The Experts below are selected from a list of 102234 Experts worldwide ranked by ideXlab platform
Jan Hannemann - One of the best experts on this subject based on the ideXlab platform.
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xeml lab a tool that supports the design of experiments at a Graphical Interface and generates computer readable metadata files which capture information about genotypes growth conditions environmental perturbations and sampling strategy
Plant Cell and Environment, 2009Co-Authors: Jan Hannemann, Hendrik Poorter, Bjorn Usadel, Oliver Blasing, Alex Finck, Francois Tardieu, Owen K Atkin, Thijs L Pons, Mark StittAbstract:Data mining depends on the ability to access machine-readable metadata that describe genotypes, environmental conditions, and sampling times and strategy. This article presents Xeml Lab. The Xeml Interactive Designer provides an interactive Graphical Interface at which complex experiments can be designed, and concomitantly generates machine-readable metadata files. It uses a new eXtensible Mark-up Language (XML)-derived dialect termed XEML. Xeml Lab includes a new ontology for environmental conditions, called Xeml Environment Ontology. However, to provide versatility, it is designed to be generic and also accepts other commonly used ontology formats, including OBO and OWL. A review summarizing important environmental conditions that need to be controlled, monitored and captured as metadata is posted in a Wiki (http://www.codeplex.com/XeO) to promote community discussion. The usefulness of Xeml Lab is illustrated by two meta-analyses of a large set of experiments that were performed with Arabidopsis thaliana during 5 years. The first reveals sources of noise that affect measurements of metabolite levels and enzyme activities. The second shows that Arabidopsis maintains remarkably stable levels of sugars and amino acids across a wide range of photoperiod treatments, and that adjustment of starch turnover and the leaf protein content contribute to this metabolic homeostasis.
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Xeml Lab: a tool that supports the design of experiments at a Graphical Interface and generates computer‐readable metadata files, which capture information about genotypes, growth conditions, environmental perturbations and sampling strategy
Plant cell & environment, 2009Co-Authors: Jan Hannemann, Hendrik Poorter, Bjorn Usadel, Oliver Blasing, Alex Finck, Francois Tardieu, Owen K Atkin, Thijs L Pons, Mark Stitt, Yves GibonAbstract:Data mining depends on the ability to access machine-readable metadata that describe genotypes, environmental conditions, and sampling times and strategy. This article presents Xeml Lab. The Xeml Interactive Designer provides an interactive Graphical Interface at which complex experiments can be designed, and concomitantly generates machine-readable metadata files. It uses a new eXtensible Mark-up Language (XML)-derived dialect termed XEML. Xeml Lab includes a new ontology for environmental conditions, called Xeml Environment Ontology. However, to provide versatility, it is designed to be generic and also accepts other commonly used ontology formats, including OBO and OWL. A review summarizing important environmental conditions that need to be controlled, monitored and captured as metadata is posted in a Wiki (http://www.codeplex.com/XeO) to promote community discussion. The usefulness of Xeml Lab is illustrated by two meta-analyses of a large set of experiments that were performed with Arabidopsis thaliana during 5 years. The first reveals sources of noise that affect measurements of metabolite levels and enzyme activities. The second shows that Arabidopsis maintains remarkably stable levels of sugars and amino acids across a wide range of photoperiod treatments, and that adjustment of starch turnover and the leaf protein content contribute to this metabolic homeostasis.
Mark Stitt - One of the best experts on this subject based on the ideXlab platform.
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xeml lab a tool that supports the design of experiments at a Graphical Interface and generates computer readable metadata files which capture information about genotypes growth conditions environmental perturbations and sampling strategy
Plant Cell and Environment, 2009Co-Authors: Jan Hannemann, Hendrik Poorter, Bjorn Usadel, Oliver Blasing, Alex Finck, Francois Tardieu, Owen K Atkin, Thijs L Pons, Mark StittAbstract:Data mining depends on the ability to access machine-readable metadata that describe genotypes, environmental conditions, and sampling times and strategy. This article presents Xeml Lab. The Xeml Interactive Designer provides an interactive Graphical Interface at which complex experiments can be designed, and concomitantly generates machine-readable metadata files. It uses a new eXtensible Mark-up Language (XML)-derived dialect termed XEML. Xeml Lab includes a new ontology for environmental conditions, called Xeml Environment Ontology. However, to provide versatility, it is designed to be generic and also accepts other commonly used ontology formats, including OBO and OWL. A review summarizing important environmental conditions that need to be controlled, monitored and captured as metadata is posted in a Wiki (http://www.codeplex.com/XeO) to promote community discussion. The usefulness of Xeml Lab is illustrated by two meta-analyses of a large set of experiments that were performed with Arabidopsis thaliana during 5 years. The first reveals sources of noise that affect measurements of metabolite levels and enzyme activities. The second shows that Arabidopsis maintains remarkably stable levels of sugars and amino acids across a wide range of photoperiod treatments, and that adjustment of starch turnover and the leaf protein content contribute to this metabolic homeostasis.
