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4. BioConvert: a comprehensive format converter for life sciences

Author

Caro, Hugo, primary, Dollin, Sulyvan, additional, Biton, Anne, additional, Brancotte, Bryan, additional, Desvillechabrol, Dimitri, additional, Dufresne, Yoann, additional, Li, Blaise, additional, Kornobis, Etienne, additional, Lemoine, Frédéric, additional, Maillet, Nicolas, additional, Perrin, Amandine, additional, Traut, Nicolas, additional, Néron, Bertrand, additional, and Cokelaer, Thomas, additional

Published
2023
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5. The IFB Catalogue

Author

Brancotte, Bryan, Kengni, Hippolyte, Rosnet, Thomas, Bouri, Laurent, Ison, Jon, Sand, Olivier, Chiapello, Hélène, Gaignard, Alban, Milanesi, Sylvain, van Helden, Jacques, and Ménager, Hervé

Abstract

The IFB Catalogue is a centralized database developed as part of the IFB Distributed national environment of services in Bioinformatics. Its aim is to ensure the visibility and accessibility of the Bioinformatics resources provided and maintained by the french community, whether these are research labs or service platforms, in a structured and open database that guarantees their FAIRness. Such resources can be software tools, databases, computing resources, individual expertises, platforms, trainings and training materials. This catalogue stores the metadata describing their properties (e.g. the licence of a software tool) and linking them (e.g. the publication of a database by a given team). The primary role of the Catalogue is to help users of Bioinformatics services. Through the integration of the data in the IFB website (https://www.france-bioinformatique.fr), it provides an overview of the various resources provided by the community, and supports the needs of end-users (who can perform a given kind of analysis? where is a tool available?). It is also synchronized with related international catalogues (e.g. ELIXIR bio.tools[1] , TeSS[2]), and promotes the reusability of the data through the publication of Bioschemas[3] markup and REST APIs as well as the use of the EDAM ontology[4]. The backend server is available at https://catalogue.france-bioinformatique.fr/. The code of the Catalogue database backend is openly available on https://github.com/IFB-ElixirFr/ifbcat

Published
2022
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6. The iPPI-DB initiative: a community-centered database of protein–protein interaction modulators

Author

Torchet, Rachel, Druart, Karen, Ruano, Luis Checa, Moine-Franel, Alexandra, Borges, Hélène, Doppelt-Azeroual, Olivia, Brancotte, Bryan, Mareuil, Fabien, Nilges, Michael, Ménager, Hervé, Sperandio, Olivier, Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Département de Biologie structurale et Chimie - Department of Structural Biology and Chemistry, Institut Pasteur [Paris] (IP), none declared, This work used the computational and storage services (TARS cluster, VMHosting) provided by the IT department at Institut Pasteur, Paris. The authorswish to acknowledge in particular the help and technical advice of Eric Deveaud,Emmanuel Guichard, Thomas Me ́nard and Youssef Ghorbal (IT Department,Institut Pasteur). They also want to acknowledge the technical help of Tru Huynh(Structural Bioinformatics Unit, Institut Pasteur). They thank Jon Ison, BenjaminBardiaux and Pascal Campagne for their proofreading of the paper.Marvin JS (20.5.0, 2020, http://www.chemaxon.com) is used for drawingand displaying chemical structures in both Query mode and Contributionmode of iPPI-DB. Pipeline Pilot (server 19.1) is used to prepare the DrugBankdatabase from a SDF file prior to chemical similarity search 202 (2020), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Centre National de la Recherche Scientifique (CNRS)-Centre de Ressources et de Recherche Technologique - Center for Technological Resources and Research (C2RT), Institut Pasteur [Paris]-Institut Pasteur [Paris], Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Etude de la dynamique des protéomes (EDyP), BioSanté (UMR BioSanté), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Biologie Computationnelle (ex C3BI), Bioinformatique structurale - Structural Bioinformatics, and Druart, Karen

