Search Results - "Sallou, Olivier"

BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers by Bai, Jingwen, Bandla, Chakradhar, Guo, Jiaxin, Vera Alvarez, Roberto, Bai, Mingze, Vizcaíno, Juan Antonio, Moreno, Pablo, Grüning, Björn, Sallou, Olivier, Perez-Riverol, Yasset

“…BioContainers is an open-source project that aims to create, store, and distribute bioinformatics software containers and packages. The BioContainers community…”
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The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community by Darde, Thomas A, Sallou, Olivier, Becker, Emmanuelle, Evrard, Bertrand, Monjeaud, Cyril, Le Bras, Yvan, Jégou, Bernard, Collin, Olivier, Rolland, Antoine D, Chalmel, Frédéric

“…We report the development of the ReproGenomics Viewer (RGV), a multi- and cross-species working environment for the visualization, mining and comparison of…”
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The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes by Ouedraogo, Marion, Bettembourg, Charles, Bretaudeau, Anthony, Sallou, Olivier, Diot, Christian, Demeure, Olivier, Lecerf, Frédéric

“…There has been a surge in studies linking genome structure and gene expression, with special focus on duplicated genes. Although initially duplicated from the…”
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Recommendations for the packaging and containerizing of bioinformatics software [version 2; peer review: 2 approved, 1 approved with reservations] by Gruening, Bjorn, Sallou, Olivier, Moreno, Pablo, da Veiga Leprevost, Felipe, Ménager, Hervé, Søndergaard, Dan, Röst, Hannes, Sachsenberg, Timo, O'Connor, Brian, Madeira, Fábio, Dominguez Del Angel, Victoria, Crusoe, Michael R, Varma, Susheel, Blankenberg, Daniel, Jimenez, Rafael C, Perez-Riverol, Yasset

“…Software Containers are changing the way scientists and researchers develop, deploy and exchange scientific software. They allow labs of all sizes to easily…”
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BioShaDock: a community driven bioinformatics shared Docker-based tools registry [version 1; peer review: 2 approved] by Moreews, François, Sallou, Olivier, Ménager, Hervé, Le bras, Yvan, Monjeaud, Cyril, Blanchet, Christophe, Collin, Olivier

“…Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific…”
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Seqcrawler: biological data indexing and browsing platform by Sallou, Olivier, Bretaudeau, Anthony, Roult, Aurelien

“…Seqcrawler takes its roots in software like SRS or Lucegene. It provides an indexing platform to ease the search of data and meta-data in biological banks and…”
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High-Resolution Profiling of Novel Transcribed Regions During Rat Spermatogenesis1 by Chalmel, Frédéric, Lardenois, Aurélie, Evrard, Bertrand, Rolland, Antoine D, Sallou, Olivier, Dumargne, Marie-Charlotte, Coiffec, Isabelle, Collin, Olivier, Primig, Michael, Jégou, Bernard

“…Mammalian spermatogenesis is a complex and highly orchestrated combination of processes in which male germline proliferation and differentiation result in the…”
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SRD: a Staphylococcus regulatory RNA database by Sassi, Mohamed, Augagneur, Yoann, Mauro, Tony, Ivain, Lorraine, Chabelskaya, Svetlana, Hallier, Marc, Sallou, Olivier, Felden, Brice

“…An overflow of regulatory RNAs (sRNAs) was identified in a wide range of bacteria. We designed and implemented a new resource for the hundreds of sRNAs…”
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GO-Docker: A Batch Scheduling System with Docker Containers by Sallou, Olivier, Monjeaud, Cyril

“…Multi user open source batch scheduling software based on Docker containers with custom scheduler and executor plugin mechanisms…”
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High-resolution profiling of novel transcribed regions during rat spermatogenesis by Chalmel, Frédéric, Lardenois, Aurélie, Evrard, Bertrand, Rolland, Antoine D, Sallou, Olivier, Dumargne, Marie-Charlotte, Coiffec, Isabelle, Collin, Olivier, Primig, Michael, Jégou, Bernard

“…Mammalian spermatogenesis is a complex and highly orchestrated combination of processes in which male germline proliferation and differentiation result in the…”
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TOXsIgN: a cross-species repository for toxicogenomic signatures by Darde, Thomas A, Gaudriault, Pierre, Beranger, Rémi, Lancien, Clément, Caillarec-Joly, Annaëlle, Sallou, Olivier, Bonvallot, Nathalie, Chevrier, Cécile, Mazaud-Guittot, Séverine, Jégou, Bernard, Collin, Olivier, Becker, Emmanuelle, Rolland, Antoine D, Chalmel, Frédéric

“…Abstract Motivation At the same time that toxicologists express increasing concern about reproducibility in this field, the development of dedicated databases…”
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GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development by Britto, Ramona, Sallou, Olivier, Collin, Olivier, Michaux, Grégoire, Primig, Michael, Chalmel, Frédéric

“…We present gene prioritization system (GPSy), a cross-species gene prioritization system that facilitates the arduous but critical task of prioritizing genes…”
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Community-driven development for computational biology at Sprints, Hackathons and Codefests by Möller, Steffen, Afgan, Enis, Banck, Michael, Bonnal, Raoul J P, Booth, Timothy, Chilton, John, Cock, Peter J A, Gumbel, Markus, Harris, Nomi, Holland, Richard, Kalaš, Matúš, Kaján, László, Kibukawa, Eri, Powel, David R, Prins, Pjotr, Quinn, Jacqueline, Sallou, Olivier, Strozzi, Francesco, Seemann, Torsten, Sloggett, Clare, Soiland-Reyes, Stian, Spooner, William, Steinbiss, Sascha, Tille, Andreas, Travis, Anthony J, Guimera, Roman, Katayama, Toshiaki, Chapman, Brad A

“…Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the…”
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The GAG database: A new resource to gather genomic annotation cross-references by Obadia, T., Sallou, O., Ouedraogo, M., Guernec, G., Lecerf, F.

“…Several institutions provide genomic annotation data, and therefore these data show a significant segmentation and redundancy. Public databases allow access,…”
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PepPSy: a web server to prioritize gene products in experimental and biocuration workflows by Sallou, Olivier, Duek, Paula D, Darde, Thomas A, Collin, Olivier, Lane, Lydie, Chalmel, Frédéric

“…Among the 20 000 human gene products predicted from genome annotation, about 3000 still lack validation at protein level. We developed PepPSy, a user-friendly…”
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Recommendations for the packaging and containerizing of bioinformatics software [version 1; peer review: 2 approved with reservations] by Gruening, Bjorn, Sallou, Olivier, Moreno, Pablo, da Veiga Leprevost, Felipe, Ménager, Hervé, Søndergaard, Dan, Röst, Hannes, Sachsenberg, Timo, O'Connor, Brian, Madeira, Fábio, Dominguez Del Angel, Victoria, Crusoe, Michael R, Varma, Susheel, Blankenberg, Daniel, Jimenez, Rafael C, Perez-Riverol, Yasset

“…Software Containers are changing the way scientists and researchers develop, deploy and exchange scientific software. They allow labs of all sizes to easily…”
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AnnotQTL: a new tool to gather functional and comparative information on a genomic region by Lecerf, F., Bretaudeau, A., Sallou, O., Desert, C., Blum, Y., Lagarrigue, S., Demeure, O.

“…AnnotQTL is a web tool designed to aggregate functional annotations from different prominent web sites by minimizing the redundancy of information. Although…”
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