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Xeml Lab: a tool that supports the design of experiments at a Graphical Interface and generates computer‐readable metadata files, which capture information about genotypes, growth conditions, environmental perturbations and sampling strategy
Plant cell & environment, 2009Co-Authors: Jan Hannemann, Hendrik Poorter, Bjorn Usadel, Oliver Blasing, Alex Finck, Francois Tardieu, Owen K Atkin, Thijs L Pons, Mark Stitt, Yves GibonAbstract:Data mining depends on the ability to access machine-readable metadata that describe genotypes, environmental conditions, and sampling times and strategy. This article presents Xeml Lab. The Xeml Interactive Designer provides an interactive Graphical Interface at which complex experiments can be designed, and concomitantly generates machine-readable metadata files. It uses a new eXtensible Mark-up Language (XML)-derived dialect termed XEML. Xeml Lab includes a new ontology for environmental conditions, called Xeml Environment Ontology. However, to provide versatility, it is designed to be generic and also accepts other commonly used ontology formats, including OBO and OWL. A review summarizing important environmental conditions that need to be controlled, monitored and captured as metadata is posted in a Wiki (http://www.codeplex.com/XeO) to promote community discussion. The usefulness of Xeml Lab is illustrated by two meta-analyses of a large set of experiments that were performed with Arabidopsis thaliana during 5 years. The first reveals sources of noise that affect measurements of metabolite levels and enzyme activities. The second shows that Arabidopsis maintains remarkably stable levels of sugars and amino acids across a wide range of photoperiod treatments, and that adjustment of starch turnover and the leaf protein content contribute to this metabolic homeostasis.
Emmanuel Talla - One of the best experts on this subject based on the ideXlab platform.
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VisualTE: a Graphical Interface for transposable element analysis at the genomic scale
BMC genomics, 2015Co-Authors: Sébastien Tempel, Emmanuel TallaAbstract:Transposable elements are mobile DNA repeat sequences, known to have high impact on genes, genome structure and evolution. This has stimulated broad interest in the detailed biological studies of transposable elements. Hence, we have developed an easy-to-use tool for the comparative analysis of the structural organization and functional relationships of transposable elements, to help understand their functional role in genomes. We named our new software VisualTE and describe it here. VisualTE is a JAVA stand-alone Graphical Interface that allows users to visualize and analyze all occurrences of transposable element families in annotated genomes. VisualTE reads and extracts transposable elements and genomic information from annotation and repeat data. Result analyses are displayed in several Graphical panels that include location and distribution on the chromosome, the occurrence of transposable elements in the genome, their size distribution, and neighboring genes’ features and ontologies. With these hallmarks, VisualTE provides a convenient tool for studying transposable element copies and their functional relationships with genes, at the whole-genome scale, and in diverse organisms. VisualTE Graphical Interface makes possible comparative analyses of transposable elements in any annotated sequence as well as structural organization and functional relationships between transposable elements and other genetic object. This tool is freely available at: http://lcb.cnrs-mrs.fr/spip.php?article867 .
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SOFTWARE Open Access VisualTE: a Graphical Interface for transposable element analysis at the genomic scale
BMC Genomics, 2015Co-Authors: Sébastien Tempel, Emmanuel TallaAbstract:Background: Transposable elements are mobile DNA repeat sequences, known to have high impact on genes, genome structure and evolution. This has stimulated broad interest in the detailed biological studies of transposable elements. Hence, we have developed an easy-to-use tool for the comparative analysis of the structural organization and functional relationships of transposable elements, to help understand their functional role in genomes. Results: We named our new software VisualTE and describe it here. VisualTE is a JAVA stand-alone Graphical Interface that allows users to visualize and analyze all occurrences of transposable element families in annotated genomes. VisualTE reads and extracts transposable elements and genomic information from annotation and repeat data. Result analyses are displayed in several Graphical panels that include location and distribution on the chromosome, the occurrence of transposable elements in the genome, their size distribution, and neighboring genes' features and ontologies. With these hallmarks, VisualTE provides a convenient tool for studying transposable element copies and their functional relationships with genes, at the whole-genome scale, and in diverse organisms. Conclusions: VisualTE Graphical Interface makes possible comparative analyses of transposable elements in any annotated sequence as well as structural organization and functional relationships between transposable elements and other genetic object. This tool is freely available at: http://lcb.cnrs-mrs.fr/spip.php?article867.
Yves Gibon - One of the best experts on this subject based on the ideXlab platform.
