News archive 2017

22 Nov 2017

UniProt release 2017_11

Release 2017_11 out with 99261416 proteins! Browse poteins through www.uniprot.org or download data programatically from our APIs.

InterPro logo

22 Nov 2017

New releases: InterPro 66.0 and InterProScan 5.27-66.0

InterPro database version 66.0 and InterProScan version 5.27-66.0 for functional analysis are now available. InterPro now covers over 81% of the UniProt Knowledgebase and predicts GO terms for over 58 million proteins.

Food security and bioinformatics: Illustration by Spencer Phillips, EMBL-EBI

21 Nov 2017

Food security and bioinformatics

EMBL-EBI supports data-driven research into plants, pathogens, pollinators and pests. What’s next?

Gametocytes of malaria-causing Plasmodium parasites

21 Nov 2017

How malaria parasites reproduce: new insights

Study into the reproduction of malaria parasites reveals faster and broader protein regulation than expected

Europe PMC annotations API provides programmatic access to annotations text-mined from biomedical abstracts and open-access, full-text articles in Europe PMC.

14 Nov 2017

New literature API: Europe PMC Annotations

Looking for text-mined annotations from biomedical literature? Try the new Europe PMC Annotations API.

10 Nov 2017

BioModels Model of the Month: Calmodulin

Computational model of calmodulin helps researchers investigate calcium signalling in the brain

Global Alliance for Genomics and Health logo

09 Nov 2017

Driving genomics: EMBL-EBI and GA4GH

EMBL-EBI is involved in three GA4GH Driver Projects, which are developing and testing the data standards needed to enable genomics in healthcare.

25 genomes logo and image of robin. Image credit: Wikimedia Commons and Sanger Institute, Genome Research Ltd.

07 Nov 2017

Public to vote in 25 Genomes Project

The story

  • EMBL-EBI is helping celebrate the 25th anniversary of its close collaborator, the Wellcome Trust Sanger Institute, by participating in the 25 Genomes Project.
  • The project will sequence the genomes of 25 UK resident species and make them available to the public through Ensembl
  • The Wellcome Trust Sanger Institutes invites members of the public, including school children to vote for the final five species in a competition organised with the "I'm a Scientist, Get Me Out of Here" programme
EMBL-EBI databases reimagined as cabinet of curiosities

07 Nov 2017

A smart cabinet of curiosities

How open data is changing our pursuit of discovery

Manual entitled PDX standards with albino mouse on cover

31 Oct 2017

FAIR mouse cancer models

Minimal information standard makes Patient-Derived Xenograft models easy to find, access, integrate and reuse

Open Access illustration by Spencer Phillips, EMBL-EBI

27 Oct 2017

Open access: transforming science

EMBL’s open access policy aims to make EMBL research widely and freely accessible. Its research ourputs are available for both reading and reuse, providing opportunities to enrich the scientific literature and transform the life and health sciences.

UniProt

25 Oct 2017

UniProt release 2017_10

Release 2017_10 has 93.8 million protein entries! New this release: changes to keywords and updates to our controlled vocabularies for Human Diseases and PTMs. Headline article: "Of Smell and Social Life," about new species annotations. 

Mouse and soundwave

12 Oct 2017

Novel hearing loss genes identified

Scientists link 52 genes to hearing loss in mice for first time; could lead to insights into deafness in humans

11 Oct 2017

Read data download issues resolved

Read data download issues previously affecting ftp.sra.ebi.ac.uk and fasp.sra.ebi.ac.uk services now resolved.

06 Oct 2017

ENA read data download issues

Issues with read data download from ftp.sra.ebi.ac.uk and fasp.sra.ebi.ac.uk

04 Oct 2017

ENA Release 133

Release 133 of ENA's assembled/annotated sequences now available

Image of whipworm. Credits: Wellcome Trust Sanger Institute

28 Sep 2017

UK pupils and scientists explore parasite problem

Summary

  • Challenge: The human whipworm infects approximately 500 million people globally, mainly children, but there is no vaccine against it.
  • Solution: Understanding the whipworm genome will help scientists develop vaccines and treatments effectively.
  • Event: UK school students will work alongside scientists on the Wellcome Genome Campus near Cambridge to produce the first fully annotated genome sequence for the human whipworm.
InterPro logo

26 Sep 2017

New releases: InterPro 65.0 and InterProScan 5.26-65.0

New releases: InterPro database (v. 65.0) and InterProScan (v. 5.26-65.0) for functional analysis. InterPro now covers over 80.7% of the UniProt Knowledgebase and predicts GO terms for over 53 million proteins.

Aerial shot of participants during 10 year anniversary Training Symposium

21 Sep 2017

Ten years of training at EMBL-EBI

International experts gather at EMBL-EBI to reflect on the future of bioinformatics training

14 Sep 2017

EMBL-EBI to be HTTPS by default from 1-October

On the 1st of October the majority of services hosted on www.ebi.ac.uk will be served over HTTPS by default. Services that are becoming HTTPS by default will automatically redirect users accessing the site on insecure HTTP URLs to secure HTTPS URLs.

