scholarly journals TreeGenes: A Forest Tree Genome Database

2008 ◽  
Vol 2008 ◽  
pp. 1-7 ◽  
Author(s):  
Jill L. Wegrzyn ◽  
Jennifer M. Lee ◽  
Brandon R. Tearse ◽  
David B. Neale
Keyword(s):  
Data Retrieval ◽  
Forest Tree ◽  
Research Community ◽  
Genetic Maps ◽  
Data Types ◽  
Genome Database ◽  
Access Points ◽  
Web Resource ◽  
Wide Range ◽  
Visualization Tools

The Dendrome Project and associated TreeGenes database serve the forest genetics research community through a curated and integrated web-based relational database. The research community is composed of approximately 2 000 members representing over 730 organizations worldwide. The database itself is composed of a wide range of genetic data from many forest trees with focused efforts on commercially important members of the Pinaceae family. The primary data types curated include species, publications, tree and DNA extraction information, genetic maps, molecular markers, ESTs, genotypic, and phenotypic data. There are currently ten main search modules or user access points within this PostgreSQL database. These access points allow users to navigate logically through the related data types. The goals of the Dendrome Project are to (1) provide a comprehensive resource for forest tree genomics data to facilitate gene discovery in related species, (2) develop interfaces that encourage the submission and integration of all genomic data, and to (3) centralize and distribute existing and novel online tools for the research community that both support and ease analysis. Recent developments have focused on increasing data content, functional annotations, data retrieval, and visualization tools. TreeGenes was developed to provide a centralized web resource with analysis and visualization tools to support data storage and exchange.

scholarly journals SorghumBase: a web-based portal for sorghum genetic information and community advancement

Planta ◽  
2022 ◽  
Vol 255 (2) ◽  
Author(s):  
Nicholas Gladman ◽  
Andrew Olson ◽  
Sharon Wei ◽  
Kapeel Chougule ◽  
Zhenyuan Lu ◽  
...  
Keyword(s):  
Resource Sharing ◽  
Content Management ◽  
Research Community ◽  
Data Types ◽  
Training Materials ◽  
Wide Range ◽  
Variant Information ◽  
Data Collation ◽  
Genome Assemblies ◽  
User Friendly

Abstract Main conclusion SorghumBase provides a community portal that integrates genetic, genomic, and breeding resources for sorghum germplasm improvement. Abstract Public research and development in agriculture rely on proper data and resource sharing within stakeholder communities. For plant breeders, agronomists, molecular biologists, geneticists, and bioinformaticians, centralizing desirable data into a user-friendly hub for crop systems is essential for successful collaborations and breakthroughs in germplasm development. Here, we present the SorghumBase web portal (https://www.sorghumbase.org), a resource for the sorghum research community. SorghumBase hosts a wide range of sorghum genomic information in a modular framework, built with open-source software, to provide a sustainable platform. This initial release of SorghumBase includes: (1) five sorghum reference genome assemblies in a pan-genome browser; (2) genetic variant information for natural diversity panels and ethyl methanesulfonate (EMS)-induced mutant populations; (3) search interface and integrated views of various data types; (4) links supporting interconnectivity with other repositories including genebank, QTL, and gene expression databases; and (5) a content management system to support access to community news and training materials. SorghumBase offers sorghum investigators improved data collation and access that will facilitate the growth of a robust research community to support genomics-assisted breeding.

scholarly journals FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs

2020 ◽  
Vol 49 (D1) ◽  
pp. D892-D898
Author(s):  
Imad Abugessaisa ◽  
Jordan A Ramilowski ◽  
Marina Lizio ◽  
Jesicca Severin ◽  
Akira Hasegawa ◽  
...  
Keyword(s):  
Functional Annotation ◽  
Research Community ◽  
Dermal Fibroblasts ◽  
Data Types ◽  
Web Interfaces ◽  
Web Resource ◽  
Non Coding Rna ◽  
Mammalian Genomes ◽  
Non Coding Rnas ◽  
Genome Assemblies

