data and new features, including Human gene set GENCODE 24 and annotations available in RDF format. Read more
The Ensembl Genome Explorer
7 Dec 2015

Target Validation Platform launches

A web interface to help researchers find therapeutic targets for new and repurposed medicines has been launched by the Centre for Therapeutic Target Validation. Read more
The CTTV launches its new Target Validation Platform
3 Dec 2015

InterPro 55.0 and InterProScan 5.16-55.0 released

InterPro 55.0 integrates hundreds of new methods from the Pfam, SUPERFAMILY, PANTHER, CATH-Gene3D, HAMAP and ProDom databases. InterProScan 5.16-55.0 uses data from the newly released InterPro 55.0. Read more
InterPro: protein sequence analysis & classification

November

23 Nov 2015

Proposed improvements to the GWAS Catalog: REST API and genomic mapping

As part of our on-going efforts to improve the information available to users from the GWAS Catalog we are planning to make a few changes and would be very interested in hearing your feedback. Read more
NHGRI-EBI GWAS Catalog
12 Nov 2015

UniProt 2015_11 release

UniProt 2015_11 out now with 55,090,633 proteins! This release, read the headline about the visual sense of motion' and related updates to Sdk2 UniProtKB entries, UniProtKB news and more at http://www.uniprot.org/help/2015/11/11/release.     Read more
UniProt logo
9 Nov 2015

Unpacking embryonic pluripotency

Research from EMBL-EBI and the University of Cambridge shines a light on the pathways that give rise to pluripotent cells in rodents and primates. The findings have implications for reprogramming and in vitro fertilisation. Read more
Bertone and Smith: Unpacking embryonic pluripotency
2 Nov 2015

Change to Globus endpoint for public ENA data

The Globus endpoint for public ENA data is changing from ebi#ena to ebi#public ('ena' subfolder). Read more

October

30 Oct 2015

Allergy: the price of immunity?

A study by Nick Furnham et al. provides tools that will make it easier for scientists to predict proteins in food and the environment that are likely to cause allergy. Read more
Nick Furnham PLoS Comp Biol 2015
27 Oct 2015

Enzyme research made easier

The freely available Enzyme Portal helps researchers study enzymatic activity by making it easier to explore all enzyme-related information in EMBL-EBI’s public data resources. Read more
Enzyme Portal relaunched at EMBL-EBI
21 Oct 2015

Ensembl Genomes 29 is out!

Ensembl Genomes 29 features pairwise alignments for over 50 plant genomes, new protist and fungi genomes and much, much more. Read more
Ensembl Genomes 29 - explore nonvertebrate genomes
15 Oct 2015

New version of UniProtJAPI client released

We have been working on a new version of the UniProt JAPI and have now moved this from beta to production! The new JAPI client is downloadable via: http://www.ebi.ac.uk/uniprot/japi/index.html The old client will be able to access up to date UniProt data up to release 2015_12. After this, the old client moves into disposition phase, and will work on stale data until May of 2016, when it will be permanently shut down. It is therefore important that you update you programs to use the new client. Read more
15 Oct 2015

Reactome Pathway Browser: packed with new features

We are pleased to announce the release of the new Reactome pathway browser, which now provides faster, more reliable navigation of our content and better access to our analysis tools. There are lots of new features in this release, all of which are covered in a video at https://youtu.be/ogJn_pgEjHY Read more
Reactome pathway browser
14 Oct 2015

UniProt release 2015_10

UniProt release 2015_10  The latest UniProt release is out now with 53,333,247 proteins in the UniProt Knowledgebase! Read more
12 Oct 2015

Mini DNA sequencer tests true

The performance of the MinION™ miniature DNA sequencing device has been evaluated by an open, international consortium, and the resulting recommendations and protocols published before peer-review on the F1000Research platform. Read more
Oxford Nanopore’s MinION™ USB-attached miniature sensing device. [Photo: Oxford Nanopore Technologies]
6 Oct 2015

New releases: InterPro 54.0 and InterProScan 5.15-54.0

InterPro version 54.0 InterPro 54.0 integrates 2138 new methods from the CATH-Gene3D (2), Pfam (1319), SUPERFAMILY (5), ProDom (7) and PANTHER (805) databases. Read more
InterPro: protein sequence analysis & classification
1 Oct 2015