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Xeml Lab: a tool that supports the design of experiments at a Graphical Interface and generates computer‐readable metadata files, which capture information about genotypes, growth conditions, environmental perturbations and sampling strategy
Plant cell & environment, 2009Co-Authors: Jan Hannemann, Hendrik Poorter, Bjorn Usadel, Oliver Blasing, Alex Finck, Francois Tardieu, Owen K Atkin, Thijs L Pons, Mark Stitt, Yves GibonAbstract:Data mining depends on the ability to access machine-readable metadata that describe genotypes, environmental conditions, and sampling times and strategy. This article presents Xeml Lab. The Xeml Interactive Designer provides an interactive Graphical Interface at which complex experiments can be designed, and concomitantly generates machine-readable metadata files. It uses a new eXtensible Mark-up Language (XML)-derived dialect termed XEML. Xeml Lab includes a new ontology for environmental conditions, called Xeml Environment Ontology. However, to provide versatility, it is designed to be generic and also accepts other commonly used ontology formats, including OBO and OWL. A review summarizing important environmental conditions that need to be controlled, monitored and captured as metadata is posted in a Wiki (http://www.codeplex.com/XeO) to promote community discussion. The usefulness of Xeml Lab is illustrated by two meta-analyses of a large set of experiments that were performed with Arabidopsis thaliana during 5 years. The first reveals sources of noise that affect measurements of metabolite levels and enzyme activities. The second shows that Arabidopsis maintains remarkably stable levels of sugars and amino acids across a wide range of photoperiod treatments, and that adjustment of starch turnover and the leaf protein content contribute to this metabolic homeostasis.
Hendrik Poorter - One of the best experts on this subject based on the ideXlab platform.
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xeml lab a tool that supports the design of experiments at a Graphical Interface and generates computer readable metadata files which capture information about genotypes growth conditions environmental perturbations and sampling strategy
Plant Cell and Environment, 2009Co-Authors: Jan Hannemann, Hendrik Poorter, Bjorn Usadel, Oliver Blasing, Alex Finck, Francois Tardieu, Owen K Atkin, Thijs L Pons, Mark StittAbstract:Data mining depends on the ability to access machine-readable metadata that describe genotypes, environmental conditions, and sampling times and strategy. This article presents Xeml Lab. The Xeml Interactive Designer provides an interactive Graphical Interface at which complex experiments can be designed, and concomitantly generates machine-readable metadata files. It uses a new eXtensible Mark-up Language (XML)-derived dialect termed XEML. Xeml Lab includes a new ontology for environmental conditions, called Xeml Environment Ontology. However, to provide versatility, it is designed to be generic and also accepts other commonly used ontology formats, including OBO and OWL. A review summarizing important environmental conditions that need to be controlled, monitored and captured as metadata is posted in a Wiki (http://www.codeplex.com/XeO) to promote community discussion. The usefulness of Xeml Lab is illustrated by two meta-analyses of a large set of experiments that were performed with Arabidopsis thaliana during 5 years. The first reveals sources of noise that affect measurements of metabolite levels and enzyme activities. The second shows that Arabidopsis maintains remarkably stable levels of sugars and amino acids across a wide range of photoperiod treatments, and that adjustment of starch turnover and the leaf protein content contribute to this metabolic homeostasis.
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Xeml Lab: a tool that supports the design of experiments at a Graphical Interface and generates computer‐readable metadata files, which capture information about genotypes, growth conditions, environmental perturbations and sampling strategy
Plant cell & environment, 2009Co-Authors: Jan Hannemann, Hendrik Poorter, Bjorn Usadel, Oliver Blasing, Alex Finck, Francois Tardieu, Owen K Atkin, Thijs L Pons, Mark Stitt, Yves GibonAbstract:Data mining depends on the ability to access machine-readable metadata that describe genotypes, environmental conditions, and sampling times and strategy. This article presents Xeml Lab. The Xeml Interactive Designer provides an interactive Graphical Interface at which complex experiments can be designed, and concomitantly generates machine-readable metadata files. It uses a new eXtensible Mark-up Language (XML)-derived dialect termed XEML. Xeml Lab includes a new ontology for environmental conditions, called Xeml Environment Ontology. However, to provide versatility, it is designed to be generic and also accepts other commonly used ontology formats, including OBO and OWL. A review summarizing important environmental conditions that need to be controlled, monitored and captured as metadata is posted in a Wiki (http://www.codeplex.com/XeO) to promote community discussion. The usefulness of Xeml Lab is illustrated by two meta-analyses of a large set of experiments that were performed with Arabidopsis thaliana during 5 years. The first reveals sources of noise that affect measurements of metabolite levels and enzyme activities. The second shows that Arabidopsis maintains remarkably stable levels of sugars and amino acids across a wide range of photoperiod treatments, and that adjustment of starch turnover and the leaf protein content contribute to this metabolic homeostasis.
