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Fernández JM, de la Torre V, Richardson D, Royo R, Puiggròs M, Moncunill V, Fragkogianni S, Clarke L, Flicek P, Rico D, Torrents D, Carrillo de Santa Pau E, Valencia A. The BLUEPRINT Data Analysis Portal. Cell Syst 2016; 3:491-495.e5. [PMID: 27863955 PMCID: PMC5919098 DOI: 10.1016/j.cels.2016.10.021] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/10/2016] [Accepted: 10/24/2016] [Indexed: 10/20/2022]
Abstract
The impact of large and complex epigenomic datasets on biological insights or clinical applications is limited by the lack of accessibility by easy, intuitive, and fast tools. Here, we describe an epigenomics comparative cyber-infrastructure (EPICO), an open-access reference set of libraries to develop comparative epigenomic data portals. Using EPICO, large epigenome projects can make available their rich datasets to the community without requiring specific technical skills. As a first instance of EPICO, we implemented the BLUEPRINT Data Analysis Portal (BDAP). BDAP provides a desktop for the comparative analysis of epigenomes of hematopoietic cell types based on results, such as the position of epigenetic features, from basic analysis pipelines. The BDAP interface facilitates interactive exploration of genomic regions, genes, and pathways in the context of differentiation of hematopoietic lineages. This work represents initial steps toward broadly accessible integrative analysis of epigenomic data across international consortia. EPICO can be accessed at https://github.com/inab, and BDAP can be accessed at http://blueprint-data.bsc.es.
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Affiliation(s)
- José María Fernández
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain; Spanish Bioinformatics Institute INB-ISCIII ES-ELIXIR, Madrid 28029, Spain
| | - Victor de la Torre
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain; Spanish Bioinformatics Institute INB-ISCIII ES-ELIXIR, Madrid 28029, Spain
| | - David Richardson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Romina Royo
- Spanish Bioinformatics Institute INB-ISCIII ES-ELIXIR, Madrid 28029, Spain; Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB, Research Program in Computational Biology, BSC - CRG - IRB, Barcelona 08028, Spain
| | - Montserrat Puiggròs
- Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB, Research Program in Computational Biology, BSC - CRG - IRB, Barcelona 08028, Spain
| | - Valentí Moncunill
- Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB, Research Program in Computational Biology, BSC - CRG - IRB, Barcelona 08028, Spain
| | - Stamatina Fragkogianni
- Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB, Research Program in Computational Biology, BSC - CRG - IRB, Barcelona 08028, Spain
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Rico
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - David Torrents
- Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB, Research Program in Computational Biology, BSC - CRG - IRB, Barcelona 08028, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | | | - Alfonso Valencia
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain; Spanish Bioinformatics Institute INB-ISCIII ES-ELIXIR, Madrid 28029, Spain.
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Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SCE, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res 2015; 44:D38-47. [PMID: 26538599 PMCID: PMC4702812 DOI: 10.1093/nar/gkv1116] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 10/13/2015] [Indexed: 01/24/2023] Open
Abstract
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand. Here we present a community-driven curation effort, supported by ELIXIR—the European infrastructure for biological information—that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners. As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.
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Affiliation(s)
- Jon Ison
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | - Kristoffer Rapacki
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | - Hervé Ménager
- Centre d'Informatique pour la Biologie, C3BI, Institut Pasteur, France
| | - Matúš Kalaš
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
| | - Emil Rydza
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | - Piotr Chmura
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | - Christian Anthon
- Department of Veterinary Clinical and Animal Sciences, Faculty for Health and Medical Sciences, University of Copenhagen, Denmark
| | - Niall Beard
- School of Computer Science, University of Manchester, UK
| | - Karel Berka
- Department of Physical Chemistry, RCPTM, Faculty of Science, Palacky University, Czech Republic
| | - Dan Bolser
- The European Bioinformatics Institute (EMBL-EBI), UK
| | - Tim Booth
- NEBC Wallingford, Centre for Ecology and Hydrology, UK
| | - Anthony Bretaudeau
- INRA, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), France INRIA, IRISA, GenOuest Core Facility, France
| | - Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Czech Republic
| | - Rita Casadio
- Bologna Biocomputing Group, University of Bologna, Italy
| | | | - Frederik Coppens
- Department of Plant Systems Biology, VIB, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium
| | | | | | - Kristian Davidsen
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | | | - Tunca Dogan
- UniProt, European Bioinformatics Institute (EMBL-EBI), UK
| | | | - Laura Emery
- The European Bioinformatics Institute (EMBL-EBI), UK
| | | | - Thomas Gatter
- Faculty of Technology and Center for Biotechnology, Universität Bielefeld, Germany
| | | | - Marie Grosjean
- Institut Français de Bioinformatique (French Institute of Bioinformatics), CNRS, UMS3601, France
| | - Björn Grüning
- Albert-Ludwigs-Universität Freiburg, Fahnenbergplatz, 79085 Freiburg
| | | | - Hans Ienasescu
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Denmark
| | | | - Martin Closter Jespersen
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | | | - Nick Juty
- The European Bioinformatics Institute (EMBL-EBI), UK
| | - Peter Juvan
- Centre for Functional Genomics and Biochips, Faculty of Medicine, University of Ljubljana, Slovenia
| | | | - Camille Laibe
- The European Bioinformatics Institute (EMBL-EBI), UK
| | - Jing-Woei Li
- Faculty of Medicine, The Chinese University of Hong Kong, China Hong Kong Bioinformatics Centre, School of Life Sciences,The Chinese University of Hong Kong, China
| | - Luana Licata
- Dept. of Biology, University of Rome Tor Vergata, Italy
| | - Fabien Mareuil
- Centre d'Informatique pour la Biologie, C3BI, Institut Pasteur, France
| | - Ivan Mičetić
- Department of Biomedical Sciences, University of Padua, Italy
| | | | - Sebastien Moretti
- SIB Swiss Institute of Bioinformatics, Switzerland Department of Ecology and Evolution, Biophore, Evolutionary Bioinformatics group, University of Lausanne, Switzerland
| | | | - Steffen Möller
- Department of Dermatology, University of Lübeck, Germany Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Germany
| | | | - Hedi Peterson
- Institute of Computer Science, University of Tartu, Estonia
| | | | - Peter Rice
- Department of Computing, William Penney Laboratory, Imperial College London, UK
| | | | | | - Rabie Saidi
- UniProt, European Bioinformatics Institute (EMBL-EBI), UK
| | | | - Veit Schwämmle
- Protein Research Group, Department for Biochemistry and Molecular Biology, University of Southern Denmark, Denmark
| | | | - Maria Maddalena Sperotto
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | | | | | | | - Victor de la Torre
- National Bioinformatics Institute Unit (INB), Fundacion Centro Nacional de Investigaciones Oncologicas, Spain
| | | | - Allegra Via
- Dept. of Physics, Sapienza University, Italy
| | - Guy Yachdav
- Department of Informatics, Bioinformatics-I12, TUM, Germany
| | - Federico Zambelli
- Institute of Biomembranes and Bioenergetics, National Research Council (CNR), and Dept. of Biosciences, University of Milano, Italy
| | - Gert Vriend
- Radboud University Medical Centre, CMBI, Netherlands
| | - Burkhard Rost
- Department of Informatics, Bioinformatics-I12, TUM, Germany
| | | | - Peter Løngreen
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark
| | - Søren Brunak
- Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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