scholarly journals TaxonWorks: An experience of migrating large datasets into the new cybertaxonomic infrastructure

2019 ◽  
Vol 3 ◽  
Author(s):  
Dmitry Dmitriev
Keyword(s):  
Web Application ◽  
Data Entry ◽  
Large Datasets ◽  
Character Trait ◽  
Data Migration ◽  
Data Types ◽  
Web Interfaces ◽  
Illinois Natural History Survey ◽  
Efficient Data ◽  
History Survey

TaxonWorks (http://taxonworks.org) in an integrated, open-source, cybertaxonomic web application serving taxonomists and biodiversity scientists. It is designed to facilitate efficient data capture, storage, manipulation, and retrieval. It integrates a wide variety of data types used by biodiversity scientists, including, but not limited to, taxonomy (with validation based on codes of zoological, botanical, bacterial, and viral nomenclature), specimen data, bibliographies, media (images, PDFs, sounds, videos), morphology (character/trait matrices), distribution, biological associations. Available TaxonWorks web interfaces currently provide various data entry forms for simple and advanced querying of the database. TaxonWorks has integrated batch uploader functionality. But, for larger datasets, specialized migration scripts were used. Several projects, historically build in 3i (http://dmitriev.speciesfile.org), MX (http://mx.phenomix.org), SpeciesFiles (http://software.speciesfile.org), and other databases, have been or are being migrated into TaxonWorks. Of the projects moving into TaxonWorks, it is worth mentioning several: 3i World Auchenorrhyncha Database, LepIndex, Universal Chalcidoidea Database, Orthoptera SpeciesFile, Plecoptera SpeciesFile, Illinois Natural History Survey Insect Collection database, and several others. An experience of the data migration will be shared during the presentation.

scholarly journals When Data Management Meets Project Management

2019 ◽  
Vol 3 ◽  
Author(s):  
Evgeniy Meyke
Keyword(s):  
User Interfaces ◽  
Web Application ◽  
Laboratory Data ◽  
Data Entry ◽  
Data Types ◽  
Laboratory Notebook ◽  
Data Repositories ◽  
Institutional Infrastructure ◽  
Feature Request ◽  
High Flexibility

Complex projects that collect, curate and analyse biodiversity data are often presented with the challenge of accommodating diverse data types, various curation and output workflows, and evolving project logistics that require rapid changes in the applications and data structures. At the same time, sustainability concerns and maintenance overheads pose a risk to the long term viability of such projects. We advocate the use of flexible, multiplatform tools that adapt to operational, day-to-day challenges while providing a robust, cost efficient, and maintainable framework that serves the needs data collectors, managers and users. EarthCape is a highly versatile platform for managing biodiversity research and collections data, associated molecular laboratory data (Fig. 1), multimedia, structured ecological surveys and monitoring schemes, and more. The platform includes a fully functional Windows client as well as a web application. The data are stored in the cloud or on-premises and can be accessed by users with various access and editing rights. Ease of customization (making changes to user interface and functionality) is critical for most environments that deal with operational research processes. For active researchers and curators, there is rarely time to wait for a cycle of development that follows a change or feature request. In EarthCape, most of the changes to the default setup can be implemented by the end users with minimum effort and require no programming skills. High flexibility and a range of customisation options is complemented with mapping to Darwin Core standard and integration with GBIF, Geolocate, Genbank, and Biodiversity Heritage Library APIs. The system is currently used daily for rapid data entry, digitization and sample tracking, by such organisations as Imperial College, University of Cambridge, University of Helsinki, University of Oxford. Being an operational data entry and retrieval tool, EarthCape sits at the bottom of Virtual Research Environments ecosystem. It is not a software or platform to build data repositories, but rather a very focused tool falling under "back office" software category. Routine label printing, laboratory notebook maintenance, rapid data entry set up, or any other of relatively loaded user interfaces make use of any industry standard relational database back end. This opens a wide scope for IT designers to implement desired integrations within their institutional infrastructure. APIs and developer access to core EarthCape libraries to build own applications and modules are under development. Basic data visualisation (charts, pivots, dashboards), mapping (full featured desktop GIS module), data outputs (report and label designer) are tailored not only to research analyses, but also for managing logistics and communication when working on (data) papers. The presentation will focus on the software platform featuring most prominent use cases from two areas: ecological research (managing complex network data digitization project) and museum collections management (herbarium and insect collections).

