http://www.ebi.ac.uk/Information/News/news.html EBI News feed en-gb Tue, 7 Feb 2012 12:08:28 +0000 http://www.ebi.ac.uk/Information/images/newsfeed.jpg http://www.ebi.ac.uk/Information/News/news.html http://www.ebi.ac.uk/Information/News/database_releases.html#dat_0102 In this release, 68 new models have been published and numerous models updated - http://bit.ly/w9RsDu BioModels Database now publicly provides 409 models in the curated and 420 in the non-curated branch. Together, these 829 models comprise 130800 species, 151274 relationships (which include reactions, rate rules, events and assignment rules), and 106210 cross-references. Important changes are happening or announced, so please read the release notes: http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=release_20120208 Wed, 08 Feb 2012 19:33:21 +0000 http://www.ebi.ac.uk/Information/News/database_releases.html#dat_0102 http://www.ebi.ac.uk/Information/News/database_releases.html#dat_0101 Our new release offers 27,184 fully annotated entities and 2 term changes - http://bit.ly/z5Z4Pc As part of our efforts to align ChEBI with the Gene Ontology, two ontological terms have changed: 'carbohydrate' and 'carbohydrate derivative'. Now, the term 'carbohydrate' is restricted to sugars (aldoses, ketoses etc.) that are composed solely of the elements C, H and O. The term 'carbohydrate derivative' encompasses amino sugars (thiosugars, phosphosugars, acylated sugars, glycosides, etc.). We would also like to announce that protein entities within ChEBI will be removed by June 2012. Learn more about (+)-artemisinin here: http://www.ebi.ac.uk/chebi/entityMonthForward.do Tue, 7 Feb 2012 12:08:28 +0000 http://www.ebi.ac.uk/Information/News/database_releases.html#dat_0101 http://www.ebi.ac.uk/Information/News/press_releases.html#pre_0019 Genetic switches called enhancers and the molecules that activate them can be used to draw a cell's family tree, EMBL scientists have found. Fri, 3 Feb 2012 10:10:05 +0000 http://www.ebi.ac.uk/Information/News/press_releases.html#pre_0019 http://www.ebi.ac.uk/Information/News/press_releases.html#pre_0018 In a high-powered study of several genome-wide association studies, a consortium including members of EMBL-EBI's Reactome and IntAct teams have shed light on novel gene functions that control fate- determining events during the formation of blood platelets and their progenitor cells. Thu, 2 Feb 2012 10:02:30 +0000 http://www.ebi.ac.uk/Information/News/press_releases.html#pre_0018 http://www.ebi.ac.uk/Information/News/database_releases.html#dat_0100 Get your 19,968,487 fresh protein records today! New this release: "What's in a species name?" and Clustal Omega replaces Clustal W as UniProt's alignment program. Follow this link to find out more http://bit.ly/y5QeLp. Thu, 26 Jan 2012 14:28:32 +0000 http://www.ebi.ac.uk/Information/News/database_releases.html#dat_0100 http://www.ebi.ac.uk/Information/News/press_releases.html#pre_0017 A team of geneticists and computational biologists in the UK today reveal how an ancient mechanism is involved in gene control and continues to drive genome evolution. The new study is published in the journal Cell. Thu, 12 Jan 2012 17:00:00 +0000 http://www.ebi.ac.uk/Information/News/press_releases.html#pre_0017 http://www.ebi.ac.uk/Information/News/database_releases.html#dat_0099 UniProt-GOA has vastly improved the HAMAP2GO annotation set. The HAMAP source predicts 3,458,519 GO annotations and the HAMAP2GO pipeline can now use the full complexity of manually curated UniProtKB HAMAP rules. Tue, 10 Jan 2012 14:28:32 +0000 http://www.ebi.ac.uk/Information/News/database_releases.html#dat_0099 http://www.ebi.ac.uk/Information/News/press_releases.html#pre_0016 Researchers from EMBL-EBI, the University of Oxford and The Genome Analysis Centre in the UK have developed a new way to analyse genetic variants. In a paper published in Nature Genetics, the team introduces Cortex, the first de novo assembly software capable of assembling multiple eukaryotic genomes simultaneously. Tue, 10 Jan 2012 16:12:15 +0000 http://www.ebi.ac.uk/Information/News/press_releases.html#pre_0016 http://www.ebi.ac.uk/Information/News/press_releases.html#pre_0015 Together with Rothamsted Research, we bring you PhytoPath: a new resource that integrates genome-scale