Abstract The Functional ANnoTation Of the Mammalian genome (FANTOM) Consortium has continued to provide extensive resources in the pursuit of understanding the transcriptome, and transcriptional regulation, of mammalian genomes for the last 20 years. To share these resources with the research community, the FANTOM web-interfaces and databases are being regularly updated, enhanced and expanded with new data types. In recent years, the FANTOM Consortium's efforts have been mainly focused on creating new non-coding RNA datasets and resources. The existing FANTOM5 human and mouse miRNA atlas was supplemented with rat, dog, and chicken datasets. The sixth (latest) edition of the FANTOM project was launched to assess the function of human long non-coding RNAs (lncRNAs). From its creation until 2020, FANTOM6 has contributed to the research community a large dataset generated from the knock-down of 285 lncRNAs in human dermal fibroblasts; this is followed with extensive expression profiling and cellular phenotyping. Other updates to the FANTOM resource includes the reprocessing of the miRNA and promoter atlases of human, mouse and chicken with the latest reference genome assemblies. To facilitate the use and accessibility of all above resources we further enhanced FANTOM data viewers and web interfaces. The updated FANTOM web resource is publicly available at https://fantom.gsc.riken.jp/.

scholarly journals Carbon Nanotube Films for Energy Applications

Energies ◽  
2021 ◽  
Vol 14 (7) ◽  
pp. 1890
Author(s):  
Monika Rdest ◽  
Dawid Janas
Keyword(s):  
Carbon Nanotube ◽  
Mechanical Energy ◽  
Research Community ◽  
Thermal Interface Materials ◽  
Thermal Interface ◽  
Conductive Coatings ◽  
Storage Devices ◽  
Energy Applications ◽  
Wide Range ◽  
Interface Materials

This perspective article describes the application opportunities of carbon nanotube (CNT) films for the energy sector. Up to date progress in this regard is illustrated with representative examples of a wide range of energy management and transformation studies employing CNT ensembles. Firstly, this paper features an overview of how such macroscopic networks from nanocarbon can be produced. Then, the capabilities for their application in specific energy-related scenarios are described. Among the highlighted cases are conductive coatings, charge storage devices, thermal interface materials, and actuators. The selected examples demonstrate how electrical, thermal, radiant, and mechanical energy can be converted from one form to another using such formulations based on CNTs. The article is concluded with a future outlook, which anticipates the next steps which the research community will take to bring these concepts closer to implementation.

scholarly journals Using Satellite Data for CBRN (Chemical, Biological, Radiological, and Nuclear) Threat Detection, Monitoring, and Modelling

2021 ◽  
Author(s):  
Gary Sutlieff ◽  
Lucy Berthoud ◽  
Mark Stinchcombe
Keyword(s):  
Satellite Data ◽  
Meteorological Data ◽  
Atmospheric Composition ◽  
Chemical Detection ◽  
List Type ◽  
Data Types ◽  
Wide Range ◽  
Future Technologies ◽  
The Impact ◽  
Near Future

Abstract CBRN (Chemical, Biological, Radiological, and Nuclear) threats are becoming more prevalent, as more entities gain access to modern weapons and industrial technologies and chemicals. This has produced a need for improvements to modelling, detection, and monitoring of these events. While there are currently no dedicated satellites for CBRN purposes, there are a wide range of possibilities for satellite data to contribute to this field, from atmospheric composition and chemical detection to cloud cover, land mapping, and surface property measurements. This study looks at currently available satellite data, including meteorological data such as wind and cloud profiles, surface properties like temperature and humidity, chemical detection, and sounding. Results of this survey revealed several gaps in the available data, particularly concerning biological and radiological detection. The results also suggest that publicly available satellite data largely does not meet the requirements of spatial resolution, coverage, and latency that CBRN detection requires, outside of providing terrain use and building height data for constructing models. Lastly, the study evaluates upcoming instruments, platforms, and satellite technologies to gauge the impact these developments will have in the near future. Improvements in spatial and temporal resolution as well as latency are already becoming possible, and new instruments will fill in the gaps in detection by imaging a wider range of chemicals and other agents and by collecting new data types. This study shows that with developments coming within the next decade, satellites should begin to provide valuable augmentations to CBRN event detection and monitoring. Article Highlights There is a wide range of existing satellite data in fields that are of interest to CBRN detection and monitoring. The data is mostly of insufficient quality (resolution or latency) for the demanding requirements of CBRN modelling for incident control. Future technologies and platforms will improve resolution and latency, making satellite data more viable in the CBRN management field

scholarly journals Technology-enhanced and game based learning for children with special needs: a systematic mapping study

