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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital. |
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Data corrente: |
05/10/2020 |
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Data da última atualização: |
06/10/2020 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
MUDADU, M. de A.; ZERLOTINI NETO, A. |
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Afiliação: |
MAURICIO DE ALVARENGA MUDADU, CNPTIA; ADHEMAR ZERLOTINI NETO, CNPTIA. |
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Título: |
Machado: open source genomics data integration framework. |
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Ano de publicação: |
2020 |
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Fonte/Imprenta: |
GigaScience, v. 9, n. 9, p. 1-16, Sept. 2020. |
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DOI: |
10.1093/gigascience/giaa097 |
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Idioma: |
Inglês |
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Notas: |
Na publicação: Adhemar Zerlotini. |
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Conteúdo: |
Abstract. Background: Genome projects and multiomics experiments generate huge volumes of data that must be stored, mined, and transformed into useful knowledge. All this information is supposed to be accessible and, if possible, browsable afterwards. Computational biologists have been dealing with this scenario for more than a decade and have been implementing software and databases to meet this challenge. The GMOD's (Generic Model Organism Database) biological relational database schema, known as Chado, is one of the few successful open source initiatives; it is widely adopted and many software packages are able to connect to it. Findings: We have been developing an open source software package named Machado, a genomics data integration framework implemented in Python, to enable research groups to both store and visualize genomics data. The framework relies on the Chado database schema and, therefore, should be very intuitive for current developers to adopt it or have it running on top of already existing databases. It has several data-loading tools for genomics and transcriptomics data and also for annotation results from tools such as BLAST, InterproScan, OrthoMCL, and LSTrAP. There is an API to connect to JBrowse, and a web visualization tool is implemented using Django Views and Templates. The Haystack library integrated with the ElasticSearch engine was used to implement a Google-like search, i.e., single auto-complete search box that provides fast results and filters. Conclusion: Machado aims to be a modern object-relational framework that uses the latest Python libraries to produce an effective open source resource for genomics research. MenosAbstract. Background: Genome projects and multiomics experiments generate huge volumes of data that must be stored, mined, and transformed into useful knowledge. All this information is supposed to be accessible and, if possible, browsable afterwards. Computational biologists have been dealing with this scenario for more than a decade and have been implementing software and databases to meet this challenge. The GMOD's (Generic Model Organism Database) biological relational database schema, known as Chado, is one of the few successful open source initiatives; it is widely adopted and many software packages are able to connect to it. Findings: We have been developing an open source software package named Machado, a genomics data integration framework implemented in Python, to enable research groups to both store and visualize genomics data. The framework relies on the Chado database schema and, therefore, should be very intuitive for current developers to adopt it or have it running on top of already existing databases. It has several data-loading tools for genomics and transcriptomics data and also for annotation results from tools such as BLAST, InterproScan, OrthoMCL, and LSTrAP. There is an API to connect to JBrowse, and a web visualization tool is implemented using Django Views and Templates. The Haystack library integrated with the ElasticSearch engine was used to implement a Google-like search, i.e., single auto-complete search box that provides fast results and filters... Mostrar Tudo |
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Palavras-Chave: |
Chado; Dados genômicos; Multiomics. |
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Thesagro: |
Base de Dados. |
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Thesaurus Nal: |
Genomics; Python. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/216418/1/AP-Machado-2020.pdf
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Marc: |
LEADER 02322naa a2200229 a 4500
001 2125289
005 2020-10-06
008 2020 bl uuuu u00u1 u #d
024 7 $a10.1093/gigascience/giaa097$2DOI
100 1 $aMUDADU, M. de A.
245 $aMachado$bopen source genomics data integration framework.$h[electronic resource]
260 $c2020
500 $aNa publicação: Adhemar Zerlotini.
520 $aAbstract. Background: Genome projects and multiomics experiments generate huge volumes of data that must be stored, mined, and transformed into useful knowledge. All this information is supposed to be accessible and, if possible, browsable afterwards. Computational biologists have been dealing with this scenario for more than a decade and have been implementing software and databases to meet this challenge. The GMOD's (Generic Model Organism Database) biological relational database schema, known as Chado, is one of the few successful open source initiatives; it is widely adopted and many software packages are able to connect to it. Findings: We have been developing an open source software package named Machado, a genomics data integration framework implemented in Python, to enable research groups to both store and visualize genomics data. The framework relies on the Chado database schema and, therefore, should be very intuitive for current developers to adopt it or have it running on top of already existing databases. It has several data-loading tools for genomics and transcriptomics data and also for annotation results from tools such as BLAST, InterproScan, OrthoMCL, and LSTrAP. There is an API to connect to JBrowse, and a web visualization tool is implemented using Django Views and Templates. The Haystack library integrated with the ElasticSearch engine was used to implement a Google-like search, i.e., single auto-complete search box that provides fast results and filters. Conclusion: Machado aims to be a modern object-relational framework that uses the latest Python libraries to produce an effective open source resource for genomics research.
