Workflows Community Summit 2022: A Roadmap Revolution

Authors: da Silva, Rafael Ferreira, Badia, Rosa M., Bala, Venkat, Bard, Debbie, Bremer, Peer-Timo, Buckley, Ian, Caino-Lores, Silvina, Chard, Kyle, Goble, Carole, Jha, Shantenu, Katz, Daniel S., Laney, Daniel, Parashar, Manish, Suter, Frederic, Tyler, Nick, Uram, Thomas, Altintas, Ilkay, Andersson, Stefan, Arndt, William, Aznar, Juan, Bader, Jonathan, Balis, Bartosz, Blanton, Chris, Braghetto, Kelly Rosa, Brodutch, Aharon, Brunk, Paul, Casanova, Henri, Lierta, Alba Cervera, Chigu, Justin, Coleman, Taina, Collier, Nick, Colonnelli, Iacopo, Coppens, Frederik, Crusoe, Michael, Cunningham, Will, Kinoshita, Bruno de Paula, Di Tommaso, Paolo, Doutriaux, Charles, Downton, Matthew, Elwasif, Wael, Enders, Bjoern, Erdmann, Chris, Fahringer, Thomas, Figueiredo, Ludmilla, Filgueira, Rosa, Foltin, Martin, Fouilloux, Anne, Gadelha, Luiz, Gallo, Andy, Saez, Artur Garcia, Garijo, Daniel, Gerlach, Roman, Grant, Ryan, Grayson, Samuel, Grubel, Patricia, Gustafsson, Johan, Hayot-Sasson, Valerie, Hernandez, Oscar, Hilbrich, Marcus, Justine, AnnMary, Laflotte, Ian, Lehmann, Fabian, Luckow, Andre, Luettgau, Jakob, Maheshwari, Ketan, Matsuda, Motohiko, Medic, Doriana, Mendygral, Pete, Michalewicz, Marek, Nonaka, Jorji, Pawlik, Maciej, Pottier, Loic, Pouchard, Line, Putz, Mathias, Radha, Santosh Kumar, Ramakrishnan, Lavanya, Ristov, Sashko, Romano, Paul, Rosendo, Daniel, Ruefenacht, Martin, Rycerz, Katarzyna, Saurabh, Nishant, Savchenko, Volodymyr, Schulz, Martin, Simpson, Christine, Sirvent, Raul, Skluzacek, Tyler, Soiland-Reyes, Stian, Souza, Renan, Sukumar, Sreenivas Rangan, Sun, Ziheng, Sussman, Alan, Thain, Douglas, Titov, Mikhail, Tovar, Benjamin, Tripathy, Aalap, Turilli, Matteo, Tuznik, Bartosz, van Dam, Hubertus, Vivas, Aurelio, Ward, Logan, Widener, Patrick, Wilkinson, Sean, Zawalska, Justyna, Zulfiqar, Mahnoor

Subject Terms: Computer Science - Distributed, Parallel, and Cluster Computing

Access URL: http://arxiv.org/abs/2304.00019

Workflows Community Summit: Bringing the Scientific Workflows Community Together

Authors: da Silva, Rafael Ferreira, Casanova, Henri, Chard, Kyle, Laney, Dan, Ahn, Dong, Jha, Shantenu, Goble, Carole, Ramakrishnan, Lavanya, Peterson, Luc, Enders, Bjoern, Thain, Douglas, Altintas, Ilkay, Babuji, Yadu, Badia, Rosa M., Bonazzi, Vivien, Coleman, Taina, Crusoe, Michael, Deelman, Ewa, Di Natale, Frank, Di Tommaso, Paolo, Fahringer, Thomas, Filgueira, Rosa, Fursin, Grigori, Ganose, Alex, Gruning, Bjorn, Katz, Daniel S., Kuchar, Olga, Kupresanin, Ana, Ludascher, Bertram, Maheshwari, Ketan, Mattoso, Marta, Mehta, Kshitij, Munson, Todd, Ozik, Jonathan, Peterka, Tom, Pottier, Loic, Randles, Tim, Soiland-Reyes, Stian, Tovar, Benjamin, Turilli, Matteo, Uram, Thomas, Vahi, Karan, Wilde, Michael, Wolf, Matthew, Wozniak, Justin