Subjects
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], AcademicSubjects/SCI01060, Databases and Ontologies, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [INFO.INFO-DB] Computer Science [cs]/Databases [cs.DB], [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Original Papers, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [CHIM.CHEM]Chemical Sciences/Cheminformatics
Abstract

International audience; Abstract Motivation One avenue to address the paucity of clinically testable targets is to reinvestigate the druggable genome by tackling complicated types of targets such as Protein-Protein Interactions (PPIs). Given the challenge to target those interfaces with small chemical compounds, it has become clear that learning from successful examples of PPI modulation is a powerful strategy. Freely accessible databases of PPI modulators that provide the community with tractable chemical and pharmacological data, as well as powerful tools to query them, are therefore essential to stimulate new drug discovery projects on PPI targets. Results Here, we present the new version iPPI-DB, our manually curated database of PPI modulators. In this completely redesigned version of the database, we introduce a new web interface relying on crowdsourcing for the maintenance of the database. This interface was created to enable community contributions, whereby external experts can suggest new database entries. Moreover, the data model, the graphical interface, and the tools to query the database have been completely modernized and improved. We added new PPI modulators, new PPI targets and extended our focus to stabilizers of PPIs as well. Availability and implementation The iPPI-DB server is available at https://ippidb.pasteur.fr The source code for this server is available at https://gitlab.pasteur.fr/ippidb/ippidb-web/ and is distributed under GPL licence (http://www.gnu.org/licences/gpl). Queries can be shared through persistent links according to the FAIR data standards. Data can be downloaded from the website as csv files. Supplementary information Supplementary data are available at Bioinformatics online.

Published
2021
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7. Viral Host Range database, an online tool for recording, analyzing and disseminating virus-host interactions

Author

Lamy-Besnier, Quentin, Brancotte, Bryan, Ménager, Hervé, Debarbieux, Laurent, Bactériophage, bactérie, hôte - Bacteriophage, bacterium, host, Institut Pasteur [Paris] (IP), Université Paris Cité (UPCité), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), This work has been supported by grant ANR-19-AMRB-0002, ANR-19-AMRB-0002,MAPVAP,Évaluation préclinique et mécanistique de deux cocktails de bactériophages ciblant Pseudomonas aeruginosa et Escherichia coli multirésistants pour le traitement des pneumonies acquises sous ventilation(2019), Institut Pasteur [Paris], Université de Paris (UP), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)

Subjects
AcademicSubjects/SCI01060, viruses, [SDV]Life Sciences [q-bio], Databases and Ontologies, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], complex mixtures, Applications Notes
Abstract

Abstrtact Motivation Viruses are ubiquitous in the living world, and their ability to infect more than one host defines their host range. However, information about which virus infects which host, and about which host is infected by which virus, is not readily available. Results We developed a web-based tool called the Viral Host Range database to record, analyze and disseminate experimental host range data for viruses infecting archaea, bacteria and eukaryotes. Availability and implementation The ViralHostRangeDB application is available from https://viralhostrangedb.pasteur.cloud. Its source code is freely available from the Gitlab instance of Institut Pasteur (https://gitlab.pasteur.fr/hub/viralhostrangedb).

Published
2020
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8. High-Resolution Typing of Staphylococcus epidermidis Based on Core Genome Multilocus Sequence Typing To Investigate the Hospital Spread of Multidrug-Resistant Clones

Author

Jamet, Anne, primary, Guglielmini, Julien, additional, Brancotte, Bryan, additional, Coureuil, Mathieu, additional, Euphrasie, Daniel, additional, Meyer, Julie, additional, Roux, Johanna, additional, Barnier, Jean-Philippe, additional, Bille, Emmanuelle, additional, Ferroni, Agnès, additional, Magny, Jean-François, additional, Bôle-Feysot, Christine, additional, Charbit, Alain, additional, Nassif, Xavier, additional, and Brisse, Sylvain, additional

