RHdb: the radiation hybrid database

Since July 1995, the European Bioinformatics Institute (EBI) has maintained RHdb (http://www.ebi.ac.uk/RHdb ), a public database for radiation hybrid data. Radiation hybrid mapping is an important technique for determining high resolution maps. RHdb is also served by CORBA servers. The EBI is an Outstation of the European Molecular Biology Laboratory (EMBL).     

RHdb: the Radiation Hybrid database

Since July 1995, the European Bioinformatics Institute (EBI) has maintained RHdb (http://www.ebi.ac.uk/RHdb), a public database for radiation hybrid data. Radiation hybrid mapping is an important technique for determining high resolution maps. RHdb is also served by CORBA servers. The EBI is an Outstation of the European Molecular Biology Laboratory (EMBL).     

The radiation hybrid database.

Since July 1995, the European Bioinformatics Institute (EBI) has maintained the Radiation Hybrid database (RHdb; http://www.ebi.ac. uk/RHdb ), a public database for radiation hybrid data. Radiation hybrid mapping is an important technique for determining high resolution maps. Recently, CORBA access has been added to RHdb. The EBI is an Outstation of the European Molecular Biology Laboratory (EMBL).     

The Radiation Hybrid Database.

Since July 1995, the European Bioinformatics Institute (EBI) has maintained RHdb, a public database for radiation hybrid data. Radiation hybrid data are used in the generation of alternative genetic maps as they can include non-polymorphic markers and are also powerful enough to order unresolved genetic clusters of polymorphic STSs. The EBI is an Outstation of the European Molecular Biology Laboratory (EMBL).     

HuGeMap: a distributed and integrated Human Genome Map database.

The HuGeMap database stores the major genetic and physical maps of the human genome. It is also interconnected with the gene radiation hybrid mapping database RHdb. HuGeMap is accessible through a Web server for interactive browsing at URL http://www.infobiogen. fr/services/Hugemap , as well as through a CORBA server for effective programming. HuGeMap is intended as an attempt to build open, interconnected databases, that is databases that distribute their objects worldwide in compliance with a recognized standard of distribution. Maps can be displayed and compared with a java applet (http://babbage.infobiogen.fr:15000/Mappet/Show. html ) that queries the HuGeMap ORB server as well as the RHdb ORB server at the EBI.     

A proposal for a standard CORBA interface for genome maps

MOTIVATION: The scientific community urgently needs to standardize the exchange of biological data. This is helped by the use of a common protocol and the definition of shared data structures. We have based our standardization work on CORBA, a technology that has become a standard in the past years and allows interoperability between distributed objects. RESULTS: We have defined an IDL specification for genome maps and present it to the scientific community. We have implemented CORBA servers based on this IDL to distribute RHdb and HuGeMap maps. The IDL will co-evolve with the needs of the mapping community. AVAILABILITY: The standard IDL for genome maps is available at http:// corba.ebi.ac.uk/RHdb/EUCORBA/MapIDL.htm l. The IORs to browse maps from Infobiogen and EBI are at http://www.infobiogen.fr/services/Hugemap/IOR and http://corba.ebi.ac.uk/RHdb/EUCORBA/IOR CONTACT: manu@infobiogen.fr, tome@ebi.ac.uk     

The EBI SRS server-new features

MOTIVATION: Here we report on recent developments at the EBI SRS server (http://srs.ebi.ac.uk). SRS has become an integration system for both data retrieval and sequence analysis applications. The EBI SRS server is a primary gateway to major databases in the field of molecular biology produced and supported at EBI as well as European public access point to the MEDLINE database provided by US National Library of Medicine (NLM). It is a reference server for latest developments in data and application integration. The new additions include: concept of virtual databases, integration of XML databases like the Integrated Resource of Protein Domains and Functional Sites (InterPro), Gene Ontology (GO), MEDLINE, Metabolic pathways, etc., user friendly data representation in 'Nice views', SRSQuickSearch bookmarklets. AVAILABILITY: SRS6 is a licensed product of LION Bioscience AG freely available for academics. The EBI SRS server (http://srs.ebi.ac.uk) is a free central resource for molecular biology data as well as a reference server for the latest developments in data integration.     

The European Bioinformatics Institute (EBI) databases.

This paper describes the databases and services of the European Bioinformatics Institute (EBI). In collaboration with DDBJ and GenBank/NCBI, the EBI maintains and distributes the EMBL Nucleotide Sequence Database, Europe's primary nucleotide sequence data resource. The EBI also maintains and distributes the SWISS-PROT Protein Sequence Database, in collaboration with Amos Bairoch of the University of Geneva. Over thirty additional specialist molecular biology databases, as well as software and documentation of interest to molecular biologists, are also available. The EBI network services include database searching, entry retrieval, and sequence similarity searching facilities.     

