scholarly journals IDbSV: An Open-Access Repository for Monitoring SARS-CoV-2 Variations and Evolution

2021 ◽  
Vol 8 ◽  
Author(s):  
Abdelmounim Essabbar ◽  
Souad Kartti ◽  
Tarek Alouane ◽  
Mohammed Hakmi ◽  
Lahcen Belyamani ◽  
...  
Keyword(s):  
Continuous Monitoring ◽  
New Records ◽  
International Database ◽  
Genetic Lineages ◽  
Functional Annotations ◽  
Interactive Data ◽  
Health Communities ◽  
Metadata Association ◽  
User Friendly ◽  
Data Visualizations

Ending COVID-19 pandemic requires a collaborative understanding of SARS-CoV-2 and COVID-19 mechanisms. Yet, the evolving nature of coronaviruses results in a continuous emergence of new variants of the virus. Central to this is the need for a continuous monitoring system able to detect potentially harmful variants of the virus in real-time. In this manuscript, we present the International Database of SARS-CoV-2 Variations (IDbSV), the result of ongoing efforts in curating, analyzing, and sharing comprehensive interpretation of SARS-CoV-2's genetic variations and variants. Through user-friendly interactive data visualizations, we aim to provide a novel surveillance tool to the scientific and public health communities. The database is regularly updated with new records through a 4-step workflow (1—Quality control of curated sequences, 2—Call of variations, 3—Functional annotation, and 4—Metadata association). To the best of our knowledge, IDbSV provides access to the largest repository of SARS-CoV-2 variations and the largest analysis of SARS-CoV-2 genomes with over 60 thousand annotated variations curated from the 1,808,613 genomes alongside their functional annotations, first known appearance, and associated genetic lineages, enabling a robust interpretation tool for SARS-CoV-2 variations to help understanding SARS-CoV-2 dynamics across the world.

scholarly journals metaXplor: an interactive viral and microbial metagenomic data manager

GigaScience ◽  
2021 ◽  
Vol 10 (2) ◽  
Author(s):  
Guilhem Sempéré ◽  
Adrien Pétel ◽  
Magsen Abbé ◽  
Pierre Lefeuvre ◽  
Philippe Roumagnac ◽  
...  
Keyword(s):  
Heterogeneous Data ◽  
Metagenomic Data ◽  
Online Data ◽  
Data Repositories ◽  
Ongoing Research ◽  
Efficient Management ◽  
Public Data ◽  
Reference Databases ◽  
Interactive Data ◽  
User Friendly

Abstract Background Efficiently managing large, heterogeneous data in a structured yet flexible way is a challenge to research laboratories working with genomic data. Specifically regarding both shotgun- and metabarcoding-based metagenomics, while online reference databases and user-friendly tools exist for running various types of analyses (e.g., Qiime, Mothur, Megan, IMG/VR, Anvi'o, Qiita, MetaVir), scientists lack comprehensive software for easily building scalable, searchable, online data repositories on which they can rely during their ongoing research. Results metaXplor is a scalable, distributable, fully web-interfaced application for managing, sharing, and exploring metagenomic data. Being based on a flexible NoSQL data model, it has few constraints regarding dataset contents and thus proves useful for handling outputs from both shotgun and metabarcoding techniques. By supporting incremental data feeding and providing means to combine filters on all imported fields, it allows for exhaustive content browsing, as well as rapid narrowing to find specific records. The application also features various interactive data visualization tools, ways to query contents by BLASTing external sequences, and an integrated pipeline to enrich assignments with phylogenetic placements. The project home page provides the URL of a live instance allowing users to test the system on public data. Conclusion metaXplor allows efficient management and exploration of metagenomic data. Its availability as a set of Docker containers, making it easy to deploy on academic servers, on the cloud, or even on personal computers, will facilitate its adoption.

scholarly journals OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species

2019 ◽  
Vol 47 (W1) ◽  
pp. W52-W58 ◽  
Author(s):  
Ling Xu ◽  
Zhaobin Dong ◽  
Lu Fang ◽  
Yongjiang Luo ◽  
Zhaoyuan Wei ◽  
...  
Keyword(s):  
Web Server ◽  
Venn Diagram ◽  
Orthologous Group ◽  
Genome Comparison ◽  
Species Number ◽  
Whole Genome ◽  
Functional Annotations ◽  
Occurrence Pattern ◽  
Multiple Species ◽  
User Friendly

Abstract OrthoVenn is a powerful web platform for the comparison and analysis of whole-genome orthologous clusters. Here we present an updated version, OrthoVenn2, which provides new features that facilitate the comparative analysis of orthologous clusters among up to 12 species. Additionally, this update offers improvements to data visualization and interpretation, including an occurrence pattern table for interrogating the overlap of each orthologous group for the queried species. Within the occurrence table, the functional annotations and summaries of the disjunctions and intersections of clusters between the chosen species can be displayed through an interactive Venn diagram. To facilitate a broader range of comparisons, a larger number of species, including vertebrates, metazoa, protists, fungi, plants and bacteria, have been added in OrthoVenn2. Finally, a stand-alone version is available to perform large dataset comparisons and to visualize results locally without limitation of species number. In summary, OrthoVenn2 is an efficient and user-friendly web server freely accessible at https://orthovenn2.bioinfotoolkits.net.

scholarly journals Students’ multimodal knowledge sharing in school: Spatial repertoires and semiotic assemblages

2021 ◽  
Author(s):  
Linnea Stenliden ◽  
Jörgen Nissen
Keyword(s):  
Social Science ◽  
Elementary School Students ◽  
Visual Analytics ◽  
Intervention Study ◽  
Science Classroom ◽  
Knowledge Building ◽  
School Students ◽  
Building Process ◽  
Interactive Data ◽  
Data Visualizations

