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 | Acceso al texto completo restringido a Biblioteca INIA Las Brujas. Por información adicional contacte bibliolb@inia.org.uy. |
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Registro completo
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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha : |
29/09/2014 |
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Actualizado : |
09/10/2019 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Autor : |
COLE, J.B.; NEWMAN, S.; FOERTTER, F.; AGUILAR, I. |
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Afiliación : |
IGNACIO AGUILAR GARCIA, Instituto Nacional de Investigación Agropecuaria (INIA), Uruguay. |
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Título : |
Breeding and genetics symposium: Really big data: Processing and analysis of very large data sets. |
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Fecha de publicación : |
2012 |
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Fuente / Imprenta : |
Journal of Animal Science, 2012, v.90, no.3, p.723-733. |
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ISSN : |
0021-8812 |
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DOI : |
10.2527/jas.2011-4584 |
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Idioma : |
Inglés |
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Notas : |
Article history: Received: 11 August 2011 / Accepted: 13 November 2011 / Published: 01 March 2012 . |
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Contenido : |
ABSTRACT.
Modern animal breeding data sets are large and getting larger, due in part to recent availability of high-density SNP arrays and cheap sequencing technology. High-performance computing methods for efficient data warehousing and analysis are under development. Financial and security considerations are important when using shared clusters. Sound software engineering practices are needed, and it is better to use existing solutions when possible. Storage requirements for genotypes are modest, although full-sequence data will require greater storage capacity. Storage requirements for intermediate and results files for genetic evaluations are much greater, particularly when multiple runs must be stored for research and validation studies. The greatest gains in accuracy from genomic selection have been realized for traits of low heritability, and there is increasing interest in new health and management traits. The collection of sufficient phenotypes to produce accurate evaluations may take many years, and high-reliability proofs for older bulls are needed to estimate marker effects. Data mining algorithms applied to large data sets may help identify unexpected relationships in the data, and improved visualization tools will provide insights. Genomic selection using large data requires a lot of computing power, particularly when large fractions of the population are genotyped. Theoretical improvements have made possible the inversion of large numerator relationship matrices, permitted the solving of large systems of equations, and produced fast algorithms for variance component estimation. Recent work shows that single-step approaches combining BLUP with a genomic relationship (G) matrix have similar computational requirements to traditional BLUP, and the limiting factor is the construction and inversion of G for many genotypes. A naïve algorithm for creating G for 14,000 individuals required almost 24 h to run, but custom libraries and parallel computing reduced that to 15 m. Large data sets also create challenges for the delivery of genetic evaluations that must be overcome in a way that does not disrupt the transition from conventional to genomic evaluations. Processing time is important, especially as real-time systems for on-farm decisions are developed. The ultimate value of these systems is to decrease time-to-results in research, increase accuracy in genomic evaluations, and accelerate rates of genetic improvement.
© 2012 American Society of Animal Science. All rights reserved. MenosABSTRACT.
Modern animal breeding data sets are large and getting larger, due in part to recent availability of high-density SNP arrays and cheap sequencing technology. High-performance computing methods for efficient data warehousing and analysis are under development. Financial and security considerations are important when using shared clusters. Sound software engineering practices are needed, and it is better to use existing solutions when possible. Storage requirements for genotypes are modest, although full-sequence data will require greater storage capacity. Storage requirements for intermediate and results files for genetic evaluations are much greater, particularly when multiple runs must be stored for research and validation studies. The greatest gains in accuracy from genomic selection have been realized for traits of low heritability, and there is increasing interest in new health and management traits. The collection of sufficient phenotypes to produce accurate evaluations may take many years, and high-reliability proofs for older bulls are needed to estimate marker effects. Data mining algorithms applied to large data sets may help identify unexpected relationships in the data, and improved visualization tools will provide insights. Genomic selection using large data requires a lot of computing power, particularly when large fractions of the population are genotyped. Theoretical improvements have made possible the inversion of large numerator relationship matri... Presentar Todo |
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Thesagro : |
EVALUACIONES GENÉTICAS; FENOTIPOS; GENETICA ANIMAL; MEJORAMIENTO GENETICO ANIMAL. |
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Asunto categoría : |
L10 Genética y mejoramiento animal |
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Marc : |
LEADER 03346naa a2200241 a 4500
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005 2019-10-09
008 2012 bl uuuu u00u1 u #d
022 $a0021-8812
024 7 $a10.2527/jas.2011-4584$2DOI
100 1 $aCOLE, J.B.
