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1. mdx: A Cloud Platform for Supporting Data Science and Cross-Disciplinary Research Collaborations

Author

Suzumura, Toyotaro, Sugiki, Akiyoshi, Takizawa, Hiroyuki, Imakura, Akira, Nakamura, Hiroshi, Taura, Kenjiro, Kudoh, Tomohiro, Hanawa, Toshihiro, Sekiya, Yuji, Kobayashi, Hiroki, Matsushima, Shin, Kuga, Yohei, Nakamura, Ryo, Jiang, Renhe, Kawase, Junya, Hanai, Masatoshi, Miyazaki, Hiroshi, Ishizaki, Tsutomu, Shimotoku, Daisuke, Miyamoto, Daisuke, Aida, Kento, Takefusa, Atsuko, Kurimoto, Takashi, Sasayama, Koji, Kitagawa, Naoya, Fujiwara, Ikki, Tanimura, Yusuke, Aoki, Takayuki, Endo, Toshio, Ohshima, Satoshi, Fukazawa, Keiichiro, Date, Susumu, and Uchibayashi, Toshihiro

Subjects
Computer Science - Machine Learning, Computer Science - Computers and Society, Computer Science - Distributed, Parallel, and Cluster Computing
Abstract

The growing amount of data and advances in data science have created a need for a new kind of cloud platform that provides users with flexibility, strong security, and the ability to couple with supercomputers and edge devices through high-performance networks. We have built such a nation-wide cloud platform, called "mdx" to meet this need. The mdx platform's virtualization service, jointly operated by 9 national universities and 2 national research institutes in Japan, launched in 2021, and more features are in development. Currently mdx is used by researchers in a wide variety of domains, including materials informatics, geo-spatial information science, life science, astronomical science, economics, social science, and computer science. This paper provides an the overview of the mdx platform, details the motivation for its development, reports its current status, and outlines its future plans.

Published
2022

8. Multi-GPU Scaling of a Conservative Weakly Compressible Solver for Large-Scale Two-Phase Flow Simulation

Author

Yang, Kai, Aoki, Takayuki, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Takizawa, Hiroyuki, editor, Shen, Hong, editor, Hanawa, Toshihiro, editor, Hyuk Park, Jong, editor, Tian, Hui, editor, and Egawa, Ryusuke, editor

Published
2023
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9. Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a Monophyletic Fusarium that Includes the Fusarium solani Species Complex.

Author

Geiser, David M, Al-Hatmi, Abdullah MS, Aoki, Takayuki, Arie, Tsutomu, Balmas, Virgilio, Barnes, Irene, Bergstrom, Gary C, Bhattacharyya, Madan K, Blomquist, Cheryl L, Bowden, Robert L, Brankovics, Balázs, Brown, Daren W, Burgess, Lester W, Bushley, Kathryn, Busman, Mark, Cano-Lira, José F, Carrillo, Joseph D, Chang, Hao-Xun, Chen, Chi-Yu, Chen, Wanquan, Chilvers, Martin, Chulze, Sofia, Coleman, Jeffrey J, Cuomo, Christina A, de Beer, Z Wilhelm, de Hoog, G Sybren, Del Castillo-Múnera, Johanna, Del Ponte, Emerson M, Diéguez-Uribeondo, Javier, Di Pietro, Antonio, Edel-Hermann, Véronique, Elmer, Wade H, Epstein, Lynn, Eskalen, Akif, Esposto, Maria Carmela, Everts, Kathryne L, Fernández-Pavía, Sylvia P, da Silva, Gilvan Ferreira, Foroud, Nora A, Fourie, Gerda, Frandsen, Rasmus JN, Freeman, Stanley, Freitag, Michael, Frenkel, Omer, Fuller, Kevin K, Gagkaeva, Tatiana, Gardiner, Donald M, Glenn, Anthony E, Gold, Scott E, Gordon, Thomas R, Gregory, Nancy F, Gryzenhout, Marieka, Guarro, Josep, Gugino, Beth K, Gutierrez, Santiago, Hammond-Kosack, Kim E, Harris, Linda J, Homa, Mónika, Hong, Cheng-Fang, Hornok, László, Huang, Jenn-Wen, Ilkit, Macit, Jacobs, Adriaana, Jacobs, Karin, Jiang, Cong, Jiménez-Gasco, María Del Mar, Kang, Seogchan, Kasson, Matthew T, Kazan, Kemal, Kennell, John C, Kim, Hye-Seon, Kistler, H Corby, Kuldau, Gretchen A, Kulik, Tomasz, Kurzai, Oliver, Laraba, Imane, Laurence, Matthew H, Lee, Theresa, Lee, Yin-Won, Lee, Yong-Hwan, Leslie, John F, Liew, Edward CY, Lofton, Lily W, Logrieco, Antonio F, S López-Berges, Manuel, Luque, Alicia G, Lysøe, Erik, Ma, Li-Jun, Marra, Robert E, Martin, Frank N, May, Sara R, McCormick, Susan P, McGee, Chyanna, Meis, Jacques F, Migheli, Quirico, Mohamed Nor, NMI, Monod, Michel, Moretti, Antonio, Mostert, Diane, and Mulè, Giuseppina

