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5. Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts

Author

Gallone, Brigida, Steensels, Jan, Prahl, Troels, Soriaga, Leah, Saels, Veerle, Herrera-Malaver, Beatriz, Merlevede, Adriaan, Roncoroni, Miguel, Voordeckers, Karin, Miraglia, Loren, Teiling, Clotilde, Steffy, Brian, Taylor, Maryann, Schwartz, Ariel, Richardson, Toby, White, Christopher, Baele, Guy, Maere, Steven, and Verstrepen, Kevin J.

Published
2016
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7. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

Author

Afgan, Enis, Nekrutenko, Anton, Grüning, Bjórn, Blankenberg, Daniel, Goecks, Jeremy, Schatz, Michael, Ostrovsky, Alexander, Mahmoud, Alexandru, Lonie, Andrew, Syme, Anna, Fouilloux, Anne, Bretaudeau, Anthony, Kumar, Anup, Eschenlauer, Arthur, Desanto, Assunta, Guerler, Aysam, Serrano-Solano, Beatriz, Batut, Bérénice, Grüning, Björn, Langhorst, Bradley, Carr, Bridget, Raubenolt, Bryan, Hyde, Cameron, Bromhead, Catherine, Barnett, Christopher, Royaux, Coline, Gallardo, Cristóbal, Fornika, Daniel, Baker, Dannon, Bouvier, Dave, Clements, Dave, de Lima Morais, David, Tabernero, David Lopez, Lariviere, Delphine, Nasr, Engy, Zambelli, Federico, Heyl, Florian, Psomopoulos, Fotis, Coppens, Frederik, Price, Gareth, Cuccuru, Gianmauro, Corguillé, Gildas Le, von Kuster, Greg, Akbulut, Gulsum Gudukbay, Rasche, Helena, Hotz, Hans-Rudolf, Eguinoa, Ignacio, Makunin, Igor, Ranawaka, Isuru, Taylor, James, Joshi, Jayadev, Hillman-Jackson, Jennifer, Chilton, John, Kamali, Kaivan, Suderman, Keith, Poterlowicz, Krzysztof, Yvan, Le Bras, Lopez-Delisle, Lucille, Sargent, Luke, Bassetti, Madeline, Tangaro, Marco Antonio, van den Beek, Marius, Čech, Martin, Bernt, Matthias, Fahrner, Matthias, Tekman, Mehmet, Föll, Melanie, Crusoe, Michael, Roncoroni, Miguel, Kucher, Natalie, Coraor, Nate, Stoler, Nicholas, Rhodes, Nick, Soranzo, Nicola, Pinter, Niko, Goonasekera, Nuwan, Moreno, Pablo, Videm, Pavankumar, Melanie, Petera, Mandreoli, Pietro, Jagtap, Pratik, Gu, Qiang, Weber, Ralf, Lazarus, Ross, Vorderman, Ruben, Hiltemann, Saskia, Golitsynskiy, Sergey, Garg, Shilpa, Bray, Simon, Gladman, Simon, Leo, Simone, Mehta, Subina, Griffin, Timothy, Jalili, Vahid, Yves, Vandenbrouck, Wen, Victor, Nagampalli, Vijay, Bacon, Wendi, de Koning, Willem, Maier, Wolfgang, Briggs, Peter, Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Pathology, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
[SDV]Life Sciences [q-bio], Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology
Abstract

Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with >230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations. Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with >230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.

Published
2022
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8. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses:2022 update