scholarly journals A Secure and Efficient Data Migration Over Cloud Computing

2021 ◽  
Vol 1099 (1) ◽  
pp. 012082
Author(s):  
G. Madhukar Rao ◽  
K. Srinivas ◽  
Sayyad Samee ◽  
K Venkatesh ◽  
Pankaj Dadheech ◽  
...  
Keyword(s):  
Cloud Computing ◽  
Data Migration ◽  
Efficient Data

scholarly journals Nextstrain: real-time tracking of pathogen evolution

2017 ◽  
Author(s):  
James Hadfield ◽  
Colin Megill ◽  
Sidney M. Bell ◽  
John Huddleston ◽  
Barney Potter ◽  
...  
Keyword(s):  
Public Health ◽  
Real Time ◽  
Web Application ◽  
Sequence Data ◽  
Data Types ◽  
Bioinformatics Pipeline ◽  
Public Health Importance ◽  
Viral Genomes ◽  
Effective Public Health ◽  
Interactive Visualisation

AbstractSummaryUnderstanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualisation platform. Together these present a real-time view into the evolution and spread of a range of viral pathogens of high public health importance. The visualization integrates sequence data with other data types such as geographic information, serology, or host species. Nextstrain compiles our current understanding into a single accessible location, publicly available for use by health professionals, epidemiologists, virologists and the public alike.Availability and implementationAll code (predominantly JavaScript and Python) is freely available from github.com/nextstrain and the web-application is available at nextstrain.org.

scholarly journals Descriptions of Nearctic Caddis Flies (Trichoptera)

1938 ◽  
Vol 21 (1-8) ◽  
pp. 101-183 ◽  
Author(s):  
T. H. Frison
Keyword(s):  
New Species ◽  
North America ◽  
Natural History ◽  
Aquatic Insects ◽  
Initial Report ◽  
Illinois Natural History Survey ◽  
Caddis Flies ◽  
History Survey

This paper, describing new species of caddis flies from Illinois and other localities in North America, is the initial report on a project of the Illinois Natural History Survey pertaining to these aquatic insects.

scholarly journals LandScape: a web application for interactive genomic summary visualization

2019 ◽  
Author(s):  
Wenlong Jia ◽  
Hechen Li ◽  
Shiying Li ◽  
Shuaicheng Li
Keyword(s):  
Genetic Information ◽  
Web Application ◽  
Genomic Research ◽  
File Format ◽  
Data Types ◽  
Web Based ◽  
Link Type ◽  
Level Data ◽  
Real Time Visualization ◽  
Information Landscape

ABSTRACTSummaryVisualizing integrated-level data from genomic research remains a challenge, as it requires sufficient coding skills and experience. Here, we present LandScapeoviz, a web-based application for interactive and real-time visualization of summarized genetic information. LandScape utilizes a well-designed file format that is capable of handling various data types, and offers a series of built-in functions to customize the appearance, explore results, and export high-quality diagrams that are available for publication.Availability and implementationLandScape is deployed at bio.oviz.org/demo-project/analyses/landscape for online use. Documentation and demo data are freely available on this website and GitHub (github.com/Nobel-Justin/Oviz-Bio-demo)[email protected]

scholarly journals AUTOMATED INFORMA¬TION SYSTEM FOR GPS MONITORING DATA PROCESSING

2021 ◽  
Vol 2 (37) ◽  
pp. 88-92
Author(s):  
K. Yalova ◽  
K. Yashyna ◽  
O. Tarasiyk
Keyword(s):  
User Interface ◽  
Data Processing ◽  
System Architecture ◽  
Web Application ◽  
Gps Tracking ◽  
System Software ◽  
Web Interfaces ◽  
Application Service ◽  
Functional Features ◽  
Tion System

Using of automated information systems in the field of geolocation data processing increases the control and management efficiency of freight and passenger traffic. The article presents the results of design and software implementation of the automated information system that allows monitoring of GPS tracking data in real time, build routes and set control points for it, generate system messages about the status of vehicles on the route and generate reporting information on the base of user requests. The design of the system architecture and interface was carried out on the basis of developed object and functional data domain models, which take into account its structural and functional features. The microservice approach principles were applied during the developing of the system architecture. The system software is a set of independent services that work in their own process, implement a certain business logic algorithm and communicate with other services through the HTTP protocol. The set of the system software services consists of: a service for working with GPS data, a service for implementing geolocation data processing functions, and a web application service. The main algorithms of the developed system services and their functional features are described in the work. Article’s figures graphically describe developed system site map and system typical Web forms. This data displays the composition of web pages, paths between them and shows the user interface. The design of the user interface was carried out taking into account quality requirements of user graphical web interfaces.