Enzymatic hydrolysis and characterization of lignocellulosic biomass exposed to electron beam irradiation

Pretreatment of lignocellulosic biomass has been taken up as a global challenge as it comprises a large renewable source of fermentable sugars. In this study, effect of electron beam irradiation (EBI) on a hybrid grass variety investigated as a biomass pretreatment method. Dry biomass samples after characterization were exposed to EBI doses of 0, 75, 150 and 250kGy. The pretreated biomass samples were enzymatically hydrolyzed using Trichoderma reesei ATCC 26921 cellulase for 144h. The enzyme loadings were 15 and 30FPU/g of biomass. The structural changes and degree of crystallinity of the pretreated biomass were studied by FTIR, XRD and SEM analyses. The lignocellulosic biomass sample showed 12.0% extractives, 36.9% cellulose, 28.4% hemicellulose, 11.9% lignin and 8.6% ash. Significant improvements in the reducing sugar and glucose yields were observed in the hydrolysate of EBI pretreated biomass compared to the control. In 250kGy exposed samples 79% of the final reducing sugar yield was released within 48h of hydrolysis at an enzyme loading rate of 30FPU/g of biomass. The IR crystallinity index calculated from the FTIR data and degree of crystallinity (XRD) decreased in the EBI treated samples. A significant negative correlation was observed between degree of crystallinity and the glucose yield from enzymatic hydrolysis.     

The European Bioinformatics Institute web site: a new view

SUMMARY: The European Bioinformatics Institute (EBI), and outstation of the European Molecular Biology laboratory, has revamped its web site for the second time since 1997 in order to address increased user demand as well as establishing better uniformity and easier accessibility for the ever growing number of users and services it offers to the community. A GRID-like hardware infrastructure has been put in place to provide round the clock services in a redundant and reliable fashion. AVAILABILITY: http://www.ebi.ac.uk/     

The European Bioinformatics Institute (EBI) databases.

The European Bioinformatics Institute (EBI) maintains and distributes the EMBL Nucleotide Sequence database, Europe's primary nucleotide sequence data resource. The EBI also maintains and distributes the SWISS-PROT Protein Sequence database, in collaboration with Amos Bairoch of the University of Geneva. Over fifty additional specialist molecular biology databases, as well as software and documentation of interest to molecular biologists are available. The EBI network services include database searching and sequence similarity searching facilities.     

5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame

The Bioinformatics Committee of the HUPO Brain Proteome Project (HUPO BPP) meets regularly to execute the post-lab analyses of the data produced in the HUPO BPP pilot studies. On July 7, 2005 the members came together for the 5th time at the European Bioinformatics Institute (EBI) in Hinxton, UK, hosted by Rolf Apweiler. As a main result, the parameter set of the semi-automated data re-analysis of MS/MS spectra has been elaborated and the subsequent work steps have been defined.     

The EMBL Nucleotide Sequence Database: major new developments

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) incorporates, organizes and distributes nucleotide sequences from all available public sources. The database is located and maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK. In an international collaboration with DDBJ (Japan) and GenBank (USA), data are exchanged amongst the collaborating databases on a daily basis to achieve optimal synchronization. Webin is the preferred web-based submission system for individual submitters, while automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via FTP, Email and World Wide Web interfaces. EBI's Sequence Retrieval System (SRS) integrates and links the main nucleotide and protein databases plus many other specialized molecular biology databases. For sequence similarity searching, a variety of tools (e.g. Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. All resources can be accessed via the EBI home page at http://www.ebi.ac.uk.     

A fish-based assessment tool for the ecological quality of the brackish Schelde estuary in Flanders (Belgium)

This paper presents a new approach which was developed to find an optimal combination of candidate metrics for creating a fish-based estuarine biotic index (EBI) for defining the quality status of an estuarine area. The key idea was that a powerful index should minimise two prediction errors simultaneously: falsely declaring the status of a site as disturbed while it is not (Type I error) and the reverse, falsely declaring a disturbed site as undisturbed (Type II error). The balance between both errors is an inherent characteristic of an index and can be displayed as a curve. The area under this curve (AUC) is a measure of the misclassification rate (smaller = better). This criterion was the basis for a stepwise approach whereby in each step a metric resulting in the highest reduction of AUC was added. Five metrics were selected and the distribution of their average was the basis to derive the thresholds for the classes of the EBI. This paper presents the fish-based index (EBI) for the brackish Schelde estuary in Flanders (Belgium). The index was calibrated against fyke net data from five sites during the period from 1995 to 2004. The sites ranged in quality from moderately impacted to very disturbed, classes 3 to 5 respectively. Despite there being neither of the highest classes 1 (high) and 2 (good), the EBI presented can serve as an evaluation tool in the highly impacted situation in Flanders as it discriminates well between moderate and highly impacted sites. In addition, its definition complies with the biological status classes of the European Water Framework Directive (WFD). Handling Editor: K. Martens     

The EMBL Nucleotide Sequence Database.