Published
2021
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11. Community curation of bioinformatics software and data resources

Author

Ison, Jon, Ménager, Hervé, Brancotte, Bryan, Jaaniso, Erik, Salumets, Ahto, Raček, Tomáš, Lamprecht, Anna-Lena, Palmblad, Magnus, Kalaš, Matúš, Chmura, Piotr, Hancock, John M, Schwämmle, Veit, Ienasescu, Hans-Ioan, Sub Software Technology, Software Technology, Sub Software Technology, Software Technology, National Life Science Supercomputing Center [Kongens Lyngby, Denmark] (Computerome), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institute of Computer Science [University of Tartu, Estonie], University of Tartu, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Faculty of Informatics [Brno] (FI / MUNI), Masaryk University [Brno] (MUNI), Department of Information and Computing Sciences [Utrecht], Utrecht University [Utrecht], Center for Proteomics and Metabolomics [Leiden] (CPM), Leiden University Medical Center (LUMC), Universiteit Leiden-Universiteit Leiden, Department of Informatics [Bergen] (UiB), University of Bergen (UiB), Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), ELIXIR Hub [Cambridge], University of Southern Denmark (SDU), We acknowledge with gratitude the support of our funders: The Danish Ministry of Higher Education and Science and ELIXIR-EXCELERATE under the European Union’s Horizon 2020 research and innovation programme (grant agreement number 676559), European Project: 676559,H2020,H2020-INFRADEV-1-2015-1,ELIXIR-EXCELERATE(2015), Technical University of Denmark [Lyngby] (DTU), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)

Subjects
AcademicSubjects/SCI01060, Computer science, community driven, registry, 03 medical and health sciences, Software, Bioinformatics software, Humans, Molecular Biology, database, 030304 developmental biology, Life Scientists, 0303 health sciences, business.industry, software, 030302 biochemistry & molecular biology, Community Participation, Computational Biology, bioinformatics, curation, Service provider, Data science, Data resources, Europe, Database Management Systems, Problem Solving Protocol, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, Information Systems
Abstract

The corpus of bioinformatics resources is huge and expanding rapidly, presenting life scientists with a growing challenge in selecting tools that fit the desired purpose. To address this, the European Infrastructure for Biological Information is supporting a systematic approach towards a comprehensive registry of tools and databases for all domains of bioinformatics, provided under a single portal (https://bio.tools). We describe here the practical means by which scientific communities, including individual developers and projects, through major service providers and research infrastructures, can describe their own bioinformatics resources and share these via bio.tools.

Published
2019
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12. Community curation of bioinformatics software and data resources

Author

Ison, Jon, Ménager, Hervé, Brancotte, Bryan, Jaaniso, Erik, Salumets, Ahto, Raček, Tomáš, Lamprecht, Anna-Lena, Palmblad, Magnus, Kalaš, Matúš, Chmura, Piotr Jaroslaw, Hancock, John M, Schwämmle, Veit, Ioan Ienasescu, Hans, Ison, Jon, Ménager, Hervé, Brancotte, Bryan, Jaaniso, Erik, Salumets, Ahto, Raček, Tomáš, Lamprecht, Anna-Lena, Palmblad, Magnus, Kalaš, Matúš, Chmura, Piotr Jaroslaw, Hancock, John M, Schwämmle, Veit, and Ioan Ienasescu, Hans

Abstract

The corpus of bioinformatics resources is huge and expanding rapidly, presenting life scientists with a growing challenge in selecting tools that fit the desired purpose. To address this, the European Infrastructure for Biological Information is supporting a systematic approach towards a comprehensive registry of tools and databases for all domains of bioinformatics, provided under a single portal (https://bio.tools). We describe here the practical means by which scientific communities, including individual developers and projects, through major service providers and research infrastructures, can describe their own bioinformatics resources and share these via bio.tools.

