News archive 2013

17 Dec 2013

ENA release 118

Release 118 of ENA's assembled/annotated seqences now available

ELIXIR consortium agreement

16 Dec 2013

ELIXIR launches as legal entity

Estonia is the fifth country to ratify the ELIXIR Consortium Agreement. This marks the formal launch of the infrastructure for biological data in Europe, supporting life science research and its translation to medicine, the bioindustries and society.
SureChEMBL

10 Dec 2013

Digital Science transfers SureChem patent chemistry data to EMBL-EBI

Transfer of complete patent chemistry collection - over 15 million compounds - set to advance drug discovery
Perturbation of the mutated EGFR interactome identifies vulnerabilities and resistance mechanisms

10 Dec 2013

IntAct Update: December 2013

Dataset of the month

Li, J., et al. (2013) Perturbation of the mutated EGFR interactome identifies vulnerabilities and resistance mechanisms.  Molecular Systems Biology.

Ensembl logo

04 Dec 2013

Ensembl version 74 release

Ensembl version 74 has been released, offering updated data and new features.
InterPro: protein sequence analysis & classification

15 Nov 2013

InterProScan 5.2-45.0 and InterPro 45.0 released

InterProScan 5 version 5.2-45

We are pleased to announce the release of InterProScan 5.2-45.0 (please find the full release notes here).

InterProScan 5.2-45.0 uses data from the newly released InterPro 45.0, which contains 25,326 entries and includes updates to PROSITE patterns (20.97), PROSITE profiles (20.97) and HAMAP (201310.09).

13 Nov 2013

UniProt release 2013_11

UniProt 2013_11 release is out now. Get your new protein records today! This release contains headline article 'Forever young and cancer-free… in a black hole' and the latest news about new changes to controlled volabularies and keywords. In the coming months, UniProt will extend the length of accession codes to 10 characters. Details at http://www.uniprot.org/docs/sp_soon.htm.
NEWHOUSE_Steven

11 Nov 2013

Steven Newhouse joins EMBL-EBI as Head of Technical Services

We are pleased to welcome Steven Newhouse, founding director of the European Grid Infrastructure, as our new Head of Technical Services.
IntAct: the open-source protein-interaction database

05 Nov 2013

IntAct Update: November 2013

Dataset of the Month

Dolan, P.T., et al. (2013) Identification and comparative analysis of hepatitis C virus-host cell protein interactions. Mol. BioSys. 9:3199-3209. DOI: 10.1039/c3mb70343f.

Data for this study were submitted directly to IntAct as part of the publication process, and can be searched using IMEx ID IM-21137 on the IntAct website and the IMEx Consortium pages.

Bertone et al. Nat Methods 2013

03 Nov 2013

Large-scale assessment of transcriptome analysis software

A systematic assessment of RNA-seq programs, published in Nature Methods, may inspire new computing approaches to handle current and future technologies for gene expression analysis.
BioLayout Express3D

31 Oct 2013

BioLayout Express 3D for visualising biological networks

Researchers at EMBL-EBI and the University of Edinburgh have released a new version of BioLayout Express3D, an open-source tool for visualising and analysing biological networks.

European Nucleotide Archive (ENA)

29 Oct 2013

First bulk CRAM submission to ENA

The first large-scale read data set in the CRAM compressed format has been submitted, undergone processing and been made public in the European Nucleotide Archive (ENA).

29 Oct 2013

First bulk CRAM submission to ENA

The first large-scale read data set in the CRAM compressed format has been submitted, undergone processing and been made public at ENA. Using CRAM in lossless mode, the submission represents a pre-publication data release from the Wellcome Trust Sanger Insitute and comprises around 4,000 run records covering a number of pathogen species. Data are available for download in both CRAM and FASTQ formats. The data set in CRAM format consumes 80% of the disk space or network bandwidth for download required for its gzipped FASTQ equivalent.

Janet Thornton and David Willetts

28 Oct 2013

Cambridge celebrates £75M investment in bioinformatics

Monday, 28 October: UK Minister for Universities and Science David Willetts joins key stakeholders in the Cambridge biotechnology cluster to celebrate the opening of EMBL-EBI's new building on the Genome Campus.

17 Oct 2013

UniProt release 2013_10

UniProt 2013_10 is out. Get your 45,288,084 protein records today! Read headline article 'When the cat's away...' and the latest news about new cross-references and more at http://www.uniprot.org/news/2013/10/16/release. UniProt has also announced that the cross-references to IPI will be removed from UniProtKB records by the begining of 2014 http://www.uniprot.org/docs/sp_soon.htm.