245 $aBreeding and genetics symposium$bReally big data: Processing and analysis of very large data sets.$h[electronic resource]
260 $c2012
500 $aArticle history: Received: 11 August 2011 / Accepted: 13 November 2011 / Published: 01 March 2012 .
520 $aABSTRACT. Modern animal breeding data sets are large and getting larger, due in part to recent availability of high-density SNP arrays and cheap sequencing technology. High-performance computing methods for efficient data warehousing and analysis are under development. Financial and security considerations are important when using shared clusters. Sound software engineering practices are needed, and it is better to use existing solutions when possible. Storage requirements for genotypes are modest, although full-sequence data will require greater storage capacity. Storage requirements for intermediate and results files for genetic evaluations are much greater, particularly when multiple runs must be stored for research and validation studies. The greatest gains in accuracy from genomic selection have been realized for traits of low heritability, and there is increasing interest in new health and management traits. The collection of sufficient phenotypes to produce accurate evaluations may take many years, and high-reliability proofs for older bulls are needed to estimate marker effects. Data mining algorithms applied to large data sets may help identify unexpected relationships in the data, and improved visualization tools will provide insights. Genomic selection using large data requires a lot of computing power, particularly when large fractions of the population are genotyped. Theoretical improvements have made possible the inversion of large numerator relationship matrices, permitted the solving of large systems of equations, and produced fast algorithms for variance component estimation. Recent work shows that single-step approaches combining BLUP with a genomic relationship (G) matrix have similar computational requirements to traditional BLUP, and the limiting factor is the construction and inversion of G for many genotypes. A naïve algorithm for creating G for 14,000 individuals required almost 24 h to run, but custom libraries and parallel computing reduced that to 15 m. Large data sets also create challenges for the delivery of genetic evaluations that must be overcome in a way that does not disrupt the transition from conventional to genomic evaluations. Processing time is important, especially as real-time systems for on-farm decisions are developed. The ultimate value of these systems is to decrease time-to-results in research, increase accuracy in genomic evaluations, and accelerate rates of genetic improvement. © 2012 American Society of Animal Science. All rights reserved.
650 $aEVALUACIONES GENÉTICAS
650 $aFENOTIPOS
650 $aGENETICA ANIMAL
650 $aMEJORAMIENTO GENETICO ANIMAL
700 1 $aNEWMAN, S.
700 1 $aFOERTTER, F.
700 1 $aAGUILAR, I.
773 $tJournal of Animal Science, 2012$gv.90, no.3, p.723-733.
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INIA Las Brujas (LB) |
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| Registros recuperados : 218 | |
| 21. |  | LEGARRA, A.; AGUILAR, I.; MISZTAL, I. Single step methods with a view towards poultry breeding. Volume Species Breeding: Poultry, 324. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 10., Vancouver, BC, Canada, August 17-22, 2014. p.324. Acknowledgements: This work has been financed by X-Gen and GenSSeq actions from SelGen metaprogram (INRA).| Tipo: Trabajos en Congresos/Conferencias |
| Biblioteca(s): INIA Las Brujas. |
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| 25. | | LEGARRA, A.; AGUILAR, I.; COLLEAU, J.J. Short communication: Methods to compute genomic inbreeding for ungenotyped individuals. Journal of Dairy Science, April 2020, Volume 103, Issue 4, Pages 3363-3367. Doi: https://doi.org/10.3168/jds.2019-17750 Article history: Received October 15, 2019. / Accepted December 18, 2019.