Published
2020

13. Community curation of bioinformatics software and data resources

Author

Sub Software Technology, Software Technology, Ison, Jon, Ménager, Hervé, Brancotte, Bryan, Jaaniso, Erik, Salumets, Ahto, Raček, Tomáš, Lamprecht, Anna-Lena, Palmblad, Magnus, Kalaš, Matúš, Chmura, Piotr, Hancock, John M, Schwämmle, Veit, Ienasescu, Hans-Ioan, Sub Software Technology, Software Technology, Ison, Jon, Ménager, Hervé, Brancotte, Bryan, Jaaniso, Erik, Salumets, Ahto, Raček, Tomáš, Lamprecht, Anna-Lena, Palmblad, Magnus, Kalaš, Matúš, Chmura, Piotr, Hancock, John M, Schwämmle, Veit, and Ienasescu, Hans-Ioan

Published
2019

16. High-Resolution Typing of Staphylococcus epidermidisBased on Core Genome Multilocus Sequence Typing To Investigate the Hospital Spread of Multidrug-Resistant Clones

Author

Jamet, Anne, Guglielmini, Julien, Brancotte, Bryan, Coureuil, Mathieu, Euphrasie, Daniel, Meyer, Julie, Roux, Johanna, Barnier, Jean-Philippe, Bille, Emmanuelle, Ferroni, Agnès, Magny, Jean-François, Bôle-Feysot, Christine, Charbit, Alain, Nassif, Xavier, and Brisse, Sylvain

Abstract

Staphylococcus epidermidisis a pathogen emerging worldwide as a leading cause of health care-associated infections. A standardized high-resolution typing method to document transmission and dissemination of multidrug-resistant S. epidermidisstrains is needed.

Published
2020
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17. Multi-Cloud deployment for microbial genomes analysis

Author

Lorenzo, Jonathan, Brancotte, Bryan, Lacroix, Thomas, BEDRI, Mohamed, Gibrat, Jean-Francois, and BLANCHET, Christophe

Subjects
virtual environment, bacterial genomics, synteny, bioinformatics tools, cloud infrastructures
Published
2017

18. BioFlow-Insight: facilitating reuse of Nextflow workflows with structure reconstruction and visualization.

Author

Marchment G, Brancotte B, Schmit M, Lemoine F, and Cohen-Boulakia S

Abstract

Bioinformatics workflows are increasingly used for sharing analyses, serving as a cornerstone for enhancing the reproducibility and shareability of bioinformatics analyses. In particular, Nextflow is a commonly used workflow system, permitting the creation of large workflows while offering substantial flexibility. An increasing number of Nextflow workflows are being shared on repositories such as GitHub. However, this tremendous opportunity to reuse existing code remains largely underutilized. In cause, the increasing complexity of workflows constitute a major obstacle to code reuse. Consequently, there is a rising need for tools that can help bioinformaticians extract valuable information from their own and others' workflows. To facilitate workflow inspection and reuse, we developed BioFlow-Insight to automatically analyze the code of Nextflow workflows and generate useful information, particularly in the form of visual graphs depicting the workflow's structure and representing its individual analysis steps. BioFlow-Insight is an open-source tool, available as both a command-line interface and a web service. It is accessible at https://pypi.org/project/bioflow-insight/ and https://bioflow-insight.pasteur.cloud/., (© The Author(s) 2024. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.)

Published
2024
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19. Trait selection strategy in multi-trait GWAS: Boosting SNPs discoverability.