scholarly journals Linking Norms, Ratings, and Relations of Words and Concepts Across Multiple Language Varieties

2020 ◽  
Author(s):  
Annika Tjuka ◽  
Robert Forkel ◽  
Johann-Mattis List
Keyword(s):  
Web Application ◽  
Age Of Acquisition ◽  
Data Curation ◽  
Data Sets ◽  
Data Types ◽  
Word Meanings ◽  
Language Varieties ◽  
Diverse Data ◽  
Multiple Languages ◽  
Word Frequencies

Psychologists and linguists have collected a great diversity of data for word and concept properties. In psychology, many studies accumulate norms and ratings such as word frequencies or age-of-acquisition often for a large number of words. Linguistics, on the other hand, provides valuable insights into relations of word meanings. We present a collection of those data sets for norms, ratings, and relations that cover different languages: ‘NoRaRe.’ To enable a comparison between the diverse data types, we established workflows that facilitate the expansion of the database. A web application allows convenient access to the data (https://digling.org/norare/). Furthermore, a software API ensures consistent data curation by providing tests to validate the data sets. The NoRaRe collection is linked to the database curated by the Concepticon project (https://concepticon.clld.org) which offers a reference catalog of unified concept sets. The link between words in the data sets and the Concepticon concept sets makes a cross-linguistic comparison possible. In three case studies, we test the validity of our approach, the accuracy of our workflow, and the applicability of our database. The results indicate that the NoRaRe database can be applied for the study of word properties across multiple languages. The data can be used by psychologists and linguists to benefit from the knowledge rooted in both research disciplines.

Visualizing Sedimentary Condensation , Dilution, and Erosion using Shiny Apps

2021 ◽  
Author(s):  
Niklas Hohmann ◽  
Emilia Jarochowska
Keyword(s):  
Web Application ◽  
Science Communication ◽  
Student Understanding ◽  
Large Datasets ◽  
Sedimentation Rates ◽  
Web Interface ◽  
High Input ◽  
R Software ◽  
Self Study ◽  
Versatile Tool

<p>Fossil accumulations can be generated by (1) high input of organism remains or (2) by low sedimentation rates, reducing the volume of sediment between individual fossils. This creates a paradox, in which shell beds may form in environments with low biomass production. This effect of sedimentary condensation on fossil abundance is easy to understand, however, its implications are hard to grasp and visualize.</p><p>We present the shellbed condensator ( https://stratigraphicpaleobiology.shinyapps.io/shellbed_condensator/ ), a web application that allows to interactively visualize and animate the effects of sedimentary condensation and erosion on fossil abundance and proxies recorded by the sedimentary record. It is an adaptation of the seminal computer simulation by Kidwell (1985). The application is written in R Software and uses the shiny package for the construction of the web interface and the DAIME package for the sedimentological model (Hohmann, 2021). It allows creating stratigraphic expressions and age models for combinations of fossil input and sedimentation rates defined by the user.</p><p>To assess the utility of shiny apps for teaching purposes, we examine student understanding of sedimentary condensation after unsupervised studying and after unsupervised usage of the app. Due to their strong visual and interactive components, shiny apps are a powerful and versatile tool for science communication, teaching, self-study, the visualization of large datasets, and the promotion of scientific findings.</p><p> </p>

VoiceWeb

2011 ◽  
pp. 340-359 ◽  
Author(s):  
Dimitris Spiliotopoulos ◽  
Georgios Kouroupetroglou ◽  
Pepi Stavropoulou
Keyword(s):  
Resource Management ◽  
Web Application ◽  
State Of The Art ◽  
Theoretical Perspective ◽  
Usability Evaluation ◽  
Design Issues ◽  
Web Interfaces ◽  
Conversational Interfaces ◽  
Hands On ◽  
Technical Issues

This chapter presents the state-of-the-art in usability issues and methodologies for VoiceWeb interfaces. It undertakes a theoretical perspective to the usability methodology and provides a framework description for creating and testing usable content and applications for conversational interfaces. The methodologies and their uses are discussed as well as certain technical issues that are of specific importance for each type of system. Moreover, it discusses the hands-on approaches for applying usability methodologies in a spoken dialogue web application environment, including methodological and design issues, resource management, implementation using existing technologies for usability evaluation in several stages of the design and deployment. Finally, the challenging usability issues and parameters of the emerging advanced speech-enabled web interfaces are presented.

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