650 $aGenomics
650 $aPython
650 $aBase de Dados
653 $aChado
653 $aDados genômicos
653 $aMultiomics
700 1 $aZERLOTINI NETO, A.
773 $tGigaScience$gv. 9, n. 9, p. 1-16, Sept. 2020.
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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Registro Completo
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Biblioteca(s): |
Embrapa Soja. |
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Data corrente: |
09/10/2013 |
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Data da última atualização: |
04/04/2022 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
A - 2 |
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Autoria: |
MORAES, M. T. de; DEBIASI, H.; FRANCHINI, J. C.; SILVA, V. R. da. |
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Afiliação: |
MOACIR T. DE MORAES, UFRGS; HENRIQUE DEBIASI, CNPSO; JULIO CEZAR FRANCHINI DOS SANTOS, CNPSO; VANDERLEI R. DA SILVA, UFSM. |
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Título: |
Soil penetration resistance in a rhodic eutrudox affected by machinery traffic and soil water content. |
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Ano de publicação: |
2013 |
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Fonte/Imprenta: |
Engenharia Agrícola, Jaboticabal, v. 33, n. 4, p. 748-757, jul./ago. 2013. |
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ISSN: |
0100-6916 |
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Idioma: |
Inglês |
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Conteúdo: |
ABSTRACT: Soil compaction caused by machinery traffic reduces crop yields. This study aimed to evaluate the effects of intensive traffic, and the soil water content, on the soil penetration resistance (PR) of a Rhodic Eutrudox (Distroferric Red Latosol, Brazilian Classification), managed under no-tillage (NT). The experiment consisted of six treatments: NT with recent chiseling, NT without additional compaction, and NT with additional compaction by 4, 8, 10 and 20 passes of a harvester with a weight of 100 kN (70 kN on the front axle). Undisturbed soil samples were collected at 5.5-10.5 cm and 13.5-18.5 cm depth to quantify the soil bulk density (BD). The PR was assessed in four periods, using an impact penetrometer, inserted in the soil to a depth of 46 cm. The effect of traffic intensities on the PR was small when this variable was assessed with the soil in the plastic consistency. Differences in PR among treatments increased as the soil water content decreased. The increase in the values of PR and BD was higher in the first passes, but the increase in the number of traffics resulted in deeper soil compaction. The machinery traffic effects on PR are better characterized in the friable soil consistency. RESUMO: A compactação do solo causada pelo tráfego de máquinas reduz a produtividade das culturas. O objetivo deste trabalho foi avaliar os efeitos do tráfego intensivo e do conteúdo de água do solo na resistência à penetração (PR) de um Latossolo Vermelho distroférrico, muito argiloso, manejado em sistema plantio direto (NT). O experimento foi composto por seis tratamentos: NT escarificado; NT sem compactação adicional; e NT com compactação adicional pelo tráfego de uma colhedora com massa de 100 kN (70 kN no eixo dianteiro) por 4; 8; 10 e 20 passadas. A densidade do solo (BD) foi determinada utilizando amostras indeformadas, coletadas nas camadas de 5,5-10,5 cm e 13,5-18,5 cm. A RP foi determinada em quatro épocas, utilizando um penetrômetro de impacto, inserido no solo até a profundidade de 46 cm. O efeito das intensidades de tráfego no NT sobre a PR foi pequeno quando esta variável foi avaliada com o solo na consistência plástica. As diferenças na PR entre os tratamentos aumentaram à medida que o conteúdo de água no momento da avaliação diminuiu. O aumento nos valores de PR e BD foi maior nas primeiras passadas, mas o incremento do número de tráfegos aumentou a profundidade de compactação do solo. O aumento da PR proporcionado pelo tráfego de máquinas é mais bem caracterizado quando determinado com o solo na consistência friável. MenosABSTRACT: Soil compaction caused by machinery traffic reduces crop yields. This study aimed to evaluate the effects of intensive traffic, and the soil water content, on the soil penetration resistance (PR) of a Rhodic Eutrudox (Distroferric Red Latosol, Brazilian Classification), managed under no-tillage (NT). The experiment