Author

Suzuki Y, Ménager H, Brancotte B, Vernet R, Nerin C, Boetto C, Auvergne A, Linhard C, Torchet R, Lechat P, Troubat L, Cho MH, Bouzigon E, Aschard H, and Julienne H

Abstract

Since the first Genome-Wide Association Studies (GWAS), thousands of variant-trait associations have been discovered. However, the sample size required to detect additional variants using standard univariate association screening is increasingly prohibitive. Multi-trait GWAS offers a relevant alternative: it can improve statistical power and lead to new insights about gene function and the joint genetic architecture of human phenotypes. Although many methodological hurdles of multi-trait testing have been discussed, the strategy to select trait, among overwhelming possibilities, has been overlooked. In this study, we conducted extensive multi-trait tests using JASS (Joint Analysis of Summary Statistics) and assessed which genetic features of the analysed sets were associated with an increased detection of variants as compared to univariate screening. Our analyses identified multiple factors associated with the gain in the association detection in multi-trait tests. Together, these factors of the analysed sets are predictive of the gain of the multi-trait test (Pearson's ρ equal to 0.43 between the observed and predicted gain, P < 1.6 × 10 -60 ). Applying an alternative multi-trait approach (MTAG, multi-trait analysis of GWAS), we found that in most scenarios but particularly those with larger numbers of traits, JASS outperformed MTAG. Finally, we benchmark several strategies to select set of traits including the prevalent strategy of selecting clinically similar traits, which systematically underperformed selecting clinically heterogenous traits or selecting sets that issued from our data-driven models. This work provides a unique picture of the determinant of multi-trait GWAS statistical power and outline practical strategies for multi-trait testing., Competing Interests: Declaration of interests M.H.C. has received grant support from Bayer, unrelated to the current work.

Published
2023
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20. The iPPI-DB initiative: a community-centered database of protein-protein interaction modulators.

Author

Torchet R, Druart K, Ruano LC, Moine-Franel A, Borges H, Doppelt-Azeroual O, Brancotte B, Mareuil F, Nilges M, Ménager H, and Sperandio O

Abstract

Motivation: One avenue to address the paucity of clinically testable targets is to reinvestigate the druggable genome by tackling complicated types of targets such as Protein-Protein Interactions (PPIs). Given the challenge to target those interfaces with small chemical compounds, it has become clear that learning from successful examples of PPI modulation is a powerful strategy. Freely accessible databases of PPI modulators that provide the community with tractable chemical and pharmacological data, as well as powerful tools to query them, are therefore essential to stimulate new drug discovery projects on PPI targets., Results: Here, we present the new version iPPI-DB, our manually curated database of PPI modulators. In this completely redesigned version of the database, we introduce a new web interface relying on crowdsourcing for the maintenance of the database. This interface was created to enable community contributions, whereby external experts can suggest new database entries. Moreover, the data model, the graphical interface, and the tools to query the database have been completely modernized and improved. We added new PPI modulators, new PPI targets and extended our focus to stabilizers of PPIs as well., Availability and Implementation: The iPPI-DB server is available at https://ippidb.pasteur.fr The source code for this server is available at https://gitlab.pasteur.fr/ippidb/ippidb-web/ and is distributed under GPL licence (http://www.gnu.org/licences/gpl). Queries can be shared through persistent links according to the FAIR data standards. Data can be downloaded from the website as csv files., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2021. Published by Oxford University Press.)

Published
2021
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21. Community curation of bioinformatics software and data resources.

Author

Ison J, Ménager H, Brancotte B, Jaaniso E, Salumets A, Raček T, Lamprecht AL, Palmblad M, Kalaš M, Chmura P, Hancock JM, Schwämmle V, and Ienasescu HI

Subjects
Computational Biology standards, Database Management Systems, Europe, Humans, Community Participation, Computational Biology methods, Software
Abstract

The corpus of bioinformatics resources is huge and expanding rapidly, presenting life scientists with a growing challenge in selecting tools that fit the desired purpose. To address this, the European Infrastructure for Biological Information is supporting a systematic approach towards a comprehensive registry of tools and databases for all domains of bioinformatics, provided under a single portal (https://bio.tools). We describe here the practical means by which scientific communities, including individual developers and projects, through major service providers and research infrastructures, can describe their own bioinformatics resources and share these via bio.tools., (© The Author(s) 2019. Published by Oxford University Press.)

Published
2020
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