Author

Afgan, Enis, Nekrutenko, Anton, Grüning, Bjórn A., Blankenberg, Daniel, Goecks, Jeremy, Schatz, Michael C., Ostrovsky, Alexander E., Mahmoud, Alexandru, Lonie, Andrew J., Syme, Anna, Fouilloux, Anne, Bretaudeau, Anthony, Kumar, Anup, Eschenlauer, Arthur C., Desanto, Assunta D., Guerler, Aysam, Serrano-Solano, Beatriz, Batut, Bérénice, Grüning, Björn A., Langhorst, Bradley W., Carr, Bridget, Raubenolt, Bryan A., Hyde, Cameron J., Bromhead, Catherine J., Barnett, Christopher B., Royaux, Coline, Gallardo, Cristóbal, Fornika, Daniel J., Baker, Dannon, Bouvier, Dave, Clements, Dave, De Lima Morais, David A., Tabernero, D. L., Lariviere, Delphine, Nasr, Engy, Zambelli, Federico, Heyl, Florian, Psomopoulos, Fotis, Coppens, Frederik, Price, Gareth R., Cuccuru, Gianmauro, Corguillé, Gildas Le, Von Kuster, Greg, Akbulut, Gulsum Gudukbay, Rasche, Helena, Hans-Rudolf, Hotz, Eguinoa, Ignacio, Makunin, Igor, Ranawaka, Isuru J., Taylor, James P., Joshi, Jayadev, Hillman-Jackson, Jennifer, Chilton, John M., Kamali, Kaivan, Suderman, Keith, Poterlowicz, Krzysztof, Yvan, Le Bras, Lopez-Delisle, Lucille, Sargent, Luke, Bassetti, Madeline E., Tangaro, Marco Antonio, Van Den Beek, Marius, Cech, Martin, Bernt, Matthias, Fahrner, Matthias, Tekman, Mehmet, Föll, Melanie C., Crusoe, Michael R., Roncoroni, Miguel, Kucher, Natalie, Coraor, Nate, Stoler, Nicholas, Rhodes, Nick, Soranzo, Nicola, Pinter, Niko, Goonasekera, Nuwan A., Moreno, Pablo A., Videm, Pavankumar, Melanie, Petera, Mandreoli, Pietro, Jagtap, Pratik D., Gu, Qiang, Weber, Ralf J.M., Lazarus, Ross, Vorderman, Ruben H.P., Hiltemann, Saskia, Golitsynskiy, Sergey, Garg, Shilpa, Bray, Simon A., Gladman, Simon L., Leo, Simone, Mehta, Subina P., Griffin, Timothy J., Jalili, Vahid, Yves, Vandenbrouck, Wen, Victor, Nagampalli, Vijay K., Bacon, Wendi A., De Koning, Willem, Maier, Wolfgang, Briggs, Peter J., Afgan, Enis, Nekrutenko, Anton, Grüning, Bjórn A., Blankenberg, Daniel, Goecks, Jeremy, Schatz, Michael C., Ostrovsky, Alexander E., Mahmoud, Alexandru, Lonie, Andrew J., Syme, Anna, Fouilloux, Anne, Bretaudeau, Anthony, Kumar, Anup, Eschenlauer, Arthur C., Desanto, Assunta D., Guerler, Aysam, Serrano-Solano, Beatriz, Batut, Bérénice, Grüning, Björn A., Langhorst, Bradley W., Carr, Bridget, Raubenolt, Bryan A., Hyde, Cameron J., Bromhead, Catherine J., Barnett, Christopher B., Royaux, Coline, Gallardo, Cristóbal, Fornika, Daniel J., Baker, Dannon, Bouvier, Dave, Clements, Dave, De Lima Morais, David A., Tabernero, D. L., Lariviere, Delphine, Nasr, Engy, Zambelli, Federico, Heyl, Florian, Psomopoulos, Fotis, Coppens, Frederik, Price, Gareth R., Cuccuru, Gianmauro, Corguillé, Gildas Le, Von Kuster, Greg, Akbulut, Gulsum Gudukbay, Rasche, Helena, Hans-Rudolf, Hotz, Eguinoa, Ignacio, Makunin, Igor, Ranawaka, Isuru J., Taylor, James P., Joshi, Jayadev, Hillman-Jackson, Jennifer, Chilton, John M., Kamali, Kaivan, Suderman, Keith, Poterlowicz, Krzysztof, Yvan, Le Bras, Lopez-Delisle, Lucille, Sargent, Luke, Bassetti, Madeline E., Tangaro, Marco Antonio, Van Den Beek, Marius, Cech, Martin, Bernt, Matthias, Fahrner, Matthias, Tekman, Mehmet, Föll, Melanie C., Crusoe, Michael R., Roncoroni, Miguel, Kucher, Natalie, Coraor, Nate, Stoler, Nicholas, Rhodes, Nick, Soranzo, Nicola, Pinter, Niko, Goonasekera, Nuwan A., Moreno, Pablo A., Videm, Pavankumar, Melanie, Petera, Mandreoli, Pietro, Jagtap, Pratik D., Gu, Qiang, Weber, Ralf J.M., Lazarus, Ross, Vorderman, Ruben H.P., Hiltemann, Saskia, Golitsynskiy, Sergey, Garg, Shilpa, Bray, Simon A., Gladman, Simon L., Leo, Simone, Mehta, Subina P., Griffin, Timothy J., Jalili, Vahid, Yves, Vandenbrouck, Wen, Victor, Nagampalli, Vijay K., Bacon, Wendi A., De Koning, Willem, Maier, Wolfgang, and Briggs, Peter J.

Abstract

Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with >230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations., Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with >230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.

Published
2022

11. Supporting the COVID-19 Data portal: viral data cleaning from human reads and submission to ENA

Author

Frederik, Coppens, Roncoroni Miguel, Eguinoa Ignacio, and Droesbeke, Bert

Subjects
COVID-19, viral data
Abstract

Slides for the "Supporting the COVID-19 Data portal: viral data cleaning from human reads and submission to ENA” session of the 2nd Galaxy-ELIXIR webinar series: Open Data Infrastructures to tackle COVID-19 pandemic, organized in January/February 2021.