plant pathogen with literature-curated information about the phenotypes of host infection. Tue, 10 Jan 2012 11:17:23 +0000 http://www.ebi.ac.uk/Information/News/press_releases.html#pre_0015 http://www.ebi.ac.uk/Information/News/database_releases.html#dat_0098 IntAct release 150 has a whopping 290,659 binary interactions from 5,226 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. Tue, 10 Jan 2012 09:57:31 +0000 http://www.ebi.ac.uk/Information/News/database_releases.html#dat_0098 http://www.ebi.ac.uk/Information/News/database_releases.html#dat_0097 ChEBI release 87 is now available, with 26,848 fully annotated three star level. See our entity of the month, Mercury. Mon, 9 Jan 2012 16:32:38 +0000 http://www.ebi.ac.uk/Information/News/database_releases.html#dat_0097 http://www.ebi.ac.uk/Information/News/press/2011.html#pre_0014 EMBL-EBI is developing new resources for cereal researchers and plant breeders, using the Ensembl Genomes platform. Read about it on the BBSRC website Wed, 21 Dec 2011 10:02:57 http://www.ebi.ac.uk/Information/News/press/2011.html#pre_0014 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0096 EMBL-Bank was frozen to make Release 110 on 1-DEC-2011. The release contains 230,021,806 sequence entries comprising 376,471,768,435 nucleotides ...more Mon, 19 Dec 2011 15:15:12 +0000 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0096 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0095 The Ensembl Genomes Project is pleased to announce release 12 of Ensembl Genomes. This release contains 5 new genomes, bringing the total genomes supported to 335. Main highlights are: * Software migration to Ensembl 65 * Operon data from RegulonDB for E. coli K12 in Ensembl Bacteria * A new species (Ashbya gossypii) and manually curated annotation from a new resource for yeast! This is the first release of Ensembl Fungi containing data from PomBase, a new genome-centric resource (developed by Ensembl Genomes, the University of Cambridge, and University College London) for the fission yeast Schizosaccharomyces pombe. * The addition of Cyanidioschyzon merolae to Ensembl Plants and significant updates to Physcomitrella patens and the soybean Glycine max * Three new genomes in Ensembl Metazoa: Atta cephalotes, a leaf-cutting ant, Tribolium castaneum, the red flour beetle, and Bombyx mori, a domesticated silkmoth Note, EG 12 will be available on ftp next week. Happy holidays! The Ensembl Genomes Team Fri, 16 Dec 2011 14:48:59 +0000 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0095 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0094 We are pleased to announce the release of InterPro 35.0, which contains 22,361 entries and includes updates to PIRSF (2.77), HAMAP (140911) and SMART (6.2), and the integration of 322 new methods from the GENE3D, HAMAP, PANTHER, PIRSF, Pfam, SMART and SUPERFAMILY databases. The release covers 79.7% of UniProt Knowledgebase release 2011_12. UniParc (uniparc_match.tar.gz) and UniMES (unimes_match.tar.gz) matches to InterPro methods have been updated and are available from the ftp site. Fri, 16 Dec 2011 09:53:37 +0000 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0094 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0093 Existing disease-related topics HIV, Influenza, Botulinum neurotoxicity, Amyloids and Diabetes have been reorganized and two new ones, Signaling by EGFR in Cancer and ISG15 antiviral mechanism, added. New or updated events include, Prolactin receptor, Defensins, Interleukin-7 signaling, Sulfur amino acid and Sphingolipid metabolism, Mucin O-linked glycosylation, Serine biosynthesis, Signaling by ERBB2 and ERBB4, and Gene expression. Thu, 15 Dec 2011 17:09:14 +0000 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0093 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0092 UniProtKB/SwissProt Release of 14-December-2011 contains 533657 sequence entries. ... more. UniProtKB/TrEMBL Release of 14-December-2011 contains 18510272 sequence entries. This represents an increase of 4%... more. Wed, 14 Dec 2011 15:27:35 GMT http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0092 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0091 The new release of UniProtKB-GOA contains UniProt GO v103, UniProtKB-GOA Human v105, UniProtKB-GOA Mouse v91, UniProtKB-GOA