A snapshot of stem cell expression

Researchers on the Wellcome Genome Campus reveal new genes involved in stem cell pluripotency, new subpopulations of cells and new methods to find meaning in the data. Read more
A snapshot of stem cell expression [IMAGE: EMBL-EBI/Spencer Phillips]
1 Oct 2015

Finding links and missing genes

Missing a gene may be less problematic than you’d think. This is one of the conclusions that emerge from the most extensive catalogue of structural variations – changes in large sections of a person’s DNA sequence – to date. Read more
The 1000 Genomes Project tracked genetic variation across the globe. [Image: EMBL-EBI/Spencer Phillips]

September

29 Sep 2015

Ensembl version 82 release

Ensembl version 82 features a mobile website and updated phenotype data for several species, among many other improvements. Read more
Ensembl genome explorer
23 Sep 2015

ENA Release 125

Release 125 of ENA's assembled/annotated sequences now available Read more
22 Sep 2015

GWAS Catalog

The latest release of the GWAS Catalog features an updated Diagram Browser, additional ancestry information and a preview of a new genomic annotation download. Read more
GWAS Catalog
16 Sep 2015

Further tools retirements

To continue providing the most relevant and maintained tools at EMBL-EBI we periodically review and retire certain services. To that end we will be retiring the following tools in April 2016: FingerPRINTScan PROSITE Scan The debugging interface to InterProScan Please note InterProScan will continue to be available through Web Services and the InterPro website.  Read more
9 Sep 2015

Clearing a path for cancer research

EMBL-EBI researchers develop a new computational method to study biological signalling networks in healthy and cancer cells Read more
New method to study biological signalling networks
9 Sep 2015

Phenomenal: a gateway to personalised medicine

PhenoMeNal, an EU-funded project launched today and led by EMBL-EBI, is creating a secure, on-demand e-infrastructure for clinical metabolomics data. Read more
PhenoMeNal: a secure, on-demand e-infrastructure for clinical metabolomics data.
1 Sep 2015

Lanosterol and cataracts: ChEBI entity of the month

Lanosterol is a key intermediate in the biosynthesis of cholesterol, steroid hormones, and vitamin D. It may also offer a new way of treating cataracts, as ChEBI's 'entity of the month' explains. Read more
Human eye (Wikimedia Commons) with ChEBI structure 16521 - lanosterol

August

13 Aug 2015

European Variation Archive version 1.0

Version 1.0 of the European Variation Archive (EVA) includes new datasets for human, chicken, Aedes aegypti, sorghum, maize and five barley cultivars. It also offers new search tools and other features. Read more
European Variation Archive version 1.0
10 Aug 2015

Ensembl Genomes release 28

Read all about release 28 on the Ensembl blog: annotation, BioMart and software updates and new protein domains. Read more
Ensembl Genomes release 28. Image credit:

July

31 Jul 2015

Life is but a DREAM

Can we use computers to predict whether a compound will have a toxic effect on people? The DREAM challenge uses crowd sourcing to test the state of the art. Read more
DREAM challenge in systems biomedicine
16 Jul 2015

New releases: InterPro 53.0 and InterProScan 5.14-53.0

The latest version of InterProScan lets you scan sequences for matches against the InterPro database of protein families and motifs. The new release of InterPro offers over 27,500 entries, integrates 166 new methods from several databases, and predicts Gene Ontology (GO) terms for over 30 million UniProt proteins. Read more
InterPro: protein sequence analysis & classification
15 Jul 2015

Ensembl version 81 release

Ensembl version 81 has been released, offering updated data and new features. Read more
Ensembl genome explorer
6 Jul 2015

Reactome releases knowledgebase version 53

Reactome knowledgebase 53 features updates to signal transduction pathways, new immune system and disease pathways, revised topics and new pathway illustrations. Read more
1 Jul 2015

ENA release 124

Release 124 of ENA's assembled/annotated sequences now available Read more
1 Jul 2015

ChEBI's entity of the month: Butyl anthranilate

The latest ChEBI 'entity of the month' looks at the possibility of protecting crops using a naturally occurring fragrance molecule as an environmentally friendly insect repellent. Read more
Blueberries and the structure of butyl anthranilate