RDF for molecular biology

08 Oct 2013

Bioinformatics embraces Semantic Web technologies

EMBL-EBI's new Resource Description Framework (RDF) platform provides access to bioinformatics resources that support Semantic Web technologies.
Reactome knowledgebase of human biological pathways

02 Oct 2013

Reactome releases knowledgebase version 46

We are pleased to announce the third of this year's quarterly updates (v46) of the Reactome knowledgebase.

IntAct: the open-source protein-interaction database

30 Sep 2013

IntAct: October 2013 Update

Dataset of the Month

Blasche S, et al. (2013) The protein interaction network of bacteriophage lambda with its host, Escherichia coli J. Virology (in press).

Data from this study were submitted directly to IntAct as part of the publication process, and can be searched using IMEx ID IM-21394 on the IntAct website and the IMEx Consortium pages.

Reactome: A resource for molecular reactions

30 Sep 2013

Reactome launches new web interface

Reactome's new web interface for open-source, curated pathway and reaction data is a faster, more flexible tool to help researchers query, analyse and visualise molecular data.

InterPro: protein sequence analysis & classification

26 Sep 2013

InterProScan 5 and InterPro 44.0 released

InterProScan 5

We are delighted to announce the official release of InterProScan 5 (version 5-44.0). This latest version features a complete redesign of the InterProScan software that is highly flexible and allows robust protein functional analysis. To learn more about it, please visit our Introduction page: http://code.google.com/p/interproscan/wiki/Introduction.

Geuvadis RNA seq study

15 Sep 2013

Functional genetic variation in humans: comprehensive map published

GEUVADIS project presents the largest-ever dataset linking human genomes to gene activity at the level of RNA.

12 Sep 2013

ENA Release 117

About ENA Release 117

Release 117 of assembled/annotated sequences from the European Nucleotide Archive (ENA) is now available on the EBI public ftp server at ftp://ftp.ebi.ac.uk/pub/databases/embl/release/. It contains 324,201,244 sequences comprising 670,004,320,378 nucleotides. You can read the full release notes here.

12 Sep 2013

ENA release 117

Release 117 of assembled/annotated sequences from the European Nucleotide Archive (ENA) is now available on the EBI public ftp server at ftp://ftp.ebi.ac.uk/pub/databases/embl/release/.
It contains 324,201,244 sequences comprising 670,004,320,378 nucleotides. You can see the full release notes at: http://bit.ly/LKFtrE.

Ensembl logo

04 Sep 2013

Ensembl version 73 release

Ensembl version 73 has been released, offering updated data and new features.

The new Ensembl release 73 includes:

News image (EMBL-EBI)

04 Sep 2013

It's not just noise

EMBL scientists discern key gene expression patterns in the human genome
The IntAct molecular interaction database

29 Aug 2013

IntAct: September 2013 Update

Database News

Wikipedia

08 Aug 2013

ISCB Wikipedia Competition

The International Society for Computational Biology (ISCB) announces an international competition to improve the coverage on Wikipedia of any aspect of computational biology.

Mice on a path

05 Aug 2013

Wired for change

A new study of gene expression reveals the first steps of evolution in gene regulation in mice. Published in the journal Cell, the research has implications for the study of differences in gene regulation between people.
Reese-Hoyes 2013

01 Aug 2013

IntAct: August 2013 Update

Database News

The 2014 course on Networks and Pathways Bioinformatics for Biologists at EMBL-EBI, supported by the PSIMEx project (funded under the Health Theme of the EU's Seventh Framework Programme), by took place at EMBL-EBI with 39 students learning how to analyse their large-scale datasets using a variety of methods.

25 Jul 2013

New in InterPro: release 43.1

We are pleased to announce the release of InterPro 43.1. This release fixes the problem with the protein match data in InterPro release 43.0.  It includes an update to Pfam (27.0)  and 805 new methods from the GENE3D, PANTHER, Pfam, ProDom and SUPERFAMILY databases. Protein families covered by the new entries include a number of growth factors and their corresponding receptors, and families involved in actin cytoskeleton organisation.

SurvCurv: the survival database at EMBL-EBI

23 Jul 2013

Exploring survival

EMBL-EBI researchers have created a new resource that can help scientists study ageing. Published in the journal Aging Cell, SurvCurv is the first comprehensive, open resource to enable the large-scale analysis of survival data in model organisms.
GWAS catalog

16 Jul 2013

Webinar on the GWAS Catalog

On Thursday, 18 July, the NHGRI's Division of Genomic Medicine will present Current uses of and future directions for the GWAS Catalog, a webinar highlighting current uses and exploring future directions for the GWAS catalog. The webinar will examine how the catalogue's use by biomedical researchers is informing projects such as ENCODE, mouse phenotyping projects and regulatory genomics. GWAS catalog personnel will identify goals and directions for their work.

