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6 results on '"Séverine Duvaud"'

1. The ISMARA client [version 1; referees: 2 approved]

Author

Panu Artimo, Séverine Duvaud, Mikhail Pachkov, Vassilios Ioannidis, Erik van Nimwegen, and Heinz Stockinger

Subjects
Bioinformatics, Medicine, Science
Abstract

ISMARA (ismara.unibas.ch) automatically infers the key regulators and regulatory interactions from high-throughput gene expression or chromatin state data. However, given the large sizes of current next generation sequencing (NGS) datasets, data uploading times are a major bottleneck. Additionally, for proprietary data, users may be uncomfortable with uploading entire raw datasets to an external server. Both these problems could be alleviated by providing a means by which users could pre-process their raw data locally, transferring only a small summary file to the ISMARA server. We developed a stand-alone client application that pre-processes large input files (RNA-seq or ChIP-seq data) on the user's computer for performing ISMARA analysis in a completely automated manner, including uploading of small processed summary files to the ISMARA server. This reduces file sizes by up to a factor of 1000, and upload times from many hours to mere seconds. The client application is available from ismara.unibas.ch/ISMARA/client.

Published
2016
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2. Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users

Author

Heinz Stockinger, Chiara Gabella, Séverine Duvaud, Vassilios Ioannidis, Frédérique Lisacek, and Christine Durinx

Subjects
Biological data, Databases, Factual, AcademicSubjects/SCI00010, Research areas, Interface (Java), ExPASy, Computational Biology, Ontology (information science), Biology, Bioinformatics, User-Computer Interface, Resource (project management), Web Server Issue, Genetics, User interface, Software, User-centered design
Abstract

The SIB Swiss Institute of Bioinformatics (https://www.sib.swiss) creates, maintains and disseminates a portfolio of reliable and state-of-the-art bioinformatics services and resources for the storage, analysis and interpretation of biological data. Through Expasy (https://www.expasy.org), the Swiss Bioinformatics Resource Portal, the scientific community worldwide, freely accesses more than 160 SIB resources supporting a wide range of life science and biomedical research areas. In 2020, Expasy was redesigned through a user-centric approach, known as User-Centred Design (UCD), whose aim is to create user interfaces that are easy-to-use, efficient and targeting the intended community. This approach, widely used in other fields such as marketing, e-commerce, and design of mobile applications, is still scarcely explored in bioinformatics. In total, around 50 people were actively involved, including internal stakeholders and end-users. In addition to an optimised interface that meets users' needs and expectations, the new version of Expasy provides an up-to-date and accurate description of high-quality resources based on a standardised ontology, allowing to connect functionally-related resources., Graphical Abstract Graphical AbstractThe illustration of Expasy's redesign through a user-centric approach: all the elements that contributed to the process (icons) and the main strengths (stars) of the new implementation.

Published
2021
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3. The bio.tools registry of software tools and data resources for the life sciences

Author

Piotr Jaroslaw Chmura, Salvador Capella, Rob Hooft, Søren Brunak, Tomáš Raček, Inge Jonassen, Rodrigo Lopez, Jacques van Helden, Bengt Persson, Hedi Peterson, Brane Leskošek, Alfonso Valencia, Heinz Stockinger, Hervé Ménager, Emil Karol Rydza, Matúš Kalaš, Josep Lluís Gelpí, Tommi Nyrönen, Hans Ienasescu, Christophe Blanchet, Rafael C. Jimenez, Björn Grüning, Jon Ison, Babis Savakis, Radka Svobodová Vařeková, Arlindo L. Oliveira, Peter Løngreen, Niall Beard, Gert Vriend, Veit Schwämmle, Jiří Vondrášek, Séverine Duvaud, Federico Zambelli, Ahto Salumets, Kristoffer Rapacki, Olivier Collin, Technical University of Denmark [Lyngby] (DTU), University of Copenhagen = Københavns Universitet (KU), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], University of Bergen (UIB), University of Southern Denmark (SDU), Albert-Ludwigs-Universität Freiburg, University of Manchester [Manchester], European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Swiss Institute of Bioinformatics - Lausanne (SIB), Swiss Institute of Bioinformatics, Uppsala University, Central European Institute of Technology [Brno] (CEITEC), Czech Academy of Sciences [Prague] (ASCR), University of Tartu, Dutch Techcentre for Life Sciences [Utrecht], Center for Science (CSC-IT), CSC-IT Center for Science, Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Università degli studi di Milano [Milano], Biomedical Sciences Research Centre Alexander Fleming [Vari, Greece] (BSRC), University of Ljubljana, Institut Français de Bioinformatique - UMS CNRS 3601 (IFB-CORE), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA), ELIXIR Hub [Cambridge], Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa (INESC-ID), Instituto Superior Técnico, Universidade Técnica de Lisboa (IST)-Instituto de Engenharia de Sistemas e Computadores (INESC), Nijmegen Medical Centre [Nijmegen], Plateforme bioinformatique GenOuest [Rennes], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Danish Ministry of Higher Education and Science, European Project: 676559,H2020,H2020-INFRADEV-1-2015-1,ELIXIR-EXCELERATE(2015), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of Bergen (UiB), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Czech Academy of Sciences [Prague] (CAS), Università degli Studi di Milano [Milano] (UNIMI), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Plateforme Génomique Santé Biogenouest®-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), University of Copenhagen = Københavns Universitet (UCPH), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université de Lausanne = University of Lausanne (UNIL), Università degli Studi di Milano = University of Milan (UNIMI), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), and Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1)