2021 ◽  
Author(s):  
Jose A. Gallud ◽  
Monica Carreño ◽  
Ricardo Tesoriero ◽  
Andrés Sandoval ◽  
María D. Lozano ◽  
...  
Keyword(s):  
Special Needs ◽  
State Of The Art ◽  
Research Community ◽  
Systematic Mapping Study ◽  
Children With Special Needs ◽  
Game Based Learning ◽  
Mapping Study ◽  
Systematic Mapping ◽  
Wide Range ◽  
Research Questions

AbstractTechnology-based education of children with special needs has become the focus of many research works in recent years. The wide range of different disabilities that are encompassed by the term “special needs”, together with the educational requirements of the children affected, represent an enormous multidisciplinary challenge for the research community. In this article, we present a systematic literature review of technology-enhanced and game-based learning systems and methods applied on children with special needs. The article analyzes the state-of-the-art of the research in this field by selecting a group of primary studies and answering a set of research questions. Although there are some previous systematic reviews, it is still not clear what the best tools, games or academic subjects (with technology-enhanced, game-based learning) are, out of those that have obtained good results with children with special needs. The 18 articles selected (carefully filtered out of 614 contributions) have been used to reveal the most frequent disabilities, the different technologies used in the prototypes, the number of learning subjects, and the kind of learning games used. The article also summarizes research opportunities identified in the primary studies.

scholarly journals Product formalisms for measures on spaces with binary tree structures: representation, visualization, and multiscale noise

2020 ◽  
Vol 8 ◽  
Author(s):  
Devasis Bassu ◽  
Peter W. Jones ◽  
Linda Ness ◽  
David Shallcross
Keyword(s):  
Data Science ◽  
Theoretical Foundation ◽  
Continuous Functions ◽  
Noise Model ◽  
Data Types ◽  
Data Set ◽  
Tree Structures ◽  
Simple Concept ◽  
Wide Range ◽  
Computer Scientists

Abstract In this paper, we present a theoretical foundation for a representation of a data set as a measure in a very large hierarchically parametrized family of positive measures, whose parameters can be computed explicitly (rather than estimated by optimization), and illustrate its applicability to a wide range of data types. The preprocessing step then consists of representing data sets as simple measures. The theoretical foundation consists of a dyadic product formula representation lemma, and a visualization theorem. We also define an additive multiscale noise model that can be used to sample from dyadic measures and a more general multiplicative multiscale noise model that can be used to perturb continuous functions, Borel measures, and dyadic measures. The first two results are based on theorems in [15, 3, 1]. The representation uses the very simple concept of a dyadic tree and hence is widely applicable, easily understood, and easily computed. Since the data sample is represented as a measure, subsequent analysis can exploit statistical and measure theoretic concepts and theories. Because the representation uses the very simple concept of a dyadic tree defined on the universe of a data set, and the parameters are simply and explicitly computable and easily interpretable and visualizable, we hope that this approach will be broadly useful to mathematicians, statisticians, and computer scientists who are intrigued by or involved in data science, including its mathematical foundations.

scholarly journals Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir

2020 ◽  
Author(s):  
James A. Fellows Yates ◽  
Aida Andrades Valtueña ◽  
Ashild J. Vågene ◽  
Becky Cribdon ◽  
Irina M. Velsko ◽  
...  
Keyword(s):  
Large Scale ◽  
Genetic Data ◽  
Data Retrieval ◽  
Data Sources ◽  
Valuable Data ◽  
Dna And Rna ◽  
Wide Range ◽  
Evolutionary Studies ◽  
Meta Analyses ◽  
Microbial Samples

ABSTRACTAncient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual microbial taxa, microbial communities, and metagenomic assemblages. AncientMetagenomeDir (archived at https://doi.org/10.5281/zenodo.3980833) is a collection of indices of published genetic data deriving from ancient microbial samples that provides basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories. These collections are community-curated and span multiple sub-disciplines in order to ensure adequate breadth and consensus in metadata definitions, as well as longevity of the database. Internal guidelines and automated checks to facilitate compatibility with established sequence-read archives and term-ontologies ensure consistency and interoperability for future meta-analyses. This collection will also assist in standardising metadata reporting for future ancient metagenomic studies.

