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ELIXIR-EXCELERATE

Title
ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences.
Funding
EC | H2020 | RIA
Call
H2020-INFRADEV-1-2015-1
Contract (GA) number
676559
Start Date
2015/09/01
End Date
2019/08/31
Open Access mandate
yes
Data Pilot
no
Organizations
VIB, UPF, IRB BARCELONA, NBIC, UiO, SIB, CSIC, UOXF, CIRAD, CNR, UU, FORTH, INESC ID, UTARTU, UiB, EARLHAM, NTNU, FPS, CRG, INRA, UCAM, UiT, LIU, BSC, UMA, CNIO, IBET, IP, IMIM, BSRCAF, FCG-IGC, UL, EMBL, UEDIN, NIB, DTU, Athena RC, CCMAR, HWU, UMAN, FVIB, CESNET, HUJI, MU, CSC, UOCHB AVCR, CNRS
More information
Detailed project information (CORDIS)

 

  • ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services [version 1; referees: 1 approved, 2 approved with reservations]

    Espen Mikal Robertsen; Hubert Denise; Alex Mitchell; Robert D. Finn; Lars Ailo Bongo; Nils Peder Willassen (2017)
    Projects: EC | ELIXIR-EXCELERATE (676559)
    Metagenomics, the study of genetic material recovered directly from environmental samples, has the potential to provide insight into the structure and function of heterogeneous microbial communities.  There has been an increased use of metagenomics to discover and understand the diverse biosynthetic capacities of marine microbes, thereby allowing them to be exploited for industrial, food, and health care products. This ELIXIR pilot action was motivated by the need to establish dedicated data ...

    ELIXIR Advanced workshops on genome annotation

    Henrik Lantz; Bengt Persson (2017)
    Projects: EC | ELIXIR-EXCELERATE (676559)
    Genome assembly and genome annotation constitute areas where significant resources, both manpower and computational resources, are needed to come to the successful conclusion of a project. Experience, both organism-specific but also general knowledge of assembly and annotation, is necessary and this is often slowly built up over the years when working continuously on similar projects. Every project is unique, as all organisms are different and variety of different data types and tools exist. ...

    BUFET: boosting the unbiased miRNA functional enrichment analysis using bitsets

    Zagganas, Konstantinos; Vergoulis, Thanasis; Paraskevopoulou, Maria D.; Vlachos, Ioannis S.; Skiadopoulos, Spiros; Dalamagas, Theodore (2017)
    Projects: EC | ELIXIR-EXCELERATE (676559)
    Background A group of miRNAs can regulate a biological process by targeting genes involved in the process. The unbiased miRNA functional enrichment analysis is the most precise in silico approach to predict the biological processes that may be regulated by a given miRNA group. However, it is computationally intensive and significantly more expensive than its alternatives. Results We introduce BUFET, a new approach to significantly reduce the time required for the execution of the unbiased miR...

    The metagenomic data life-cycle: standards and best practices

    ten Hoopen, Petra; Finn, Robert D.; Bongo, Lars Ailo; Corre, Erwan; Fosso, Bruno; Meyer, Folker; Mitchell, Alex; Pelletier, Eric; Pesole, Graziano; Santamaria, Monica; Willassen, Nils Peder; Cochrane, Guy (2017)
    Projects: EC | ELIXIR-EXCELERATE (676559)
    International audience; Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonized way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (i) material sampling, (ii) material sequencing, (iii) data analysis, and (iv) data archiving and publishing. Taking examples from marine research, we summarize essential variables used to describe material s...

    HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering

    Bendl, Jaroslav; Stourac, Jan; Sebestova, Eva; Vavra, Ondrej; Musil, Milos; Brezovsky, Jan; Damborsky, Jiri (2016)
    Projects: EC | ELIXIR-EXCELERATE (676559)
    HotSpot Wizard 2.0 is a web server for automated identification of hot spots and design of smart libraries for engineering proteins’ stability, catalytic activity, substrate specificity and enantioselectivity. The server integrates sequence, structural and evolutionary information obtained from 3 databases and 20 computational tools. Users are guided through the processes of selecting hot spots using four different protein engineering strategies and optimizing the resulting library's size by ...

    Reference genome assessment from a population scale perspective: an accurate profile of variability and noise

    Carbonell-Caballero, José; Amadoz, Alicia; Alonso, Roberto; Hidalgo, Marta R; Çubuk, Cankut; Conesa, David; López-Quílez, Antonio; Dopazo, Joaquín (2017)
    Projects: EC | ELIXIR-EXCELERATE (676559)
    Abstract Motivation Current plant and animal genomic studies are often based on newly assembled genomes that have not been properly consolidated. In this scenario, misassembled regions can easily lead to false-positive findings. Despite quality control scores are included within genotyping protocols, they are usually employed to evaluate individual sample quality rather than reference sequence reliability. We propose a statistical model that combines quality control scores across samples in o...

    REPORT: Portfolio of ELIXIR data resources and tools for the rare diseases communities

    There is a wide range of data resources and analysis methods used in the rare-disease area. Deliverable 8.1 report the efforts undertaken from the ELIXIR-EXCELERATE WP8 rare disease use case to create a dynamic portfolio of ELIXIR data resources and analysis tools useful to the rare disease communities. Since the start of the project, we have reviewed the ELIXIR-EXCELERATE currentdata resources and evaluated their usability and potential impact on the rare disease com...

    Datasets annotated for at least 1 woody plant, cereal and solanaceous species; genotype, phenotype and sample metadata submitted to appropriate public archives

    Plant omics data is often not published, or dispersed among multiple repositories and, owing to poor annotation of submissions with descriptive metadata, effectively not FAIR (i.e. Findable, Accessible, Interoperable and Re-usable). In this work package, our goal is to make plant -omics data FAIR, and the first part of this work has involved the development of standards for the annotation of data sets, and their exemplary application to diverse data from diverse speci...

    ELIXIR-EXCELERATE: Deliverable 6.2: Report on comprehensive metagenomic data standards environment

    Guy Cochrane; Rob Finn; Nils Peder Willassen; Lars Ailo Bongo; Monica Santamaria; Bruno Fosso; Eric Pelletier; Erwan Corre; Alex Mitchell; Simon Potter (2018)
    Projects: EC | ELIXIR-EXCELERATE (676559)
    We have previously reviewed data standards and best practices in marine metagenomics and have published our review and three core recommendations (ten Hoopen et al., 2017). On our first recommendation - that scientists comply with data standards and recommended best practices, we assess in this Annex the status across sampling, sequencing, analysis and results archiving stages of metagenomics studies. We report for our second recommendation - that computational analysis process be describ...

    MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data

    Fosso, Bruno; Santamaria, Monica; D'Antonio, M.; Lovero, D.; Corrado, G.; Vizza, E.; Passaro, N.; Garbuglia, A.R.; Capobianchi, M.R.; Crescenzi, M.; Valiente Feruglio, Gabriel Alejandro; Pesole, Graziano (2017)
    Projects: EC | ELIXIR-EXCELERATE (676559)
    Abstract Summary: Shotgun metagenomics by high-throughput sequencing may allow deep and accurate characterization of host-associated total microbiomes, including bacteria, viruses, protists and fungi. However, the analysis of such sequencing data is still extremely challenging in terms of both overall accuracy and computational efficiency, and current methodologies show substantial variability in misclassification rate and resolution at lower taxonomic ranks or are limited to specific life do...
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