ISMB/ECCB 2013

10 Jul 2013

EMBL-EBI staff at ISMB/ECCB 2013, Berlin

Friday, 19 July 2013

Paul Flicek, SNP-SIG. Highlight presentation: Using comparative genomics to restrict the search space of regulatory variants causing rare disease. 1.05-1.55pm, room TBC

Marco Punta, 3DSIG. Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions.

02 Jul 2013

Change to EMBL-Bank flat file AC lines

Use of AC lines to denote 'WGS/TSA set membership' in addition to 'record replacement' has been a frequent cause of confusion among our users. To solve this we have moved WGS/TSA master accession numbers from AC lines to DR lines. 

27 Jun 2013

UniProt 2013_07 release

'How to go green, or red?', read the headline article this release and the latest UniProtKB news about changes to the controlled vocabulary of human diseases at http://www.uniprot.org/news/2013/06/26/release.

27 Jun 2013

ENA release 116

Release 116 of assembled/annotated sequences from the European Nucleotide Archive (ENA) is now available on the EBI public ftp server at ftp://ftp.ebi.ac.uk/pub/databases/embl/release/.
It contains 309,513,621 sequences comprising 616,248,681,624 nucleotides. You can see the full release notes at: http://bit.ly/LKFtrE.

The European Nucleotide Archive

27 Jun 2013

ENA Release 116

About ENA Release 116

Release 116 of assembled/annotated sequences from the European Nucleotide Archive (ENA) is now available on the EBI public ftp server at ftp://ftp.ebi.ac.uk/pub/databases/embl/release/. It contains 309,513,621 sequences comprising 616,248,681,624 nucleotides. You can read the full release notes at http://bit.ly/LKFtrE 

IntAct July 2013

26 Jun 2013

IntAct: July 2013 Update

Database News

Apologies for the temporary loss of our Twitter Feed onto the webpage – this was due to changes made by Twitter which has caused us some problems. We have now rectifed this but remember you can sign up to follow us and receive updates directly.

Release News

There have been 3 releases in June (R165-167). The IntAct database now contains 6520 publications, 18,909 experiments and 331,895 binary interactions.

Reactome - name badge

21 Jun 2013

The Naming of Things

The systematic renaming process

Reactome, the pathway database, often needs to represent a protein in several different forms, perhaps the initial translated form and fragments of this following processing, or after many different kinds of post-translational modification. In response to this need, we have developed a systematic nomenclature for the names of peptides.

Reactome

21 Jun 2013

Reactome release 45

Reactome release 45 offers a number of new topics and updates to existing pathways.

Ensembl logo

20 Jun 2013

Ensembl version 72 release

The new Ensembl release 72 includes:

Expression Atlas

20 Jun 2013

Expression Atlas Linked Data

Our Functional Genomics Production Team is pleased to announce the beta publication of gene expression data from the Gene Expression Atlas as RDF Linked Open Data. Linked Data is an emerging standard and best practice for exposing, sharing and connecting data on the Web. Exposing the Gene Expression Atlas data as RDF provides novel ways to both query and explore this dataset.

BioModels Database

19 Jun 2013

BioModels announces Release 25

We are pleased to announce the twenty-fifth release of our BioModels Database! This public resource now offers 143,013 computational models of biological processes, comprising 142,050 from the Path2Models project and 963 published in the literature.

13 Jun 2013

CRAM 2.0 launch

CRAM 2.0 release is now available.

IntAct: the open-source protein-interaction database

10 Jun 2013

IntAct release 165 highlight: the SH3 interactome

With release 165, IntAct now offers 314,019 binary interactions from 6485 manually curated publications.

IntAct, the open-source protein interaction database, derives its entries from literature curation or direct user submissions. The data are freely available, and you can find the latest release on the FTP site: ftp://ftp.ebi.ac.uk/pub/databases/intact/current/

Global Alliance

05 Jun 2013

A Global Alliance for sharing genomic and clinical data

EMBL and EMBL-EBI have joined the Global Alliance, a large-scale, international effort to enable the secure sharing of genomic and clinical data.
InterPro: protein sequence analysis & classification

05 Jun 2013

New in InterPro: release 43.0

We are pleased to announce the release of InterPro 43.0. InterPro now contains 24,737 entries and includes an update to Pfam (27.0).