Users of EMBL-EBI services may wish to update links, bookmarks or API clients to use the HTTPS URLs.

Ensembl logo

04 Sep 2017

Ensembl release 90 – Loads more genomes

Ensembl 90 is the biggest release yet of our genome explorer.

Artist's impression of the human bowel

01 Sep 2017

Bowel cancer study reveals impact of mutations on protein networks

Summary

  • In the UK alone, 110 people are diagnosed with bowel cancer every day
  • Scientists have completed a detailed study of many of the proteins in bowel cancer cell lines
  • The results could enable researchers to predict which drugs would be effective in treating bowel cancer
Artist's impression of metabolic models. Credit: Spencer Phillips, EMBL-EBI

22 Aug 2017

BioModels: New patient derived metabolic models

EMBL-EBI’s BioModels Database hosts 6753 new patient-derived genome-scale metabolic models

 

Map of Latin America and DNA data

22 Jul 2017

Bioinformatics in Latin America

CABANA will consolidate bioinformatics in Latin America, focussing on disease, food production and biodiversity

Icons representing data types in a biobank

20 Jul 2017

Biobanks: genetic data in demand

Enriched by successive studies and a growing amount of genetic data, biobanks are in higher demand than ever. Where are the bottlenecks?

Biological samples from a biobank. Stock image courtesy of the CRG.

19 Jul 2017

UK Biobank partners with the EGA

Genetic data from a major cohort is now distributed through the EGA, ensuring sustainable, secure delivery to approved biomedical researchers worldwide.

12 Jul 2017

Submission service maintenance - 14/7/17 to 17/7/17

Webin submission services will not be available between Friday 14/7/17 10:00 and Monday 17/7/17.  

During this time the capacity of the Webin upload area will be increased to support larger submission volumes.

 

The following services will be unavailable during the scheduled maintenance:

- FTP and Aspera Webin file uploads

- Interactive Webin submissions

- Programmatic Webin submissions

07 Jul 2017

Update to Aspera server

EBI has built a new Aspera server on up-dated hardware with the latest Aspera version and configuration. This should improve your experience in downloading data via Aspera, and also address some of the recent problems that have been linked to the use of an old Aspera server version. The current Aspera hostnames will be switched over to use the new server on the 1st August.

UniProt logo

06 Jul 2017

UniProt Release 2017_07

With release 2017_07, UniProt offers data on over 88.5 million proteins! Browse the updated data on the UniProt website, or access it programmatically using our Java API, Proteins REST API or SPARQL endpoint.

06 Jul 2017

ENA Release 132

Release 132 of ENA's assembled/annotated sequences now available

30 Jun 2017

Taxon support for sequence, WGS and assembly in ENA Browser Tools

You can now download sequence, WGS and assembly data by tax ID using ENA Browser Tools

InterPro logo

30 Jun 2017

New releases: InterPro 64.0 and InterProScan 5.25-64.0

New releases: InterPro database (v. 64.0) and InterProScan (v. 5.25-64.0) for functional analysis. InterPro now covers over 80.6% of the UniProt Knowledgebase and predicts GO terms for over 52 million proteins.

27 Jun 2017

Rfam 12.3 has been released

New Rfam release includes 101 new RNA families, new unified search and updated documentation.

Is the sex of research animals misdirecting medical research? Image: Spencer Phillips

26 Jun 2017

The sexual dimorphism dilemma

Is the sex of research animals misdirecting medical research?

Mouse genes could help decipher human disease. Image: Spencer Phillips

26 Jun 2017

Mouse genes could help decipher human disease

Characterising more than 3000 mouse genes reveals new gene functions and associations with human disease

23 Jun 2017

New tools to download data from ENA

Introducing two new tools to make retrieving data from ENA much easier: enaBrowserTools and ENA FTP Downloader.

ENA

21 Jun 2017

Guide to metagenomics data standards and best practice published

Our latest publication on data standards and best practices in metagenomics is available at https://t.co/PWjYHeWovk and includes a call for the archiving of analysis results data sets. More...

Revathi Nathaniel, UX expert at EMBL-EBI

15 Jun 2017

UX toolkit aids industry R&D

User Experience designers rarely specialise in the life sciences – EMBL-EBI and the Pistoia Alliance look to fill the gap

Image Data Resource samples

13 Jun 2017

Open imaging data for biology

The Image Data Resource: prototype of the first open, online repository linking imaging and molecular data 

Human Cell Atlas logo

01 Jun 2017

Human Cell Atlas data platform kicks off with support from CZI

EMBL-EBI, the Broad Institute and UCSC Genomics Institute will partner in developing a data coordination platform for the Human Cell Atlas, supported by CZI

Protein Data Bank in Europe logo

31 May 2017

SIFT-ing through sequence space in the PDB

The new, improved SIFTS service offers more targeted cross referencing. For example, it maps molecular structures in PDBe to the most appropriate isoform within a UniProt accession.

RNAcentral logo

16 May 2017

RNAcentral Release 7

RNAcentral release 7 overview

The latest version of the RNAcentral database is now available.