Corresponding author: A. Legarra - email: andres.legarra@inra.fr
This study was partially funded by the INRA (Paris, France) SELGEN funding metaprogram (Project...| Tipo: Artículos en Revistas Indexadas Internacionales | Circulación / Nivel : Internacional - -- |
| Biblioteca(s): INIA Las Brujas. |
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| 29. | | PRAVIA, M.I.; NAVAJAS, E.; AGUILAR, I.; RAVAGNOLO, O. Alternative models to predict residual feed intake in Hereford breed and effects on their breeding values accuracy. [48] Part 6 - Challenges - resource allocation and genetics of feed intake and efficiency. In: Proceedings of the World Congress on Genetics Applied to Livestock Production (WCGALP), 12., Rotterdam, the Netherlands, 3-8 July 2022. doi: https://doi.org/10.3920/978-90-8686-940-4_48 240-243. Article history: Published online: February 9, 2023 -- Corresponding author: María Isabel Pravia, email: mpravia@inia.org.uy| Tipo: Trabajos en Congresos/Conferencias |
| Biblioteca(s): INIA Las Brujas. |
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| 30. | | MASUDA, Y.; AGUILAR, I.; TSURUTA, S.; MISZTAL, I. Acceleration of computations in AI REML for single-step GBLUP models. Volume Methods and Tools: Statistical methods - linear and nonlinear models (Posters), 703. In: Proceedings of the World Congress on Genetics Applied to Livestock Production, 10., Vancouver, BC, Canada, August 17-22, 2014. p.703.| Tipo: Trabajos en Congresos/Conferencias |
| Biblioteca(s): INIA Las Brujas. |
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| 31. | | FRANCO, J.; FEED, O.; AGUILAR, I.; GIMENO, D.; NAVAJAS, E. ¿Afectamos la calidad del producto al cruzar? Calidad de la carne: pH y terneza. ln: INIA Tacuarembó. Seminario de actualización técnica, 23 de agosto, 2002. Cruzamientos en bovinos para carnes: Resultados FPTA 083. Tacuarembó, (Uruguay): INIA; Facultad de Agronomía, 2002. p. 63-67 (INIA Serie Actividades de Difusión ; 295) INIA Tacuarembó; Universidad de la República (Uruguay). Facultad de Agronomía; Universidad de la República (Uruguay). Facultad de Química; Frigorífico Tacuarembó; Universidad de la República (Uruguay). Facultad de Veterinaria; Caja...| Biblioteca(s): INIA Tacuarembó. |
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| 36. | | BERMANN, M.; MISZTAL, I.; LOURENCO, D.; AGUILAR, I.; LEGARRA, A. Definition of reliabilities for models with metafounders. [289] Part 17 - Challenges - improving genomic prediction. In: Proceedings of the World Congress on Genetics Applied to Livestock Production (WCGALP), 12., Rotterdam, the Netherlands, 3-8 July 2022. doi: https://doi.org/10.3920/978-90-8686-940-4_289 1217-1220. Article history: Published online: February 9, 2023. -- Corresponding author: A. Legarra, email: andres.legarra@inrae.fr -- Acknowledgment: This work received financing from European Unions' Horizon 2020 Research & Innovation Programme,...| Tipo: Trabajos en Congresos/Conferencias |
| Biblioteca(s): INIA Las Brujas. |
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| 38. | | FRANCO, J.; FEED, O.; GIMENO, D.; AGUILAR, I.; AVENDAÑO, S. Como cambia el rendimiento carnicero con los cruzamientos: calidad de la canal. ln: INIA Tacuarembó. Seminario de actualización técnica, 23 de agosto, 2002. Cruzamientos en bovinos para carnes: Resultados FPTA 083. Tacuarembó, (Uruguay): INIA; Facultad de Agronomía, 2002. p. 31-37 (INIA Serie Actividades de Difusión ; 295) INIA Tacuarembó; Universidad de la República (Uruguay). Facultad de Agronomía; Universidad de la República (Uruguay). Facultad de Química; Frigorífico Tacuarembó; Universidad de la República (Uruguay). Facultad de Veterinaria; Caja Notarial| Biblioteca(s): INIA Tacuarembó. |
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| Registros recuperados : 218 | |
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