InterPro 43.0 integrates 185 new methods from the GENE3D, PANTHER and Pfam databases, and covers 80.8% of UniProt Knowledgebase release 2013_06. It predicts Gene Ontology (GO) terms for over 22 million UniProt proteins via the InterPro2GO pipeline.

29 May 2013

UniProt 2013_06 release

In this release, read headline article 'Back to the wild' about Human THAP9 gene and the latest UniProtKB news about changes to cross-references and controlled vocabolaries at http://www.uniprot.org/news/2013/05/29/release.

Green sea turtle. Photo courtesy of RIKEN

16 May 2013

Where do turtles 'fit'?

Where do turtles fit in the evolutionary tree? Are they reptiles? How did their backbone evolve to form a shell?

Single-cell genomics - image by Thierry Voet, Wellcome Trust Sanger Institute

07 May 2013

The Single Cell Genomics Centre

EMBL-EBI and the Wellcome Trust Sanger Institute are launching the Single Cell Genomics Centre (SCGC), which seeks to answer key biological questions by exploring cellular genetics at the highest resolution possible. The centre will focus on the exploration of cell function in normal development and immune function as well as cancer.

IntAct: the open-source protein-interaction database

03 May 2013

IntAct Release 164b

With release 164b, IntAct now contains 312 133 binary interactions from 6413 manually curated publications. IntAct, the open-source protein interaction database, derives its entries from literature curation or direct user submissions. The data are freely available, and you can find the latest release on the FTP site: ftp://ftp.ebi.ac.uk/pub/databases/intact/current/

02 May 2013

UniProt 2013_05 release

The headline article this release looks at human genetic diseases in UniProtKB/Swiss-Prot. Latest news from UniProtKB: complete proteomes added for Ensembl species, removal of the cross reference to GenomeReviews and changes to keywords. Find out more at http://www.uniprot.org/news/2013/05/01/release

 

 
Children marveling at mutants of Medaka and Zebrafish

18 Apr 2013

How is a fish like a person?

Zebrafish provide valuable insights into human development and disease, and a new study promises to make this research still more effective. An international team of researchers, writing in the journal Nature, has shown exactly how our genes line up with those of this amazing fish.

InterPro: protein sequence analysis & classification

17 Apr 2013

InterPro 42.0 released

We are pleased to announce the release of InterPro 42.0 (4th April, 2013), which contains 24,622 entries and includes an update to TIGRFAMs (13.0) and HAMAP (201302.26). InterPro 42.0 integrates 439 new methods from the GENE3D, HAMAP, PANTHER, PIRSF, Pfam, SUPERFAMILY and TIGRFAMs databases, and covers 81.2% of UniProt Knowledgebase release 2013_03. It predicts GO terms for over 20 million UniProt proteins via the InterPro2GO pipeline. The new release features updates to UniParc and UniMES matches to InterPro methods.

Protein assembly - Teichmann et al.

11 Apr 2013

Perfect proteins preferred

Researchers at the EMBL-European Bioinformatics Institute (EMBL-EBI), the Medical Research Council (MRC) and the University of Oxford in the UK have shown that the specific order in which proteins assemble into complexes is extremely important to how they function. Their findings, published in the journal Cell, shed light on an important question in evolution.

European Nucleotide Archive

28 Mar 2013

CRAM 2.0: pre-launch of compression format and toolkit

Today sees the pre-launch of CRAM 2.0. Over the next two months, users can test the new version before its full launch on 1 June 2013.

IntAct

28 Mar 2013

New IntAct release

IntAct, EMBL-EBI's open-source protein interaction database, derives its entries from literature curation and direct user submissions. The data are freely available, and represent 309,567 binary interactions from 6,375 manually curated publications.

You can find the latest release on the IntAct FTP site: ftp://ftp.ebi.ac.uk/pub/databases/intact/current/

26 Mar 2013

CRAM 2.0 pre-launch

CRAM 2.0 release candidate made available and two month review period announced.

20 Mar 2013

New to Reactome: Binding and uptake of ligands by scavenger receptors

The latest news from Reactome: Plant Reactome launches and the Reactome service offers new topics and illustrations.
ChEBI entity: (–)-epigallocatechin 3-gallate (EMBL-EBI)

04 Mar 2013

ChEBI release 101 is now available, with 31651 fully annotated entities

Read about (–)-epigallocatechin 3-gallate (EGCG, CHEBI:4806), a chemical entity relevant to the study of Alzheimer's disease, on the ChEBI website: http://www.ebi.ac.uk/chebi/entityMonthForward.do

Mapping metabolism (EMBL-EBI)

03 Mar 2013

Mapping metabolism

A comprehensive map of human metabolism has been produced by a large consortium including researchers from EMBL-EBI. Published in Nature Biotechnology, the model is freely available through EMBL-EBI’s BioModels Database. It contains verified information on thousands of metabolites and reactions and represents a goldmine for systems biologists.