June

30 Jun 2015

Janet Thornton steps down

On 24 June 2015, EMBL-EBI staff gathered to celebrate Janet Thorton's 14 years as Director of the institute, as she prepares to hand over leadership to Rolf Apweiler and Ewan Birney on 1 July. Read more
Bioinformatics timeline cake, by Mr Cake!
24 Jun 2015

UniProt release 2015_07

UniProt release 2015_07 is out now. Get your 49,950,870 proteins today!  Read more
UniProt
20 Jun 2015

Sample Checklist Updates - June 2015

ENA are planning to update several sample metadata reporting checklists. Some of these changes have been carried out for harmonisation of attributes/fields between various checklist. Other changes were made to allow a standardised missing/null value reporting. All changes will come into effect as of 3rd August 2015. Read more
18 Jun 2015

Sarah Teichmann receives EMBO Gold Award

Wellcome Genome Campus research group leader Sarah Teichmann recognised for excellence in science Read more
Sarah Teichmann receives EMBO Gold Award
17 Jun 2015

Ensembl Genomes release 27 is out!

Read all about release 27 on the Ensembl blog. Read more
New fungi data in Ensembl Genomes 27
15 Jun 2015

Complex, large-scale genome analysis made easier

Researchers at EMBL-EBI speed up complex GWAS analyses with new method and algorithm Read more
mSet makes large-scale genome analysis made easier
15 Jun 2015

Lighting beacons for data access in genomic research

A new project launches to establish data-discovery services for genomics, balancing efficient data sharing and data protection. Read more
Beacon project: ELIXIR and the Global Alliance for Genomics and Health
4 Jun 2015

EMBL-EBI joins CERN openlab

CERN openlab welcomes EMBL-EBI as one of its first non-commercial partners, collaborating on future challenges in ICT. Read more
EMBL-EBI joins CERN openlab
3 Jun 2015

Changes to read data submission services 1st of October 2015

ENA will make a number of changes to submission services for raw sequence read data on first of October 2015. We continue to track an ever evolving landscape of available and preferred formats and introduce these changes with a view to overall simplification of the submission system to allow us to provide a more efficient service with faster turnaround. Read more
2 Jun 2015

ChEBI's entity of the month: Oleocanthal

The latest ChEBI 'entity of the month' looks at the remarkable properties of a compound found in extra-virgin olive oil Read more
Olive oil production and the structure of oleocanthal
1 Jun 2015

A powerful HMMER for data mining

HMMER, a fast, sensitive search tool, helps biologists find sequence relationships deep in evolutionary time. HMMER algorithms are now available through a dedicated website at EMBL-EBI. Read more
HMMER algorithm now available through EMBL-EBI

May

29 May 2015

PharmML: a flexible format for model exchange

PharmML, a flexible format for exchanging computational models in pharmaceutical R&D, opens new opportunities for drug discovery and clinical research. Read more
PharmML: a flexible format for model exchange
29 May 2015

UniProt 2015_06 release

UniProt release 2015_06 features updates relevant to POLQ and a Headline article about this potential new target for cancer therapy. The latest set of UniProt-GOA release files are also available. Read more
UniProt: The Universal Protein Resource
20 May 2015

Ensembl version 80 released

Ensembl version 80 has been released, offering updated data and new features. Read more
Ensembl: the genome explorer
20 May 2015

New releases: InterPro 52.0 and InterProScan 5.12-52.0

InterPro version 52.0 InterPro 52.0 integrates 280 new methods from the PANTHER (130), PROSITE patterns (1), PROSITE profiles (32), Pfam (4) and TIGRFAMs (113) databases, and covers 79.7% of UniProt Knowledgebase release 2015_06. It also predicts Gene Ontology (GO) terms for over 29 million UniProt proteins via the InterPro2GO pipeline. Read more
InterPro: protein sequence analysis & classification
20 May 2015

Tara Oceans: the data

Ready to explore the great unknown? 40 million previously undescribed genes and a raft of related sample data from the Tara Oceans expedition is freely available through EMBL-EBI. Read more
Tara Oceans: the data
16 May 2015

Are protein domains indivisible?