consisted of six treatments: NT with recent chiseling, NT without additional compaction, and NT with additional compaction by 4, 8, 10 and 20 passes of a harvester with a weight of 100 kN (70 kN on the front axle). Undisturbed soil samples were collected at 5.5-10.5 cm and 13.5-18.5 cm depth to quantify the soil bulk density (BD). The PR was assessed in four periods, using an impact penetrometer, inserted in the soil to a depth of 46 cm. The effect of traffic intensities on the PR was small when this variable was assessed with the soil in the plastic consistency. Differences in PR among treatments increased as the soil water content decreased. The increase in the values of PR and BD was higher in the first passes, but the increase in the number of traffics resulted in deeper soil compaction. The machinery traffic effects on PR are better characterized in the friable soil consistency. RESUMO: A compactação do solo causada pelo tráfego de máquinas reduz a produtividade das culturas. O objetivo deste trabalho foi avaliar os efeitos do tráfego intensivo e do conteúdo de água do solo na resistência à penetração (PR) de um Latossolo Vermelho distroférrico, mui... Mostrar Tudo |
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Thesagro: |
Solo. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/90726/1/soil-penetration.pdf
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Marc: |
LEADER 03185naa a2200181 a 4500
001 1968194
005 2022-04-04
008 2013 bl uuuu u00u1 u #d
022 $a0100-6916
100 1 $aMORAES, M. T. de
245 $aSoil penetration resistance in a rhodic eutrudox affected by machinery traffic and soil water content.$h[electronic resource]
260 $c2013
520 $aABSTRACT: Soil compaction caused by machinery traffic reduces crop yields. This study aimed to evaluate the effects of intensive traffic, and the soil water content, on the soil penetration resistance (PR) of a Rhodic Eutrudox (Distroferric Red Latosol, Brazilian Classification), managed under no-tillage (NT). The experiment consisted of six treatments: NT with recent chiseling, NT without additional compaction, and NT with additional compaction by 4, 8, 10 and 20 passes of a harvester with a weight of 100 kN (70 kN on the front axle). Undisturbed soil samples were collected at 5.5-10.5 cm and 13.5-18.5 cm depth to quantify the soil bulk density (BD). The PR was assessed in four periods, using an impact penetrometer, inserted in the soil to a depth of 46 cm. The effect of traffic intensities on the PR was small when this variable was assessed with the soil in the plastic consistency. Differences in PR among treatments increased as the soil water content decreased. The increase in the values of PR and BD was higher in the first passes, but the increase in the number of traffics resulted in deeper soil compaction. The machinery traffic effects on PR are better characterized in the friable soil consistency. RESUMO: A compactação do solo causada pelo tráfego de máquinas reduz a produtividade das culturas. O objetivo deste trabalho foi avaliar os efeitos do tráfego intensivo e do conteúdo de água do solo na resistência à penetração (PR) de um Latossolo Vermelho distroférrico, muito argiloso, manejado em sistema plantio direto (NT). O experimento foi composto por seis tratamentos: NT escarificado; NT sem compactação adicional; e NT com compactação adicional pelo tráfego de uma colhedora com massa de 100 kN (70 kN no eixo dianteiro) por 4; 8; 10 e 20 passadas. A densidade do solo (BD) foi determinada utilizando amostras indeformadas, coletadas nas camadas de 5,5-10,5 cm e 13,5-18,5 cm. A RP foi determinada em quatro épocas, utilizando um penetrômetro de impacto, inserido no solo até a profundidade de 46 cm. O efeito das intensidades de tráfego no NT sobre a PR foi pequeno quando esta variável foi avaliada com o solo na consistência plástica. As diferenças na PR entre os tratamentos aumentaram à medida que o conteúdo de água no momento da avaliação diminuiu. O aumento nos valores de PR e BD foi maior nas primeiras passadas, mas o incremento do número de tráfegos aumentou a profundidade de compactação do solo. O aumento da PR proporcionado pelo tráfego de máquinas é mais bem caracterizado quando determinado com o solo na consistência friável.
650 $aSolo
700 1 $aDEBIASI, H.
700 1 $aFRANCHINI, J. C.
700 1 $aSILVA, V. R. da
773 $tEngenharia Agrícola, Jaboticabal$gv. 33, n. 4, p. 748-757, jul./ago. 2013.
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