Subject Terms: Computer Science - Distributed, Parallel, and Cluster Computing

Access URL: http://arxiv.org/abs/2103.09181

Multiple Sequence Alignment Computation Using the T-Coffee Regressive Algorithm Implementation

Authors: Garriga, Edgar, Di Tommaso, Paolo, Magis, Cedrik, Erb, Ionas, Mansouri, Leila, Baltzis, Athanasios, Floden, Evan, Notredame, Cedric

Source: Methods in molecular biology. 2231:89-98

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN625406442&indx=1&recIds=ETOCRN625406442

Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty

Authors: Chatzou, Maria, Floden, Evan W., Di Tommaso, Paolo, Gascuel, Olivier, Notredame, Cedric

Source: Systematic Biology, 2018 Nov 01. 67(6), 997-1009.

Access URL: https://www.jstor.org/stable/26582223

Scalable Workflows and Reproducible Data Analysis for Genomics

Authors: Strozzi, Francesco, Janssen, Roel, Wurmus, Ricardo, Crusoe, Michael R., Githinji, George, Di Tommaso, Paolo, Belhachemi, Dominique, Möller, Steffen, Smant, Geert, Ligt, Joepde

Source: Methods in molecular biology. 1910:723-746

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN620866130&indx=1&recIds=ETOCRN620866130

Large multiple sequence alignments with a root-to-leaf regressive method

Authors: Garriga, Edgar, Di Tommaso, Paolo, Magis, Cedrik, Erb, Ionas, Mansouri, Leila, Baltzis, Athanasios, Laayouni, Hafid, Kondrashov, Fyodor, Floden, Evan, Notredame, Cedric

Source: Nature biotechnology. 37(12):1466-1470

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100193223251.0x000001&indx=1&recIds=ETOCvdc_100193223251.0x000001

Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee

Authors: Chang Jia-Ming, Di Tommaso Paolo, Taly Jean-François, Notredame Cedric

Source: BMC Bioinformatics, Vol 13, Iss Suppl 4, p S1 (2012)

Subject Terms: Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/8adc409df8e54c66a00bd63b0401b101

This result is not displayed to guests.
Login for full access.

This result is not displayed to guests.
Login for full access.

This result is not displayed to guests.
Login for full access.

Nextflow : un outil efficace pour l'amélioration de la stabilité numérique des calculs en analyse génomique. (French)

Alternate Title: Nextflow, an efficient tool to improve computation numerical stability in genomic analysis. (English)

Authors: Di Tommaso, Paolo, Floden, Evan W., Magis, Cedrik, Palumbo, Emilio, Notredame, Cedric

Source: Biologie Aujourd'hui; 2017, Vol. 211 Issue 3, p233-237, 5p

The nf-core framework for community-curated bioinformatics pipelines.

Authors: Ewels, Philip A., Peltzer, Alexander, Fillinger, Sven, Patel, Harshil, Alneberg, Johannes, Wilm, Andreas, Garcia, Maxime Ulysse, Di Tommaso, Paolo, Nahnsen, Sven

Source: Nature Biotechnology; Mar2020, Vol. 38 Issue 3, p276-278, 3p, 1 Diagram

This result is not displayed to guests.
Login for full access.

This result is not displayed to guests.
Login for full access.

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction.

Authors: Jia-Ming Chang, Di Tommaso, Paolo, Lefort, Vincent, Gascuel, Olivier, Notredame, Cedric

Source: Nucleic Acids Research; 7/1/2015, Vol. 43 Issue W1, pW3-W6, 4p

T-Coffee: Tree-Based Consistency Objective Function for Alignment Evaluation.

Authors: Magis, Cedrik, Taly, Jean-François, Bussotti, Giovanni, Chang, Jia-Ming, Di Tommaso, Paolo, Erb, Ionas, Espinosa-Carrasco, José, Notredame, Cedric

Source: Multiple Sequence Alignment Methods; 2014, p117-129, 13p

This result is not displayed to guests.
Login for full access.

This result is not displayed to guests.
Login for full access.

Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud.

Authors: Di Tommaso, Paolo, Orobitg, Miquel, Guirado, Fernando

Source: Bioinformatics; August 1 2010, Vol. 26 Issue 15, p1903-1904, 2p

This result is not displayed to guests.
Login for full access.