Subjects
evolution, fungal pathogens, Plant Biology & Botany, Microbiology, Plant Biology, Crop and Pasture Production
Abstract

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available.

Published
2021

15. No to Neocosmospora: Phylogenomic and Practical Reasons for Continued Inclusion of the Fusarium solani Species Complex in the Genus Fusarium

Author

O’Donnell, Kerry, Al-Hatmi, Abdullah MS, Aoki, Takayuki, Brankovics, Balázs, Cano-Lira, José F, Coleman, Jeffrey J, de Hoog, G Sybren, Di Pietro, Antonio, Frandsen, Rasmus JN, Geiser, David M, Gibas, Connie FC, Guarro, Josep, Kim, Hye-Seon, Kistler, H Corby, Laraba, Imane, Leslie, John F, López-Berges, Manuel S, Lysøe, Erik, Meis, Jacques F, Monod, Michel, Proctor, Robert H, Rep, Martijn, Ruiz-Roldán, Carmen, Šišić, Adnan, Stajich, Jason E, Steenkamp, Emma T, Summerell, Brett A, van der Lee, Theo AJ, van Diepeningen, Anne D, Verweij, Paul E, Waalwijk, Cees, Ward, Todd J, Wickes, Brian L, Wiederhold, Nathan P, Wingfield, Michael J, Zhang, Ning, and Zhang, Sean X

Subjects
Microbiology, Biological Sciences, Infectious Diseases, Infection, Good Health and Well Being, Antifungal Agents, Fusarium, Phylogeny, clinical mycology, evolution, fungi, phylogenetics, taxonomy, Immunology
Abstract

This article is to alert medical mycologists and infectious disease specialists of recent name changes of medically important species of the filamentous mold FusariumFusarium species can cause localized and life-threating infections in humans. Of the 70 Fusarium species that have been reported to cause infections, close to one-third are members of the Fusarium solani species complex (FSSC), and they collectively account for approximately two-thirds of all reported Fusarium infections. Many of these species were recently given scientific names for the first time by a research group in the Netherlands, but they were misplaced in the genus Neocosmospora In this paper, we present genetic arguments that strongly support inclusion of the FSSC in Fusarium There are potentially serious consequences associated with using the name Neocosmospora for Fusarium species because clinicians need to be aware that fusaria are broadly resistant to the spectrum of antifungals that are currently available.

Published
2020

16. No to Neocosmospora: Phylogenomic and Practical Reasons for Continued Inclusion of the Fusarium solani Species Complex in the Genus Fusarium.

Author

O'Donnell, Kerry, Al-Hatmi, Abdullah MS, Aoki, Takayuki, Brankovics, Balázs, Cano-Lira, José F, Coleman, Jeffrey J, de Hoog, G Sybren, Di Pietro, Antonio, Frandsen, Rasmus JN, Geiser, David M, Gibas, Connie FC, Guarro, Josep, Kim, Hye-Seon, Kistler, H Corby, Laraba, Imane, Leslie, John F, López-Berges, Manuel S, Lysøe, Erik, Meis, Jacques F, Monod, Michel, Proctor, Robert H, Rep, Martijn, Ruiz-Roldán, Carmen, Šišić, Adnan, Stajich, Jason E, Steenkamp, Emma T, Summerell, Brett A, van der Lee, Theo AJ, van Diepeningen, Anne D, Verweij, Paul E, Waalwijk, Cees, Ward, Todd J, Wickes, Brian L, Wiederhold, Nathan P, Wingfield, Michael J, Zhang, Ning, and Zhang, Sean X