Sketchnotes by Francis Rowland

03 Mar 2013

Something different

We’ve changed things a bit! On 4 March we re-launched the EMBL-EBI website, hoping to give all our visitors a warmer welcome. We’ve been working behind the scenes to give you a more consistent experience, because a big part of our mission is to make molecular data available – and accessible – to everyone.

13 Feb 2013

Changes to EMBL-CDS FTP products

The introduction of ENA Advanced Search and other recent service improvements have made a number of EMBL-CDS FTP products redundant. Any remaining users are asked to contact datasubs@ebi.ac.uk.

06 Feb 2013

The mutation police

How does our genome keep mutations in check? Reporting in the journal Cell, researchers at EMBL-EBI and the MRC show how a protein called hnRNP C suppresses pseudoexons. The finding helps in the study of diseases such as cancer and neurodegeneration, and provides insights into human evolution.

06 Feb 2013

UniProt News: The smoke's devils

Get your 30,309,136 protein records today! The latest UniProtKB news and the headline article, "The smoke's devils," is inspired by the fact that most enzymes involved in theTHC/CBD biosynthetic pathway have been identified and manually annotated in UniProtKB/Swiss-Prot

 

06 Feb 2013

Gene Ontology Annotation (UniProt-GOA) database updated

We are pleased to announce that this release of UniProt-GOA gene association files includes manual annotations for archaeal and bacterial species that have been created by the Microbial ENergy processes Gene Ontology Project (MENGO). 

Full details of our latest release are on the UniProt-GOA website.

06 Feb 2013

SwissProt and TrEMBL Protein database release

UniProtKB/SwissProt Release contains 539,165 sequence entries http://bit.ly/x5e04a
UniProtKB/TrEMBL Release contains 29,769,971 sequence entries. This represents an increase of 2%... http://bit.ly/zmCDxW

Niklas Blomberg, ELIXIR Director

05 Feb 2013

ELIXIR appoints founding director

The Interim ELIXIR Board is delighted to announce the appointment of Dr Niklas Blomberg of AstraZeneca R&D Mölndal, Sweden to the newly created post of ELIXIR Director.

04 Feb 2013

ChEBI release 100 is now available, with 31,222 fully annotated entities

We are delighted to announce that we have introduced new interactive statistic graphs and also to commemorate this 100th release we have displayed the growth of ChEBI from release 1 - 100 with the number of compounds for each release. See our entity of the month, caffeine http://www.ebi.ac.uk/chebi/entityMonthForward.do

01 Feb 2013

IntAct release 161 now contains 305,888 binary interactions from 6177 manually curated publications

IntAct, the open-source protein interaction database, derives its entries from literature curation or direct user submissions. The data are freely available, and you can find the latest release on the FTP site: ftp://ftp.ebi.ac.uk/pub/databases/intact/current/.

Nick Goldman (EMBL-EBI)

23 Jan 2013

Data storage in DNA becomes a reality

Researchers at the EMBL-European Bioinformatics Institute (EMBL-EBI) have created a way to store data in the form of DNA – a material that lasts for tens of thousands of years. The new method, published in the journal Nature, makes it possible to store at least 100 million hours of high-definition video in about a cup of DNA.

17 Jan 2013

The latest Ensembl update (e!67) has just gone live

New web features. Updated patches for the Human assembly. Reanalysed Human BodyMap data...http://www.ensembl.info/blog/2013/01/17/ensembl-70-has-been-released/

13 Jan 2013

UniProt 2013_01 is out

Get your 29,805,788 protein records today! In this release, read headline article on 'Hereditary sensory and autonomic neuropathy type IA' and news about UniRef at http://bit.ly/V8JNGv

09 Jan 2013

Gene Ontology Annotation (UniProt-GOA) Database updated

Read the release details at http://bit.ly/1p8M6q.

09 Jan 2013

SwissProt and TrEMBL Protein database release

UniProtKB/SwissProt Release contains 538,849 sequence entries http://bit.ly/x5e04a
UniProtKB/TrEMBL Release contains 29,266,939 sequence entries. This represents an increase of 3%... http://bit.ly/zmCDxW

07 Jan 2013

ChEBI release 99 is now available, with 30,797 fully annotated entities

See our entity of the month, Acrylamide http://www.ebi.ac.uk/chebi/entityMonthForward.do