Omics DI search motif

15 May 2017

Omics Discovery Index boosts FAIR data sharing

A global index led by EMBL-EBI emerges as the ‘PubMed Central of life-science datasets’

HipSci stem cell bank

09 May 2017

HipSci: The human stem cell bank of tomorrow

UK’s largest resource of human stem cells from healthy donors unveiled

The European Variation Archive logo

09 May 2017

EVA issues long-term IDs for non-human variants

dbSNP and EVA to share responsibility for maintaining reliable, long-term accession numbers for genetic variation data

InterPro logo

09 May 2017

New releases: InterPro 63.0 and InterProScan 5.24-63.0

New releases: InterPro database (version 63.0) and InterProScan (5.24-63.0) for functional analysis. InterPro now covers over 80.5% of the UniProt Knowledgebase and predicts GO terms for over 50 million proteins.

27 Apr 2017

New ENA discovery API

ENA has launched a new API to support programmatic search across all data types: https://www.ebi.ac.uk/ena/portal/api

13 Apr 2017

A race against the ageing clock

Research identifies mouse epigenetic clock that accurately predicts age and could help scientists understand the ageing process 

Deep learning for epigenetics

11 Apr 2017

Genomics reboots deep learning

Deep learning is increasingly used to understand how genomes work: a new method from EMBL-EBI provides a perfect example

03 Apr 2017

ENA Release 131

Release 131 of ENA's assembled/annotated sequences now available

Double helix stock image

31 Mar 2017

A better way to find drug targets

The ChEMBL team at EMBL-EBI collaborated on a new way to identify drug targets from Genome Wide Association Studies

Executive Master's in research infrastructure management

30 Mar 2017

When science meets management

http://emmri.unimib.it/en/Executive Master’s of Management of Research Infrastructures offers new opportunities for leadership

Artist's interpretation of the study findings: older cells losing their ability to coordinate an attack

29 Mar 2017

Ageing: cell coordination breakdown

EMBL-EBI researchers use single-cell sequencing to understand how cells age

Abstract graphic for Global Life Science Data Resources Working Group.

28 Mar 2017

Life-science data: a global responsibility

A new coalition emerges to secure global data resources for the future of open science

InterPro logo

15 Mar 2017

New releases: InterPro 62.0 and InterProScan 5.23-62.0

New releases: InterPro database (version 62.0) and InterProScan (5.23-62.0) for functional analysis. InterPro now covers over 80% of the UniProt Knowledgebase and predicts GO terms for over 48 million proteins.

The UX team at EMBL-EBI

09 Mar 2017

UX design for the life sciences: myths and realities

Laying the groundwork for EMBL-EBI’s User Experience Design community

Helen Parkinson and Ele Zeggini, Best Practice Award 2017

07 Mar 2017

Driving gender equality in science

Wellcome Genome Campus announces 2017 gender equality champions

Artist interpretation of T-cell differentiation

03 Mar 2017

Watching immune cells fight malaria

Latest genomic technology uncovers secrets of immune cells’ response to malaria

UniProt logo

15 Feb 2017

UniProt release 2017_02: Freshwater fish see red

UniProt release 2017_02 offers over 78 million protein records! Access them through our website or programmatic end-points.

30 Jan 2017

Changes to the Trace Archive at ENA

We are making some changes to capillary sequencing trace data at ENA (known as the Trace Archive).  The archive is now available in full via FTP at ftp://ftp.ebi.ac.uk/pub/databases/ena/trace.  This is a  mirror of the FTP archive at NCBI and therefore has the same directory structure (based on organism and strain) and file formats. We will update our FTP archive for new and updated files on the first Sunday of every month.

Artist's interpretation of social genetic effects: mice with different sleeping preferences

24 Jan 2017

Genetic makeup of ‘room-mate’ influences health

EMBL-EBI research shows that healing and anxiety are influenced by the genetics of one’s social partners

InterPro logo

23 Jan 2017

New releases: InterPro 61.0 and InterProScan 5.22-61.0

InterPro version 61.0

InterPro 61.0 integrates of 4239 new methods from the CDD (286), Pfam (8), SUPERFAMILY (10), PANTHER (3835), CATH-Gene3D (22), SFLD (77) and ProDom (1) databases.

InterPro now covers 80.0% of UniProt Knowledgebase release 2017_01. It predicts Gene Ontology (GO) terms for over 44 million UniProt proteins via the InterPro2GO pipeline.

Animated gif of online AML calculator (tool for research)

16 Jan 2017

Cancer genetics refine treatment decisions

How a knowledge bank could be used to find the best treatment option for people with acute myeloid leukaemia (AML)

Drosophila embryo over sea of noncoding RNA

12 Jan 2017

Buffering mechanism protects embryonic development

EMBL scientists uncover buffering mechanisms that protect an embryo’s development from detrimental effects of genetic variation

Amelie Baud, EMBL-EBI researcher, marks her journey on a map.

09 Jan 2017

Science Is Global

In the relatively new field of bioinformatics, internationality is mission-critical

06 Jan 2017

FTP Service update

FTP service is now resuming normal operation.