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl.html) constitutes Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications. While automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO), the preferred submission tool for individual submitters is Webin (WWW). Through all stages, dataflow is monitored by EBI biologists communicating with the sequencing groups. In collaboration with DDBJ and GenBank the database is produced, maintained and distributed at the European Bioinformatics Institute (EBI). Database releases are produced quarterly and are distributed on CD-ROM. Network services allow access to the most up-to-date data collection via Internet and World Wide Web interface. EBI's Sequence Retrieval System (SRS) is a Network Browser for Databanks in Molecular Biology, integrating and linking the main nucleotide and protein databases, plus many specialised databases. For sequence similarity searching a variety of tools (e.g. Blitz, Fasta, Blast etc) are available for external users to compare their own sequences against the most currently available data in the EMBL Nucleotide Sequence Database and SWISS-PROT.     

Equine dinucleotide repeat loci COR081–COR100

The nucleotide sequences data reported in this paper were submitted to the EMBL library at the European Bioinformatics Institute (EBI).     

The EMBL Nucleotide Sequence Database

The EMBL Nucleotide Sequence Database (aka EMBL-Bank; http://www.ebi.ac.uk/embl/) incorporates, organises and distributes nucleotide sequences from all available public sources. EMBL-Bank is located and maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK. In an international collaboration with DDBJ (Japan) and GenBank (USA), data are exchanged amongst the collaborating databases on a daily basis. Major contributors to the EMBL database are individual scientists and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via FTP, email and World Wide Web interfaces. EBI’s Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many other specialized databases. For sequence similarity searching, a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. All resources can be accessed via the EBI home page at http://www.ebi.ac.uk.     

Integrative proteomics: structure, function, and interaction report on the 3rd joint meeting of the British Society for Proteome Research and the European Bioinformatics Institute, July 2006

This report summarizes the highlights of the recent British Society for Proteome Research (BSPR) meeting jointly organized with the European Bioinformatics Institute (EBI) which was held at the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK in July 2006. This was the third annual scientific meeting organized by the BSPR and EBI and the theme of this years meeting was Integrative Proteomics: Structure, function and interaction. A wealth of local and overseas speakers were invited to discuss both their own work and specific challenges present in modern day proteomic based experiments.     

Increased Th17 and regulatory T cell responses in EBV-induced gene 3-deficient mice lead to marginally enhanced development of autoimmune encephalomyelitis

EBV-induced gene 3 (EBI3)-encoded protein can form heterodimers with IL-27P28 and IL-12P35 to form IL-27 and IL-35. IL-27 and IL-35 may influence autoimmunity by inhibiting Th17 differentiation and facilitating the inhibitory roles of Foxp3(+) regulatory T (Treg) cells, respectively. In this study, we have evaluated the development of experimental autoimmune encephalomyelitis (EAE) in EBI3-deficient mice that lack both IL-27 and IL-35. We found that myelin oligodendrocyte glycoprotein peptide immunization resulted in marginally enhanced EAE development in EBI3-deficient C57BL6 and 2D2 TCR-transgenic mice. EBI3 deficiency resulted in significantly increased Th17 and Th1 responses in the CNS and increased T cell production of IL-2 and IL-17 in the peripheral lymphoid organs. EBI3-deficient and -sufficient 2D2 T cells had equal ability in inducing EAE in Rag1(-/-) mice; however, more severe disease was induced in EBI3(-/-)Rag1(-/-) mice than in Rag1(-/-) mice by 2D2 T cells. EBI3-deficient mice had increased numbers of CD4(+)Foxp3(+) Treg cells in peripheral lymphoid organs. More strikingly, EBI3-deficient Treg cells had more potent suppressive functions in vitro and in vivo. Thus, our data support an inhibitory role for EBI3 in Th17, Th1, IL-2, and Treg responses. Although these observations are consistent with the known functions of IL-27, the IL-35 contribution to the suppressive functions of Treg cells is not evident in this model. Increased Treg responses in EBI3(-/-) mice may explain why the EAE development is only modestly enhanced compared with wild-type mice.