Protein domains are considered to be indivisible units – but new research shows that some can function even with big parts missing. Read more
Domain atrophy - Bateman and Prakash
11 May 2015

Teichmann and Birney elected AMS Fellows

The Academy of Medical Sciences has appointed Dr Sarah Teichmann and Dr Ewan Birney of EMBL-EBI as fellows. Read more
Ewan Birney and Sarah Teichmann elected Fellows of the Academy of Medical Sciences
1 May 2015

ChEBI's entity of the month: Neonicotinoid insectides

The latest ChEBI 'entity of the month' highlights the possible link between the use of neonicotinoid insecticides and the rapid decline in the bee population, known as colony collapse disorder. Read more
A close-up of a bee on a flower near Wembury, south-west England. Credit: Wikipedia Commons

April

30 Apr 2015

UniProt Release 2015_05

UniProt release 2015_05 is now out with over 48 million protein entries. Get your proteins today! Read headline article 'A never-ending race between evolution and genomic integrity' and the latest UniProtKB news at http://www.uniprot.org/help/2015/04/29/release. Read more
UniProt logo
30 Apr 2015

PDBe launches new website for structural biology

In their quest to make structural biology more accessible, the Protein Data Bank in Europe has launched a new, interactive website with a powerful search and sophisticated tools for analysis. Read more
PDBe’s new website for structural biology
21 Apr 2015

Clinical bioinformatics training: NHS report

NHS report sets a timeline for delivering bioinformatics training to support genomics in healthcare. Read more
Clinical bioinformatics training: NHS report
13 Apr 2015

Towards an expression atlas for an entire brain

New single-cell genomics techniques bring ‘omics to evolution-and-development research Read more
Nature Biotechnology, DOI: 10.1038/nbt.3209
9 Apr 2015

CORBEL: bridging research infrastructures

Major EU funding for ELIXIR will support efforts to facilitate access to data and biological imaging facilities for life-science research. Read more
CORBEL: facilitating access to research infrastructures
7 Apr 2015

GWAS Catalog moves to EMBL-EBI

The NHGRI-EBI GWAS Catalog has a new home at EMBL-EBI. Built on a new platform, the GWAS Catalog helps biologists explore the genomics of disease and human complexity. Read more
NHGRI-EBI GWAS Catalog moves to EMBL-EBI
2 Apr 2015

UniProt release 2015_04

 UniProt release 2015_04 is out. We've slimmed down to 47,262,724 proteins with reduced redundancy in Bacterial proteomes. The Unreviewed TrEMBL entries that were part of the redundant proteomes have been removed from the UniProt Knowledgebase but are still available in the UniParc sequence archive dataset within UniProt. From now on, we will no longer create new UniProtKB/TrEMBL records for proteomes identified as redundant. Read more
2 Apr 2015

Fireworks: Reactome's new Pathway Overview feature

The new Reactome Pathway Overview (codename: Fireworks) is a genome-wide, hierarchical visualisation of all Reactome pathways in a space-filling graph - and is integrated into the Reactome Pathway Browser. Fireworks represents pathways as nodes, and the size of the node reflects the number of entities (e.g. proteins, small molecules, genes) belonging to that pathway. The edges (lines) represent the connections between pathways in the Reactome pathway hierarchy. Read more
Fireworks: Reactome's new Pathway Overview feature

March

24 Mar 2015

Expression Atlas release

Expression Atlas release (Ensembl 79 / Ensembl Genomes 25) is out - read about new data and exciting features in Release Notes.  All Expression Atlas data is available for download on our ftp server.    This release contains 932 datasets, including: Read more
Expression Atlas
23 Mar 2015

ENA release 123

Release 123 of ENA's assembled/annotated sequences now available Read more
23 Mar 2015

New releases: InterPro 51.0 and InterProScan 5.11-51.0

InterPro version 51.0 InterPro 51.0 integrates 315 new methods from the GENE3D, HAMAP, PANTHER, PIRSF, Pfam, ProDom, SUPERFAMILY and TIGRFAMs databases, and covers 79.8% of UniProt Knowledgebase release 2015_04. It predicts Gene Ontology (GO) terms for over 28 million UniProt proteins via the InterPro2GO pipeline. Read more
InterPro: protein sequence analysis & classification
13 Mar 2015