Published
2021
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13. Additional file 9: of Dissection of the molecular bases of genotype x environment interactions: a study of phenotypic plasticity of Saccharomyces cerevisiae in grape juices

Author

Peltier, Emilien, Sharma, Vikas, Raga, Maria MartĂ­, Roncoroni, Miguel, Bernard, Margaux, Jiranek, Vladimir, Gibon, Yves, and Marullo, Philippe

Abstract

Figure S4. Linkage between translocation markers in M2xF15 and SBxGN crosses. The data represented are the number of segregant according to their genotype for the marker next to the chromosomal break point. Genotypes A strong linkage is shown with less than 10% recombinants. (PDF 4 kb)

Published
2018
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14. Additional file 13: of Dissection of the molecular bases of genotype x environment interactions: a study of phenotypic plasticity of Saccharomyces cerevisiae in grape juices

Author

Peltier, Emilien, Sharma, Vikas, Raga, Maria Martí, Roncoroni, Miguel, Bernard, Margaux, Jiranek, Vladimir, Gibon, Yves, and Marullo, Philippe

Abstract

Figure S6. Variance explained by QTL according to cross. Each dot represent a QTL. Bigger points indicate average. There is no significant difference between the two cross (Wilcoxon test pval > 0,05). (PDF 721 kb)

Published
2018
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15. Additional file 8: of Dissection of the molecular bases of genotype x environment interactions: a study of phenotypic plasticity of Saccharomyces cerevisiae in grape juices

Author

Peltier, Emilien, Sharma, Vikas, Raga, Maria MartĂ­, Roncoroni, Miguel, Bernard, Margaux, Jiranek, Vladimir, Gibon, Yves, and Marullo, Philippe

Subjects
animal diseases, genetic processes, fungi, food and beverages
Abstract

Figure S3. Heritability is correlated to the number of QTLs detected. The data represented are the number of QTLs identified according by cross and by trait according to the average heritability by cross and by trait among the three conditions. (PDF 21 kb)

Published
2018
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16. Additional file 3: of Dissection of the molecular bases of genotype x environment interactions: a study of phenotypic plasticity of Saccharomyces cerevisiae in grape juices

Author

Peltier, Emilien, Sharma, Vikas, Raga, Maria MartĂ­, Roncoroni, Miguel, Bernard, Margaux, Jiranek, Vladimir, Gibon, Yves, and Marullo, Philippe

Abstract

Figure S1. Meiosis emphases phenotypic novelty. Panel A. PCA of winemaking properties of M2xF15 and SBxGN progenies and 31 CWS in M15. Panel B. Correlation circle indicating the correlation of the variables for axes 1 and 2. Panel C. Average phenotypic distance computed from M15 condition for CWS, and the two M2xF15 and SBxGN cross. (PDF 455 kb)

Published
2018
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17. Additional file 6: of Dissection of the molecular bases of genotype x environment interactions: a study of phenotypic plasticity of Saccharomyces cerevisiae in grape juices

Author

Peltier, Emilien, Sharma, Vikas, Raga, Maria MartĂ­, Roncoroni, Miguel, Bernard, Margaux, Jiranek, Vladimir, Gibon, Yves, and Marullo, Philippe

Subjects
Nuclear Experiment
Abstract

Figure S2. Clustering of Norm of reaction for each trait. Norm of reaction of each individual is shown in dotted line and are colored and faceted according their cluster. Solid line shown the average norm of reaction of each cluster. Number of strains within each cluster is indicated by n. (PDF 2768 kb)

Published
2018
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18. Transition between fermentation and respiration determines history-dependent behavior in fluctuating carbon sources

Author

Cerulus, Bram, primary, Jariani, Abbas, additional, Perez-Samper, Gemma, additional, Vermeersch, Lieselotte, additional, Pietsch, Julian MJ, additional, Crane, Matthew M, additional, New, Aaron M, additional, Gallone, Brigida, additional, Roncoroni, Miguel, additional, Dzialo, Maria C, additional, Govers, Sander K, additional, Hendrickx, Jhana O, additional, Galle, Eva, additional, Coomans, Maarten, additional, Berden, Pieter, additional, Verbandt, Sara, additional, Swain, Peter S, additional, and Verstrepen, Kevin J, additional

Published
2018
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19. Author response: Transition between fermentation and respiration determines history-dependent behavior in fluctuating carbon sources

Author

Cerulus, Bram, primary, Jariani, Abbas, additional, Perez-Samper, Gemma, additional, Vermeersch, Lieselotte, additional, Pietsch, Julian MJ, additional, Crane, Matthew M, additional, New, Aaron M, additional, Gallone, Brigida, additional, Roncoroni, Miguel, additional, Dzialo, Maria C, additional, Govers, Sander K, additional, Hendrickx, Jhana O, additional, Galle, Eva, additional, Coomans, Maarten, additional, Berden, Pieter, additional, Verbandt, Sara, additional, Swain, Peter S, additional, and Verstrepen, Kevin J, additional

Published
2018
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21. SARS-CoV-2 sequence submission tool for the European Nucleotide Archive.