AbstractIn a world ‘flooded’ with data, students in school need adequate tools as Visual Analytics (VA), that easily process mass data, give support in drawing advanced conclusions and help to make informed predictions in relation to societal circumstances. Methods for how the students’ insights may be reformulated and presented in ‘appropriate’ modes are required as well. Therefore, the aim in this study is to analyse elementary school students’ practices of communicating visual discoveries, their insights, as the final stage in the knowledge-building process with an VA-application for interactive data visualization. A design-based intervention study is conducted in one social science classroom to explore modes for students presentation of insights, constructed from the interactive data visualizations. Video captures are used to document 30 students’ multifaceted presentations. The analyses are based on concepts from Pennycook (2018) and Deleuze and Guattari (1987). To account for how different modes interact, when students present their findings, one significant empirical sequence is described in detail. The emerging communicative dimensions (visual-, bodily- and verbal-) are embedded within broad spatial repertoires distributing flexible semiotic assemblages. These assemblages provide an incentive for the possibilities of teachers’ assessments of their students’ knowledge outcomes.

scholarly journals An Interactive Data Visualization Framework for Exploring Geospatial Environmental Datasets and Model Predictions

Water ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 2928
Author(s):  
Jeffrey D. Walker ◽  
Benjamin H. Letcher ◽  
Kirk D. Rodgers ◽  
Clint C. Muhlfeld ◽  
Vincent S. D’Angelo
Keyword(s):  
Decision Making ◽  
Case Studies ◽  
Data Visualization ◽  
Large Scale ◽  
Research Management ◽  
Web Based ◽  
Environmental Models ◽  
Potential Benefits ◽  
Interactive Data ◽  
Data Visualizations

With the rise of large-scale environmental models comes new challenges for how we best utilize this information in research, management and decision making. Interactive data visualizations can make large and complex datasets easier to access and explore, which can lead to knowledge discovery, hypothesis formation and improved understanding. Here, we present a web-based interactive data visualization framework, the Interactive Catchment Explorer (ICE), for exploring environmental datasets and model outputs. Using a client-based architecture, the ICE framework provides a highly interactive user experience for discovering spatial patterns, evaluating relationships between variables and identifying specific locations using multivariate criteria. Through a series of case studies, we demonstrate the application of the ICE framework to datasets and models associated with three separate research projects covering different regions in North America. From these case studies, we provide specific examples of the broader impacts that tools like these can have, including fostering discussion and collaboration among stakeholders and playing a central role in the iterative process of data collection, analysis and decision making. Overall, the ICE framework demonstrates the potential benefits and impacts of using web-based interactive data visualization tools to place environmental datasets and model outputs directly into the hands of stakeholders, managers, decision makers and other researchers.

Interactive Data Entry: Problems, Models, Solutions

1995 ◽  
Vol 7 (1) ◽  
pp. 30-49 ◽  
Author(s):  
Leen Breure
Keyword(s):  
Data Entry ◽  
Interface Problems ◽  
Relational Model ◽  
Intelligent Interface ◽  
Database Technology ◽  
Technical Details ◽  
Interactive Data ◽  
User Friendly ◽  
Microsoft Windows ◽  
Current Database

Interactive data entry in a database environment has often required programming to create a user-friendly, intelligent interface. This applies in particular to historical dataprocessing. The historian draws his information from documents and has to cope with inconsistencies caused by relevant differences in time and place. Because most of the current database packages are relational, first, some basics ofthe relational model are reviewed to see how this model itself has contributed to interface problems. Next, because Microsoft Windows has put its stamp on the current database technology on the PC platform, it is discussed how far this graphical user interface model has improved the situation. Although the Windows shell has certainly contributed to solving interface problems, there are still areas where historians have to find their own way. It is argued that a model-based Iapproach,which defines and discusses solutions on a conceptual level first, would be desirable to prevent entangling in less relevant technical details. Finally, implementation is considered in the form of component ware.

scholarly journals Biographika: rich interactive data visualizations on the web for the research community

2015 ◽  
Author(s):  
Pablo Pareja Tobes ◽  
Eduardo Pareja Tobes ◽  
Marina Manrique ◽  
Eduardo Pareja ◽  
Raquel Tobes
Keyword(s):  
Scientific Data ◽  
Multidimensional Data ◽  
Microsoft Excel ◽  
The Past ◽  
Static Data ◽  
Open Source Framework ◽  
Interactive Data ◽  
Interactive 3D ◽  
Data Visualizations ◽  
The Web

When visualizing scientific data one of the current bottlenecks is the lack of interactivity. There already exist many options to build static data visualizations such as R, Matlab or Microsoft Excel among others. On the other hand, we can also find many different pieces of software with a broader or more specific aim that however must be installed locally. There is therefore a gap that is not covered by any of these latter two worlds. Here is where Biographika comes in handy since it provides scientists in general, and more specifically bioinformaticians, with a way of being able to use interactive rich visualizations on the web as part of their daily research. This first version of Biographika includes a set of charts combining diverse approaches that are thought to give users different perspectives of their research data. For the sake of interoperability and expressivity among other reasons we are using D3.js, the de facto standard visualization JavaScript library for manipulating documents based on data. But not only that, we incorporate new approaches as the fact of having fully interactive 3D charts that can be easily integrated with the rest of visualizations; providing the possibility of analyzing multidimensional data in a way that could otherwise be difficult to tackle. For that we use X3DOM, an open-source framework and runtime for 3D graphics on the Web that eases the integration of HTML5 and declarative 3D content. And last but not least, Biographika is also conceived as an effort to provide the data visualization layer for Bio4j that researchers have been lacking in the past few years.

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