Subjects
lcsh:QH426-470, Databases, Factual, Bioinformatics, [SDV]Life Sciences [q-bio], MEDLINE, Biology, Biological Science Disciplines, 03 medical and health sciences, 0302 clinical medicine, Software, Bioinformàtica, lcsh:QH301-705.5, 030304 developmental biology, 0303 health sciences, Internet, business.industry, Biochemistry and Molecular Biology, Data science, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Data resources, Variety (cybernetics), lcsh:Genetics, Workflow, lcsh:Biology (General), The Internet, Open Letter, business, Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19], Biokemi och molekylärbiologi, 030217 neurology & neurosurgery
Abstract

Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue (https://bio.tools) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information. Electronic supplementary material The online version of this article (10.1186/s13059-019-1772-6) contains supplementary material, which is available to authorized users.

Published
2019
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4. ExPASy: SIB bioinformatics resource portal

Author

Heinz Stockinger, Gábor Csárdi, Robin Liechti, Aurélien Grosdidier, Manohar Jonnalagedda, Delphine Baratin, Elisabeth Gasteiger, Nicole Redaschi, Dmitry Kuznetsov, Séverine Duvaud, Konstantin Arnold, Arnaud Fortier, Grégoire Rossier, Ioannis Xenarios, Volker Flegel, Panu Artimo, Céline Hernandez, Vassilios Ioannidis, Khaled Mostaguir, Edouard de Castro, and Sébastien Moretti

Subjects
Proteomics, Internet, business.industry, media_common.quotation_subject, ExPASy, Computational Biology, Articles, Genomics, Entry point, Biology, Bioinformatics, Domain (software engineering), Systems Integration, User-Computer Interface, Resource (project management), Computer Graphics, Genetics, System integration, The Internet, User interface, business, Software, Reputation, media_common
Abstract

ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual resources (databases, web-based and downloadable software tools) are hosted in a 'decentralized' way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions. Specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by different SIB groups and external institutions. The portal features a search function across 'selected' resources. Additionally, the availability and usage of resources are monitored. The portal is aimed for both expert users and people who are not familiar with a specific domain in life sciences. The new web interface provides, in particular, visual guidance for newcomers to ExPASy.

Published
2017

5. The ISMARA client

Author

Vassilios Ioannidis, Heinz Stockinger, Panu Artimo, Erik van Nimwegen, Mikhail Pachkov, and Séverine Duvaud

Subjects
0301 basic medicine, Computer science, Bioinformatics, data analysis, computer.software_genre, General Biochemistry, Genetics and Molecular Biology, Bottleneck, 03 medical and health sciences, Upload, 0302 clinical medicine, Factor (programming language), General Pharmacology, Toxicology and Pharmaceutics, genome, computer.programming_language, Graphical user interface, General Immunology and Microbiology, business.industry, Software Tool Article, General Medicine, Articles, 030104 developmental biology, 030220 oncology & carcinogenesis, command line tool, Key (cryptography), Operating system, motif activity response analysis, Graphical User Interface, State (computer science), Raw data, business, computer
Abstract

ISMARA (ismara.unibas.ch) automatically infers the key regulators and regulatory interactions from high-throughput gene expression or chromatin state data. However, given the large sizes of current next generation sequencing (NGS) datasets, data uploading times are a major bottleneck. Additionally, for proprietary data, users may be uncomfortable with uploading entire raw datasets to an external server. Both these problems could be alleviated by providing a means by which users could pre-process their raw data locally, transferring only a small summary file to the ISMARA server. We developed a stand-alone client application that pre-processes large input files (RNA-seq or ChIP-seq data) on the user's computer for performing ISMARA analysis in a completely automated manner, including uploading of small processed summary files to the ISMARA server. This reduces file sizes by up to a factor of 1000, and upload times from many hours to mere seconds. The client application is available from ismara.unibas.ch/ISMARA/client.

Published
2016

6. The bio.tools registry of software tools and data resources for the life sciences

Author

Jon Ison, Hans Ienasescu, Piotr Chmura, Emil Rydza, Hervé Ménager, Matúš Kalaš, Veit Schwämmle, Björn Grüning, Niall Beard, Rodrigo Lopez, Severine Duvaud, Heinz Stockinger, Bengt Persson, Radka Svobodová Vařeková, Tomáš Raček, Jiří Vondrášek, Hedi Peterson, Ahto Salumets, Inge Jonassen, Rob Hooft, Tommi Nyrönen, Alfonso Valencia, Salvador Capella, Josep Gelpí, Federico Zambelli, Babis Savakis, Brane Leskošek, Kristoffer Rapacki, Christophe Blanchet, Rafael Jimenez, Arlindo Oliveira, Gert Vriend, Olivier Collin, Jacques van Helden, Peter Løngreen, and Søren Brunak

Subjects
Biology (General), QH301-705.5, Genetics, QH426-470
Abstract

Abstract Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue (https://bio.tools) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information.

Published
2019
Full Text
View/download PDF

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