Autonomous Control of Non-Silicon MEMS Flexible Micro-Assembly Line

2014 ◽  
Vol 496-500 ◽  
pp. 1468-1472
Author(s):  
Gao Yang Zhang ◽  
Xin Jin ◽  
Zhi Jing Zhang
Keyword(s):  
Assembly Line ◽  
High Volume ◽  
Research Community ◽  
Autonomous Control ◽  
Assembly System ◽  
Micro Fabrication ◽  
Micro Assembly ◽  
Wide Range ◽  
Micro Systems ◽  
Real Challenge

A wide range of micro-components can today be produced using various micro-fabrication techniques. The efficient high volume assembly of complex micro-systems consisting of vast single components (i.e., hybrid micro-systems) is, however, a difficult task that is seen to be a real challenge for the robotic research community. It is necessary to conceive flexible, highly precise and fast micro-assembly methods. In this paper, a frame of a micro-assembly system in the form of flexible micro-assembly line and its autonomous control is presented. Implementation of the control system are described and the procedure of autonomous control is described as well.

Database technology for the masses

2021 ◽  
Vol 14 (11) ◽  
pp. 2483-2490
Author(s):  
Maximilian Bandle ◽  
Jana Giceva
Keyword(s):  
Machine Learning ◽  
Relational Databases ◽  
Data Types ◽  
It Industry ◽  
Graph Data ◽  
Wide Range ◽  
Database Technology ◽  
External Interface ◽  
The Masses ◽  
Initial List

A wealth of technology has evolved around relational databases over decades that has been successfully tried and tested in many settings and use cases. Yet, the majority of it remains overlooked in the pursuit of performance (e.g., NoSQL) or new functionality (e.g., graph data or machine learning). In this paper, we argue that a wide range of techniques readily available in databases are crucial to tackling the challenges the IT industry faces in terms of hardware trends management, growing workloads, and the overall complexity of a rapidly changing application and platform landscape. However, to be truly useful, these techniques must be freed from the legacy component of database engines: relational operators. Therefore, we argue that to make databases more flexible as platforms and to extend their functionality to new data types and operations requires exposing a lower level of abstraction: instead of working with SQL it would be desirable for database engines to compile, optimize, and run a collection of sub-operators for manipulating and managing data, offering them as an external interface. In this paper, we discuss the advantages of this, provide an initial list of such sub-operators, and show how they can be used in practice.

VirES for Swarm & Virtual Research Environment: Software, guides & infrastructure to boost accessibility of Swarm

2021 ◽  
Author(s):  
Ashley Smith ◽  
Martin Pačes
Keyword(s):  
Community Involvement ◽  
Geomagnetic Field ◽  
Data Retrieval ◽  
Product Portfolio ◽  
It Services ◽  
Research Environment ◽  
Wide Range ◽  
Geomagnetic Field Models ◽  
Virtual Research Environment ◽  
Model Residuals

<p>ESA's Swarm mission continues to deliver excellent data providing insight into a wide range of geophysical phenomena. The mission is an important asset whose data are used within a number of critical resources, from geomagnetic field models to space weather services. As the product portfolio grows to better deliver on the mission's scientific goals, we face increasing complexity in accessing, processing, and visualising the data and models. ESA provides “VirES for Swarm” [1] (developed by EOX IT Services) to help solve this problem. VirES is a web-based data retrieval and visualisation tool where the majority of Swarm products are available. VirES has a graphical interface but also a machine-to-machine interface (API) for programmable use (a Python client is provided). The VirES API also provides access to geomagnetic ground observatory data, as well as forwards evaluation of geomagnetic field models to give data-model residuals. The "Virtual Research Environment" (VRE) adds utility to VirES with a free cloud-based JupyterLab interface allowing scientists to immediately program their own analysis of Swarm products using the Python ecosystem. We are augmenting this with a suite of Jupyter notebooks and dashboards, each targeting a specific use case, and seek community involvement to grow this resource.</p><p>[1] https://vires.services</p>

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