VIPERdb: A Tool for Virus Research

2018 ◽  
Vol 5 (1) ◽  
pp. 477-488 ◽  
Author(s):  
Phuong T. Ho ◽  
Daniel J. Montiel-Garcia ◽  
Jonathan. J. Wong ◽  
Mauricio Carrillo-Tripp ◽  
Charles L. Brooks ◽  
...  
Keyword(s):  
Bioinformatics Analysis ◽  
Contrast Structure ◽  
Web Based ◽  
Web Interfaces ◽  
Virus Capsids ◽  
Icosahedral Virus ◽  
Derived Properties ◽  
Virus Research ◽  
Data Visualizations ◽  
Compare And Contrast

The VIrus Particle ExploreR database (VIPERdb) ( http://viperdb.scripps.edu ) is a database and web portal for primarily icosahedral virus capsid structures that integrates structure-derived information with visualization and analysis tools accessed through a set of web interfaces. Our aim in developing VIPERdb is to provide comprehensive structure-derived information on viruses comprising simple to detailed attributes such as size (diameter), architecture ( T number), genome type, taxonomy, intersubunit association energies, and surface-accessible residues. In addition, a number of web-based tools are provided to enable users to interact with the structures and compare and contrast structure-derived properties between different viruses. Recently, we have constructed a series of data visualizations using modern JavaScript charting libraries such as Google Charts that allow users to explore trends and gain insights based on the various data available in the database. Furthermore, we now include helical viruses and nonicosahedral capsids by implementing modified procedures for data curation and analysis. This article provides an up-to-date overview of VIPERdb, describing various data and tools that are currently available and how to use them to facilitate structure-based bioinformatics analysis of virus capsids.

Trends in Web-Based Services in Academic Libraries

2011 ◽  
pp. 80-94 ◽  
Author(s):  
Lynn M. Fountain
Keyword(s):  
User Interfaces ◽  
Academic Library ◽  
Network Services ◽  
Academic Librarians ◽  
Online Learners ◽  
Electronic Journals ◽  
Web Based ◽  
Web Interfaces ◽  
Wide Range ◽  
Virtual Libraries

Change is afoot in the academic library world. The World Wide Web has expanded the types of services academic librarians are able to provide their patrons. We can now offer Web-based electronic databases, WebPACS, electronic journals, electronic reserve systems with Web-interfaces and a wide range of specialized digital library collections. Our patrons now have access to a huge variety of information, and they no longer have to leave their offices or homes to obtain it. Future developments include improved information retrieval algorithms, chic user-interfaces, advanced network services and virtual libraries created to serve the growing population of distance and online learners. Academic librarians face a world of exploding digital resources and their assistance in organizing this chaotic web of information is vital.

Developing Online Learning Portals in Low Bandwidth Communities

2011 ◽  
pp. 228-234
Author(s):  
Mae van der Merwe ◽  
Lorna Uden
Keyword(s):  
Relevant Information ◽  
Learning Processes ◽  
Web Based ◽  
Web Interfaces ◽  
Front End ◽  
Present Information ◽  
The World ◽  
The University ◽  
The Web

University portals are emerging all over the world. Portals have been perceived by many people as the technologies that are designed to enhance work and learning processes at university by making workflows simpler and information more readily available in a form in which it can be processed (Franklin, 2004). There are many benefits for having a portal in a university. First, the portal makes it easy for people to find university information targeted specifically at them. Instead of the user searching the Web for information, a person identifies himself or herself to the portal, and the portal brings all relevant information to that person. Secondly, the portal uses a single consistent Web-based front end to present information from a variety of back-end data sources. Although information about people is stored in many different databases at a university, the role of a portal is to put a consistent face to this information so that visitors do not have to deal with dozens of different Web interfaces to get their information. Usability is an important issue when designing the university portal. Principles from human computer interaction must be included in the design of portals.

scholarly journals RiboToolkit: an integrated platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution

2020 ◽  
Vol 48 (W1) ◽  
pp. W218-W229 ◽  
Author(s):  
Qi Liu ◽  
Tanya Shvarts ◽  
Piotr Sliz ◽  
Richard I Gregory
Keyword(s):  
Mrna Translation ◽  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Translational Efficiency ◽  
Translation Efficiency ◽  
Sequencing Data ◽  
Experimental Conditions ◽  
Web Based ◽  
Rna Translation ◽  
Web Interfaces