Rat v91, UniProtKB-GOA Arabidopsis v78, UniProtKB-GOA Zebrafish v78, UniProtKB-GOA Chicken v75, UniProtKB-GOA Cow v68, UniProtKB-GOA Dicty v6, UniProtKB-GOA Dog v6, UniProtKB-GOA Pig v6, UniProtKB-GOA Fly v6, UniProtKB-GOA Worm v6, UniProtKB-GOA Yeast v6, UniProtKB-GOA PDB v92 and UniProtKB-GOA Proteome Sets 80... more Tue, 13 Dec 2011 15:14:47 +0000 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0091 http://www.ebi.ac.uk/Information/News/press/2011.html#dat_0090 The EBI will introduce important changes regarding access to the existing alternative splicing resources. This concerns the Alternative Splicing Database (ASD), the Alternative Transcript Diversity Database (ATD), the Alternative Exon database (AEdb) and the Alternative Splicing and Transcript Diversity Database (ASTD). These resources will be phased out beginning of 2012... more Tue, 6 Dec 2011 10:28:41 +0000 http://www.ebi.ac.uk/Information/News/press/2011.html#dat_0090 http://www.ebi.ac.uk/Information/News/press/2011.html#pre_0013 The European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) and the Biotechnology and Biological Sciences Research Council (BBSRC) warmly welcome today's announcement from the UK Government of a GBP 75 million commitment from the Department for Business, Innovation and Skills' Large Facilities Capital Fund (LFCF) for the ELIXIR research infrastructure. Mon, 05 Dec 2011 16:14:10 +0000 http://www.ebi.ac.uk/Information/News/press/2011.html#pre_0013 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0089 ChEBI release 86 is now available, with 26,724 fully annotated three star level. See our entity of the month, Pyrrolidin-2-one. Mon, 5 Dec 2011 15:49:22 +0000 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0089 http://www.ebi.ac.uk/Information/News/press/2011.html#pre_0012 PomBase adapts the Ensembl platform to provide a valuable resource for fission yeast researchers. PomBase is a collaboration between EMBL-EBI, the University of Cambridge and University College London. Tue, 29 Nov 2011 16:16:27 +0000 http://www.ebi.ac.uk/Information/News/press/2011.html#pre_0012 http://www.ebi.ac.uk/Information/News/press/2011.html#pre_0011 The European Molecular Biology Laboratory (EMBL) is pleased to announce that Rolf Apweiler and Ewan Birney will succeed Graham Cameron as Associate Directors of the EMBL-European Bioinformatics Institute (EMBL-EBI) in 2012. Graham, a founding member of EMBL-EBI, has announced that he will retire after 30 years of working at EMBL. Mon, 28 Nov 2011 14:12:40 +0000 http://www.ebi.ac.uk/Information/News/press/2011.html#pre_0011 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0088 IntAct contains 290057 binary interactions from 5162 manually curated publications. All data is also available on the public FTP site. Mon, 21 Nov 2011 15:10:36 +0000 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0088 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0087 UniProtKB/SwissProt Release of 16-November-2011 contains 533049 sequence entries. ... more. UniProtKB/TrEMBL Release of 16-November-2011 contains 18215214 sequence entries. This represents an increase of 4%... more. Wed, 16 Nov 2011 14:54:17 GMT http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0087 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0086 The new release of UniProtKB-GOA contains UniProt GO v102, UniProtKB-GOA Human v104, UniProtKB-GOA Mouse v90, UniProtKB-GOA Rat v90, UniProtKB-GOA Arabidopsis v77, UniProtKB-GOA Zebrafish v77, UniProtKB-GOA Chicken v74, UniProtKB-GOA Cow v67, UniProtKB-GOA Dicty v5, UniProtKB-GOA Dog v5, UniProtKB-GOA Pig v5, UniProtKB-GOA Fly v5, UniProtKB-GOA Worm v5, UniProtKB-GOA Yeast v5, UniProtKB-GOA PDB v91 and UniProtKB-GOA Proteome Sets 79... more Tue, 15 Nov 2011 14:30:00 +0100 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0086 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0085 ChEBI release 85 is now available, with 26,556 fully annotated three star level. See our entity of the month, Acetylsalicylic acid. Tue, 8 Nov 2011 16:39:40 +0000 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0085 http://www.ebi.ac.uk/Information/News/press/2011.html#pre_0010 Intensive benchmark testing of a new alignment tool, Clustal Omega, was published recently in the journal Molecular Systems