Subjects
Fusarium, Antifungal Agents, Phylogeny, clinical mycology, evolution, fungi, phylogenetics, taxonomy, Infectious Diseases, Infection
Abstract

This article is to alert medical mycologists and infectious disease specialists of recent name changes of medically important species of the filamentous mold Fusarium Fusarium species can cause localized and life-threating infections in humans. Of the 70 Fusarium species that have been reported to cause infections, close to one-third are members of the Fusarium solani species complex (FSSC), and they collectively account for approximately two-thirds of all reported Fusarium infections. Many of these species were recently given scientific names for the first time by a research group in the Netherlands, but they were misplaced in the genus Neocosmospora In this paper, we present genetic arguments that strongly support inclusion of the FSSC in Fusarium There are potentially serious consequences associated with using the name Neocosmospora for Fusarium species because clinicians need to be aware that fusaria are broadly resistant to the spectrum of antifungals that are currently available.

Published
2020

18. New High Performance GPGPU Code Transformation Framework Applied to Large Production Weather Prediction Code

Author

Müller, Michel and Aoki, Takayuki

Subjects
Computer Science - Distributed, Parallel, and Cluster Computing, Physics - Atmospheric and Oceanic Physics
Abstract

We introduce "Hybrid Fortran", a new approach that allows a high performance GPGPU port for structured grid Fortran codes. This technique only requires minimal changes for a CPU targeted codebase, which is a significant advancement in terms of productivity. It has been successfully applied to both dynamical core and physical processes of ASUCA, a Japanese mesoscale weather prediction model with more than 150k lines of code. By means of a minimal weather application that resembles ASUCA's code structure, Hybrid Fortran is compared to both a performance model as well as today's commonly used method, OpenACC. As a result, the Hybrid Fortran implementation is shown to deliver the same or better performance than OpenACC and its performance agrees with the model both on CPU and GPU. In a full scale production run, using an ASUCA grid with 1581 x 1301 x 58 cells and real world weather data in 2km resolution, 24 NVIDIA Tesla P100 running the Hybrid Fortran based GPU port are shown to replace more than 50 18-core Intel Xeon Broadwell E5-2695 v4 running the reference implementation - an achievement comparable to more invasive GPGPU rewrites of other weather models., Comment: Preprint as accepted for ACM TOPC

Published
2018

23. Hybrid Fortran: High Productivity GPU Porting Framework Applied to Japanese Weather Prediction Model

Author

Müller, Michel and Aoki, Takayuki

Subjects
Computer Science - Distributed, Parallel, and Cluster Computing, Physics - Atmospheric and Oceanic Physics
Abstract

In this work we use the GPU porting task for the operative Japanese weather prediction model "ASUCA" as an opportunity to examine productivity issues with OpenACC when applied to structured grid problems. We then propose "Hybrid Fortran", an approach that combines the advantages of directive based methods (no rewrite of existing code necessary) with that of stencil DSLs (memory layout is abstracted). This gives the ability to define multiple parallelizations with different granularities in the same code. Without compromising on performance, this approach enables a major reduction in the code changes required to achieve a hybrid GPU/CPU parallelization - as demonstrated with our ASUCA implementation using Hybrid Fortran., Comment: Preprint as accepted for WACCPD 2017, final version to appear in Springer LNCS