UniProt release 2015_03

  UniProt 2015_03 is out now with 92,672,207 proteins! Read the headline article 'Regulation of translation initiation through folding' and more at http://www.uniprot.org/help/2015/03/04/release Read more
13 Mar 2015

Ensembl release 79

What's new in Ensembl 79? Human: genes updated to GENCODE 22, new assembly patches, and much more. Read more
Ensembl: the genome explorer
11 Mar 2015

Ewan Birney and Rolf Apweiler appointed Joint Directors of EMBL-EBI

Ewan Birney and Rolf Apweiler have been appointed Joint Directors of EMBL-EBI as of 1 July 2015, when Professor Dame Janet Thornton steps down after 14 years in post. Read more
Dr Rolf Apweiler (left) and Dr Ewan Birney (right) have been appointed Joint Directors of EMBL-EBI as Professor Dame Janet Thornton (centre) steps down after 14 years as Director.
8 Mar 2015

Supporting Women in Science Award 2015

John Overington of EMBL-EBI and Laura Huckins of the Wellcome Trust Sanger Institute receive the Wellcome Genome Campus Best Practice Award for Supporting Women in Science Award 2015. Read more
Laura Huckins, John Overington, Mike Stratton, Janet Thornton
2 Mar 2015

500,000 binary interactions... and growing

Building and visualising protein-interaction networks is easier and more accurate thanks to IntAct, a public database of 500,000 molecular interactions. Read more
Visualisation of all the human interactome data held in the IntAct database

February

27 Feb 2015

Upcoming tools retirements in 2015

To ensure the tools we offer at EMBL-EBI are up to date and well maintained, we periodically review and retire certain services. We will be retiring the following tools in August 2015; several of these have alternatives detailed below. Tools being retired in August 2015: Read more
Bioinformatics tools
27 Feb 2015

CTTV appoints Jeff Barrett as founding Director

Dr Jeffrey Barrett has been appointed as the founding Director of the Centre for Therapeutic Target Validation, a unique initiative between EMBL-EBI, GSK and the Wellcome Trust Sanger Institute. Read more
Dr Jeffrey Barrett, Director of CTTV
18 Feb 2015

Planned changes to ENA sequence search

Planned changes to ENA sequence search: ENA is changing to a new, BLAST-based, sequence search service. Read more
Planned changes to ENA sequence search
4 Feb 2015

UniProt 2015_02 released

 UniProt 2015_02 is out now! Get your 91,408,504 protein records today. In this release, read headline article 'Mosquitoes prefer humans' and more at http://www.uniprot.org/help/2015/02/04/release.  Read more
UniProt: The Universal Protein Resource
3 Feb 2015

New releases: InterPro 50.0 and InterProScan 5.10-50.0

InterPro version 50.0 InterPro 50.0 integrates 311 new methods from the PANTHER, PIRSF, Pfam and SUPERFAMILY databases, and covers 83.5% of UniProt Knowledgebase release 2015_02. It predicts Gene Ontology (GO) terms for over 57 million UniProt proteins via the InterPro2GO pipeline. We have also removed PfamB database, which only represented a subset of the automatically generated Pfam-B annotations and lacked any functional annotation. Read more
InterPro: protein sequence analysis & classification
3 Feb 2015

ChEMBL 20 takes the HELM

ChEMBL now incorporates the Hierarchical Editing Language for Macromolecules (HELM), the macromolecular representation standard recently released by the Pistoia Alliance. Read more
HELM in ChEMBL 20

January

20 Jan 2015

Why is a dolphin not a cat?

New research from EMBL-EBI shows how repurposing non-coding elements in the genome gave rise to the great ‘mammalian radiation’. Read more
Gene expression in 20 mammals
20 Jan 2015

Beyond COMPARE

The COMPARE project has received over €20 million from the EU to speed up the detection of and response to infectious disease outbreaks using pathogen genome sequencing and infection-control data. Read more
COMPARE project
19 Jan 2015

Hidden cell types revealed

New statistical method for RNA-seq analysis identifies and corrects for hidden structure between cells, creating order out of seeming chaos. Read more
Hidden cell types revealed
7 Jan 2015

UniProt release 2015_01

Happy New Year! UniProt's latest release 2015_01 is now available. This month's headline article focuses on Thalidomide research. Read more
UniProt: The Universal Protein Resource