Biology. Clustal Omega has the capacity to align virtually any number of protein sequences both quickly and accurately... Tue, 01 Nov 2011 12:00:00 +0100 http://www.ebi.ac.uk/Information/News/press/2011.html#pre_0010 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0084 Release 67.01 of the RESID Database of Protein Modifications is available by ftp at the EBI or at the NCIFCRF ...more Fri, 28 Oct 2011 14:51:12 +0100 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0084 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0083 UniProtKB/SwissProt Release of 19-October-2011 contains 532792 sequence entries. ... more UniProtKB/TrEMBL Release of 19-October-2011 contains 17651716 sequence entries. This represents an increase of 5%... more Wed, 19 Oct 2011 14:44:52 +0100 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0083 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0082 The new release of UniProtKB-GOA contains UniProt GO v101, UniProtKB-GOA Human v103, UniProtKB-GOA Mouse v89, UniProtKB-GOA Rat v89, UniProtKB-GOA Arabidopsis v76, UniProtKB-GOA Zebrafish v76, UniProtKB-GOA Chicken v73, UniProtKB-GOA Cow v66, UniProtKB-GOA Dicty v4, UniProtKB-GOA Dog v4, UniProtKB-GOA Pig v4, UniProtKB-GOA Fly v4, UniProtKB-GOA Worm v4, UniProtKB-GOA Yeast v4, UniProtKB-GOA PDB v90 and UniProtKB-GOA Proteome Sets 78... more Tue, 18 Oct 2011 14:30:00 +0100 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0082 http://www.ebi.ac.uk/Information/News/press/2011.html#pre_0009 A large, international collaboration including scientists at EMBL-EBI has produced a high-resolution map of 29 mammalian genomes. The study, published in Nature, provides a major resource that will help scientists understand functional elements in the human genome. Wed, 12 Oct 2011 12:00:00 +0100 http://www.ebi.ac.uk/Information/News/press/2011.html#pre_0009 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0081 Release 67.00 of the RESID Database of Protein Modifications is available by ftp at the EBI or at the NCIFCRF ...more Fri, 07 Oct 2011 15:23:04 +0100 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0081 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0080 IntEnz release 72 and Rhea release 25 are already available. UniProt 2011_09 and Reactome 38 have been used for cross-references. * 57 new EC numbers have been added in this release. * Improved graphics for reactions in Rhea. * Rhea web services (beta) available now. Next release (73/26) is flexibly scheduled for Nov 8th. Thu, 06 Oct 2011 09:23:16 +0100 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0080 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0079 IntAct contains 276,703 binary interactions from 5,054 manually curated publications. All data is also available on the public FTP site. Mon, 03 Oct 2011 15:00:48 +0100 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0079 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0078 ChEBI release 84 is now available, with 26,377 fully annotated three star level. See our entity of the month, Aminocyclopyrachlor. Mon, 3 Oct 2011 14:12:44 +0100 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0078 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0077 The Ensembl Genomes Project is pleased to announce release 11 of Ensembl Genomes This release contains 7 new genomes. Main highlights are: * Software migration to Ensembl 64 * Mycosphaerella graminicola and Phaeosphaeria nodorum (major wheat pathogens), along with Tuber melanosporum (symbiotic Perigord Truffle) included in Ensembl Fungi * Three new genomes in Ensembl Plants: Glycine max (soybean), the spikemoss Selaginella moellendorffii and the green algae Chlamydomonas reinhardti, along with updates to the Oryza glaberimma (African rice) genome and to the gene models of Vitis vinifera(grape) * Amphimedon queenslandica (demosponge) included in Ensembl Metazoa , along with updated gene models for Drosophila melanogaster and Drosophila pseudoobscura. Fri, 30 Sep 2011 11:09:37 +0100 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0077 http://www.ebi.ac.uk/Information/News/press/2011.html#pre_0008 Today marks the launch of the International Mouse Phenotyping Consortium (IMPC), a project to create one of the largest libraries of mammalian genetic function data. Thu, 29 Sep 2011 13:00:00 +0100 http://www.ebi.ac.uk/Information/News/press/2011.html#pre_0008 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0076 We are pleased to announce the release of InterPro 34.0, which contains 22245 entries, includes an update to PIRSF (2.76) and the integration of 927 new methods from the GENE3D, ProDom, Pfam, PIRSF, PANTHER and SUPERFAMILY databases. The release covers 79.6% of UniProt Knowledgebase release 2011_09. UniParc (uniparc_match.tar.gz) and UniMES (unimes_match.tar.gz) matches to InterPro methods have been updated and are available from the ftp site. For full details of the release please see the Release Notes. Sat, 24 Sep 2011 09:48:25 +0100 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0076 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0075 UniProtKB/SwissProt Release of 21-September-2011 contains 532146 sequence entries. ... more UniProtKB/TrEMBL Release of 21-September-2011 contains 16886838 sequence entries. This represents an increase of 3%... more Wed, 21 Sep 2011 15:16:52 +0100 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0075 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0074 In Version 38 of Reactome, new, revised, and substantially reorganized topics include Meiosis, specific pathways relevant to Developmental Biology, Signal transduction , Metabolism, the Immune System, Transmembrane transport of small molecules and Mitotic Cell Cycle. A Reactome tutorial has been published. Wed, 21 Sep 2011 09:00:00 +0100 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0074 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0073 The new release of UniProtKB-GOA contains UniProt GO v100, UniProtKB-GOA Human v102, UniProtKB-GOA Mouse v88, UniProtKB-GOA Rat v88, UniProtKB-GOA Arabidopsis v75, UniProtKB-GOA Zebrafish v75, UniProtKB-GOA Chicken v72, UniProtKB-GOA Cow v65, UniProtKB-GOA Dicty v3, UniProtKB-GOA Dog v3, UniProtKB-GOA Pig v3, UniProtKB-GOA Fly v3, UniProtKB-GOA Worm v3, UniProtKB-GOA Yeast v3, UniProtKB-GOA PDB v89 and UniProtKB-GOA Proteome Sets 77... more Tue, 20 Sep 2011 11:58:00 +0100 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0073 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0072 EMBL-Bank was frozen to make Release 109 on 1-SEP-2011. The release contains 220,504,007 sequence entries comprising 346,598,699,035 nucleotides ...more Wed, 14 Sep 2011 13:00:00 +0100 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0072 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0071 IntAct contains 275,144 binary interactions from 5,009 manually curated publications. All data is also available on the public FTP site. Wed, 14 Sep 2011 10:46:04 +0100 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0071 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0070 ChEBI release 83 is now available, with 26,235 fully annotated three star level. See our entity of the month, Tetraethyllead. Mon, 5 Sep 2011 14:09:26 +0100 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0070 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0069_B BioModels Database now publicly provides 366 models in the curated and 398 in the non-curated branch. Together, these 764 models comprise 119745 species, 135889 relationships (which include reactions, rate rules, events and assignment rules), and 24666 cross-references. Thu, 01 Sep 2011 18:35:58 +0100 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0069_B http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0069 The new release of UniProtKB-GOA contains UniProt GO v99, UniProtKB-GOA Human v101, UniProtKB-GOA Mouse v87, UniProtKB-GOA Rat v87, UniProtKB-GOA Arabidopsis v74, UniProtKB-GOA Zebrafish v74, UniProtKB-GOA Chicken v71, UniProtKB-GOA Cow v64, UniProtKB-GOA Dicty v2, UniProtKB-GOA Dog v2, UniProtKB-GOA Pig v2, UniProtKB-GOA Fly v2, UniProtKB-GOA Worm v2, UniProtKB-GOA Yeast v2, UniProtKB-GOA PDB v88 and UniProtKB-GOA Proteome Sets 76... more Wed, 24 Aug 2011 10:11:10 +0100 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0069 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0068 IntAct contains 268,920 binary interactions from 4,941 manually curated publications. All data is also available on the public FTP site. Tue, 16 Aug 2011 11:03:01 +0100 http://www.ebi.ac.uk/Information/News/database/2011.html#dat_0068