4 results on '"Grüning, Bjorn"'
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2. Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy
- Author
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Larivière, Delphine, primary, Abueg, Linelle, additional, Brajuka, Nadolina, additional, Gallardo-Alba, Cristóbal, additional, Grüning, Bjorn, additional, Ko, Byung June, additional, Ostrovsky, Alex, additional, Palmada-Flores, Marc, additional, Pickett, Brandon D., additional, Rabbani, Keon, additional, Balacco, Jennifer R., additional, Chaisson, Mark, additional, Cheng, Haoyu, additional, Collins, Joanna, additional, Denisova, Alexandra, additional, Fedrigo, Olivier, additional, Gallo, Guido Roberto, additional, Giani, Alice Maria, additional, Gooder, Grenville MacDonald, additional, Jain, Nivesh, additional, Johnson, Cassidy, additional, Kim, Heebal, additional, Lee, Chul, additional, Marques-Bonet, Tomas, additional, O’Toole, Brian, additional, Rhie, Arang, additional, Secomandi, Simona, additional, Sozzoni, Marcella, additional, Tilley, Tatiana, additional, Uliano-Silva, Marcela, additional, van den Beek, Marius, additional, Waterhouse, Robert M., additional, Phillippy, Adam M., additional, Jarvis, Erich D., additional, Schatz, Michael C., additional, Nekrutenko, Anton, additional, and Formenti, Giulio, additional
- Published
- 2023
- Full Text
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3. ReGaTE: Registration of Galaxy Tools in Elixir
- Author
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Doppelt-Azeroual, Olivia, Mareuil, Fabien, Deveaud, Eric, Kalaš, Matúš, Soranzo, Nicola, van den Beek, Marius, Grüning, Bjorn, Ison, Jon, Ménager, Hervé, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Computational Biology Unit [Bergen] (CBU), University of Bergen (UiB), Department of Informatics [Bergen] (UiB), Earlham Institute [Norwich], Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Center for Biological Systems Analysis - Zentrum für Biosystemanalyse [Freiburg] (ZBSA), Albert-Ludwigs-Universität Freiburg, Department of Computer Science [Freiburg], Center for Biological Sequence Analysis [Lyngby], Technical University of Denmark [Lyngby] (DTU), ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures Programme of Horizon 2020 (676559)., The authors wish to thank the developers of the bio.tools registry, especially Emil Rydza and Piotr Chmura for the technical support they provided during the development of this tool. They also thank Bertrand Néron for the contribution of his technical expertise in Python., European Project: 676559,H2020,H2020-INFRADEV-1-2015-1,ELIXIR-EXCELERATE(2015), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Mareuil, Fabien, and ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences. - ELIXIR-EXCELERATE - - H20202015-09-01 - 2019-08-31 - 676559 - VALID
- Subjects
Internet ,bioinformatics services ,bio.tools ,Computational Biology ,Reproducibility of Results ,Workflow ,Bioinformatics services ,Automation ,User-Computer Interface ,Galaxy ,Computer Systems ,Bio.Tools ,Technical Note ,[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] ,Software ,[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM] - Abstract
Background:Bioinformaticians routinely use multiple software tools and data sources in their day-to-day work, and have been guided in their choices by a number of cataloguing initiatives. The ELIXIR Tools and Data Services Registry ( bio.tools ) aims to provide a central information point, independent of any specific scientific scope within bioinformatics or technological implementation. Meanwhile, efforts to integrate bioinformatics software in workbench and workflow environments have accelerated, to enable the design, automation, and reproducibility of bioinformatics experiments. One such popular environment is the Galaxy framework, with currently more than 80 publicly available Galaxy servers around the world. In the context of a generic registry for bioinformatics software, such as bio.tools , Galaxy instances constitute a major source of valuable content. Yet there has been, to date, no convenient mechanism to register such services en masse . Findings:We present ReGaTE (Registration of Galaxy Tools in Elixir), a software utility that automates the process of registering the services available in a Galaxy instance. This utility uses the BioBlend API to extract service metadata from a Galaxy server, enhance the metadata with the scientific information required by bio.tools, and push it to the registry. Conclusion:ReGaTE provides a fast and convenient way to publish Galaxy services in bio.tools. By doing so, service providers may increase the visibility of their services, whilst enriching the software discovery function that bio.tools provides for its users. The source code of ReGaTE is freely available on Github, at https://github.com/C3BI-pasteur-fr/ReGaTE .
- Published
- 2017
4. Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy.
- Author
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Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJ, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K, Balacco JR, Chaisson M, Cheng H, Collins J, Denisova A, Fedrigo O, Gallo GR, Giani AM, Gooder GM, Jain N, Johnson C, Kim H, Lee C, Marques-Bonet T, O'Toole B, Rhie A, Secomandi S, Sozzoni M, Tilley T, Uliano-Silva M, van den Beek M, Waterhouse RM, Phillippy AM, Jarvis ED, Schatz MC, Nekrutenko A, and Formenti G
- Abstract
Improvements in genome sequencing and assembly are enabling high-quality reference genomes for all species. However, the assembly process is still laborious, computationally and technically demanding, lacks standards for reproducibility, and is not readily scalable. Here we present the latest Vertebrate Genomes Project assembly pipeline and demonstrate that it delivers high-quality reference genomes at scale across a set of vertebrate species arising over the last ~500 million years. The pipeline is versatile and combines PacBio HiFi long-reads and Hi-C-based haplotype phasing in a new graph-based paradigm. Standardized quality control is performed automatically to troubleshoot assembly issues and assess biological complexities. We make the pipeline freely accessible through Galaxy, accommodating researchers even without local computational resources and enhanced reproducibility by democratizing the training and assembly process. We demonstrate the flexibility and reliability of the pipeline by assembling reference genomes for 51 vertebrate species from major taxonomic groups (fish, amphibians, reptiles, birds, and mammals).
- Published
- 2023
- Full Text
- View/download PDF
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