Author

Roncoroni, Miguel, Droesbeke, Bert, Eguinoa, Ignacio, Ruyck, Kim De, D'Anna, Flora, Yusuf, Dilmurat, Grüning, Björn, Backofen, Rolf, and Coppens, Frederik

Subjects
*SARS-CoV-2, *COVID-19 pandemic, *GRAPHICAL user interfaces, *UPLOADING of data, *METADATA
Abstract

Summary Many aspects of the global response to the COVID-19 pandemic are enabled by the fast and open publication of SARS-CoV-2 genetic sequence data. The European Nucleotide Archive (ENA) is the European recommended open repository for genetic sequences. In this work, we present a tool for submitting raw sequencing reads of SARS-CoV-2 to ENA. The tool features a single-step submission process, a graphical user interface, tabular-formatted metadata and the possibility to remove human reads prior to submission. A Galaxy wrap of the tool allows users with little or no bioinformatics knowledge to do bulk sequencing read submissions. The tool is also packed in a Docker container to ease deployment. Availability and implementation CLI ENA upload tool is available at github.com/usegalaxy-eu/ena-upload-cli (DOI 10.5281/zenodo.4537621); Galaxy ENA upload tool at toolshed.g2.bx.psu.edu/view/iuc/ena_upload/382518f24d6d and github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload (development); and ENA upload Galaxy container at github.com/ELIXIR-Belgium/ena-upload-container (DOI 10.5281/zenodo.4730785). [ABSTRACT FROM AUTHOR]

Published
2021
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25. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

Author

Ostrovsky, Alexander E., Mahmoud, Alexandru, Lonie, Andrew J., Syme, Anna, Fouilloux, Anne, Bretaudeau, Anthony, Nekrutenko, Anton, Kumar, Anup, Eschenlauer, Arthur C., DeSanto, Assunta D., Guerler, Aysam, Serrano-Solano, Beatriz, Batut, Berenice, Gruening, Bjoern A., Langhorst, Bradley W., Carr, Bridget, Raubenolt, Bryan A., Hyde, Cameron J., Bromhead, Catherine J., Barnett, Christopher B., Royaux, Coline, Gallardo, Cristobal, Blankenberg, Daniel, Fornika, Daniel J., Baker, Dannon, Bouvier, Dave, Clements, Dave, Morais, David A. de Lima, Tabernero, David Lopez, Lariviere, Delphine, Nasr, Engy, Afgan, Enis, Zambelli, Federico, Heyl, Florian, Psomopoulos, Fotis, Coppens, Frederik, Price, Gareth R., Cuccuru, Gianmauro, Le Corguille, Gildas, Von Kuster, Greg, Akbulut, Gulsum Gudukbay, Rasche, Helena, Hans-Rudolf, Hotz, Eguinoa, Ignacio, Makunin, Igor, Ranawaka, Isuru J., Taylor, James P., Joshi, Jayadev, Hillman-Jackson, Jennifer, Goecks, Jeremy, Chilton, John M., Kamali, Kaivan, Suderman, Keith, Poterlowicz, Krzysztof, Yvan, Le Bras, Lopez-Delisle, Lucille, Sargent, Luke, Bassetti, Madeline E., Tangaro, Marco Antonio, van den Beek, Marius, Cech, Martin, Bernt, Matthias, Fahrner, Matthias, Tekman, Mehmet, Foell, Melanie C., Schatz, Michael C., Crusoe, Michael R., Roncoroni, Miguel, Kucher, Natalie, Coraor, Nate, Stoler, Nicholas, Rhodes, Nick, Soranzo, Nicola, Pinter, Niko, Goonasekera, Nuwan A., Moreno, Pablo A., Videm, Pavankumar, Melanie, Petera, Mandreoli, Pietro, Jagtap, Pratik D., Gu, Qiang, Weber, Ralf J. M., Lazarus, Ross, Vorderman, Ruben H. P., Hiltemann, Saskia, Golitsynskiy, Sergey, Garg, Shilpa, Bray, Simon A., Gladman, Simon L., Leo, Simone, Mehta, Subina P., Griffin, Timothy J., Jalili, Vahid, Yves, Vandenbrouck, Wen, Victor, Nagampalli, Vijay K., Bacon, Wendi A., de Koning, Willem, Maier, Wolfgang, and Briggs, Peter J.

Abstract

Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with >230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.

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