Published
2017

24. Considerations and consequences of allowing DNA sequence data as types of fungal taxa.

Author

Zamora, Juan, Svensson, Måns, Kirschner, Roland, Olariaga, Ibai, Ryman, Svengunnar, Parra, Luis, Geml, József, Rosling, Anna, Adamčík, Slavomír, Ahti, Teuvo, Aime, M, Ainsworth, A, Albert, László, Albertó, Edgardo, García, Alberto, Ageev, Dmitry, Agerer, Reinhard, Aguirre-Hudson, Begoña, Ammirati, Joe, Andersson, Harry, Angelini, Claudio, Antonín, Vladimír, Aoki, Takayuki, Aptroot, André, Argaud, Didier, Sosa, Blanca, Aronsen, Arne, Arup, Ulf, Asgari, Bita, Assyov, Boris, Atienza, Violeta, Bandini, Ditte, Baptista-Ferreira, João, Baral, Hans-Otto, Baroni, Tim, Barreto, Robert, Beker, Henry, Bell, Ann, Bellanger, Jean-Michel, Bellù, Francesco, Bemmann, Martin, Bendiksby, Mika, Bendiksen, Egil, Bendiksen, Katriina, Benedek, Lajos, Bérešová-Guttová, Anna, Berger, Franz, Berndt, Reinhard, Bernicchia, Annarosa, Biketova, Alona, Bizio, Enrico, Bjork, Curtis, Boekhout, Teun, Boertmann, David, Böhning, Tanja, Boittin, Florent, Boluda, Carlos, Boomsluiter, Menno, Borovička, Jan, Brandrud, Tor, Braun, Uwe, Brodo, Irwin, Bulyonkova, Tatiana, Burdsall, Harold, Buyck, Bart, Burgaz, Ana, Calatayud, Vicent, Callac, Philippe, Campo, Emanuele, Candusso, Massimo, Capoen, Brigitte, Carbó, Joaquim, Carbone, Matteo, Castañeda-Ruiz, Rafael, Castellano, Michael, Chen, Jie, Clerc, Philippe, Consiglio, Giovanni, Corriol, Gilles, Courtecuisse, Régis, Crespo, Ana, Cripps, Cathy, Crous, Pedro, da Silva, Gladstone, da Silva, Meiriele, Dam, Marjo, Dam, Nico, Dämmrich, Frank, Das, Kanad, Davies, Linda, De Crop, Eske, De Kesel, Andre, De Lange, Ruben, De Madrignac Bonzi, Bárbara, Dela Cruz, Thomas, Delgat, Lynn, Demoulin, Vincent, Desjardin, Dennis, Diederich, Paul, and Dima, Bálint

Subjects
IMC11, nomenclature, speciation, taxonomy, typification, voucherless fungi
Abstract

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.

Published
2018

27. A Perspective on the SPPEXA Collaboration from Japan

Author

Aoki, Takayuki, Barth, Timothy J., Series Editor, Griebel, Michael, Series Editor, Keyes, David E., Series Editor, Nieminen, Risto M., Series Editor, Roose, Dirk, Series Editor, Schlick, Tamar, Series Editor, Bungartz, Hans-Joachim, editor, Reiz, Severin, editor, Uekermann, Benjamin, editor, Neumann, Philipp, editor, and Nagel, Wolfgang E., editor

Published
2020
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31. Fungal taxonomy and sequence-based nomenclature

Author

Lücking, Robert, Aime, M. Catherine, Robbertse, Barbara, Miller, Andrew N., Aoki, Takayuki, Ariyawansa, Hiran A., Cardinali, Gianluigi, Crous, Pedro W., Druzhinina, Irina S., Geiser, David M., Hawksworth, David L., Hyde, Kevin D., Irinyi, Laszlo, Jeewon, Rajesh, Johnston, Peter R., Kirk, Paul M., Malosso, Elaine, May, Tom W., Meyer, Wieland, Nilsson, Henrik R., Öpik, Maarja, Robert, Vincent, Stadler, Marc, Thines, Marco, Vu, Duong, Yurkov, Andrey M., Zhang, Ning, and Schoch, Conrad L.

Published
2021
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41. How to publish a new fungal species, or name, version 3.0

Author

Aime, M. Catherine, Miller, Andrew N., Aoki, Takayuki, Bensch, Konstanze, Cai, Lei, Crous, Pedro W., Hawksworth, David L., Hyde, Kevin D., Kirk, Paul M., Lücking, Robert, May, Tom W., Malosso, Elaine, Redhead, Scott A., Rossman, Amy Y., Stadler, Marc, Thines, Marco, Yurkov, Andrey M., Zhang, Ning, and Schoch, Conrad L.

Published
2021
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43. Hybrid Fortran: High Productivity GPU Porting Framework Applied to Japanese Weather Prediction Model

Author

Müller, Michel, Aoki, Takayuki, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Chandrasekaran, Sunita, editor, and Juckeland, Guido, editor

Published
2018
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