Abstract Ribosome profiling (Ribo-seq) is a powerful technology for globally monitoring RNA translation; ranging from codon occupancy profiling, identification of actively translated open reading frames (ORFs), to the quantification of translational efficiency under various physiological or experimental conditions. However, analyzing and decoding translation information from Ribo-seq data is not trivial. Although there are many existing tools to analyze Ribo-seq data, most of these tools are designed for specific or limited functionalities and an easy-to-use integrated tool to analyze Ribo-seq data is lacking. Fortunately, the small size (26–34 nt) of ribosome protected fragments (RPFs) in Ribo-seq and the relatively small amount of sequencing data greatly facilitates the development of such a web platform, which is easy to manipulate for users with or without bioinformatic expertise. Thus, we developed RiboToolkit (http://rnabioinfor.tch.harvard.edu/RiboToolkit), a convenient, freely available, web-based service to centralize Ribo-seq data analyses, including data cleaning and quality evaluation, expression analysis based on RPFs, codon occupancy, translation efficiency analysis, differential translation analysis, functional annotation, translation metagene analysis, and identification of actively translated ORFs. Besides, easy-to-use web interfaces were developed to facilitate data analysis and intuitively visualize results. Thus, RiboToolkit will greatly facilitate the study of mRNA translation based on ribosome profiling.

A Dissection of the Protein–Protein Interfaces in Icosahedral Virus Capsids

2007 ◽  
Vol 367 (2) ◽  
pp. 574-590 ◽  
Author(s):  
Ranjit Prasad Bahadur ◽  
Francis Rodier ◽  
Joël Janin
Keyword(s):  
Protein Interfaces ◽  
Virus Capsids ◽  
Icosahedral Virus

scholarly journals Differential Expression Gene Explorer (DrEdGE): A tool for generating interactive online data visualizations for exploration of quantitative transcript abundance datasets

2019 ◽  
Author(s):  
Sophia C. Tintori ◽  
Patrick Golden ◽  
Bob Goldstein
Keyword(s):  
Data Sharing ◽  
Transcript Abundance ◽  
Rna Seq ◽  
Online Data ◽  
Web Based ◽  
Neuronal Tissue ◽  
C Elegans ◽  
Differential Expression Gene ◽  
Public Data ◽  
Data Visualizations

AbstractAs the scientific community becomes increasingly interested in data sharing, there is a growing need for tools that facilitate the querying of public data. Mining of RNA-seq datasets, for example, has value to many biomedical researchers, yet is often effectively inaccessible to non-genomicist experts, even when the raw data are available. Here we present DrEdGE (dredge.bio.unc.edu), a free Web-based tool that facilitates data sharing between genomicists and their colleagues. The DrEdGE software guides genomicists through easily creating interactive online data visualizations, which colleagues can then explore and query according to their own conditions to discover genes, samples, or patterns of interest. We demonstrate DrEdGE’s features with three example websites we generated from publicly available datasets—human neuronal tissue, mouse embryonic tissue, and a C. elegans embryonic series. DrEdGE increases the utility of large genomics datasets by removing the technical obstacles that prevent interested parties from exploring the data independently.

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.

The Marker Cluster

2016 ◽  
Vol 7 (1) ◽  
pp. 28-43 ◽  
Author(s):  
Meier Sebastian
Keyword(s):  
Spatial Data ◽  
Interface Design ◽  
Design Pattern ◽  
Empirical Evaluation ◽  
Data Sets ◽  
Web Based ◽  
Ongoing Research ◽  
Spatial Data Sets ◽  
Marker Cluster ◽  
Data Visualizations

The growing amount of gathered, stored and available data is creating a need for useful mass-data visualizations in many domains. The mapping of large spatial data sets is not only of interest for experts anymore, but, with regard to the latest advances in web cartography, also moves into the domain of public cartographic applications. One interactive web-based cartographic interface design pattern that helps with visualizing and interacting with large, high density data sets is the marker cluster; a functionality already in use in many web-based products and solutions. In this article, the author will present their ongoing research on the problem of “too many markers.” They will present an empirical evaluation and comparison of marker cluster techniques and similar approaches, including heatmaps and tiled heatmaps. They conclude with a first concept for overcoming some of the obstacles that they were able to identify in their study and thereby introduce a new direction for further research.

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