scholarly journals TaxonWorks: Character state matrices and identification tools

2021 ◽  
Vol 5 ◽  
Author(s):  
Dmitry Dmitriev ◽  
Matthew Yoder
Keyword(s):  
Phylogenetic Analysis ◽  
Measurement Unit ◽  
Free Text ◽  
Character State ◽  
External Application ◽  
Web Based ◽  
The Matrix ◽  
Application Programming ◽  
Quantitative Sample ◽  
Areas Of Interest

TaxonWorks is an integrated web-based application for practicing taxonomists and biodiversity specialists. It is focused on promoting collaboration between researchers and developers. TaxonWorks has a modular structure that enables various components of the application to target specific needs and requirements of different groups of users. Specific areas of interest may include nomenclature-related tasks (Yoder and Dmitriev 2021) designed to help assemble and validate scientific name checklists of a target group of organisms; and collection management tasks, including interfaces to create, filter, and edit collecting events, collection objects, and loans. This presentation focuses on matrix-related tools integrated into TaxonWorks. A matrix, which could either be used for phylogenetic analysis or to build an identification key, is structured as a table where columns represent numerous characters that could be used to describe a set of entities, taxa or specimens (presented as rows of the table). Each cell of the table may contain observations for specific character/entity combinations. TaxonWorks does not generate a table for each a particular matrix—all observations are stored as graphs. This structure allows building of a matrix of an unlimited size as well as reuse of individual observations in multiple matrices. For matrix columns, TaxonWorks supports a variety of different kinds of characters or descriptors: qualitative, presence/absence, quantitative, sample, gene, free text, and media. Each character may have specific properties, for example a qualitative descriptor may have numerous characters states, and a quantitative descriptor may have a measurement unit defined. For an entity in a matrix row, TaxonWorks supports either collection objects (specimens) or taxa as Operational Taxonomic Units (OTU). OTUs could either be linked to nomenclature or be stand alone entities (e.g., representing undescribed species). The matrix, once built, could serve several purposes. A matrix based on qualitative and quantitative characters could be used to build an interactive key (Fig. 1), construct standardized natural language descriptions for each entity, and determine a diagnosis (a minimal set of characters that separate one entity from all others). It could also be exported and used for phylogenetic analysis or to build an interactive key in an external application. TaxonWorks supports export files in several formats, including Nexus, TNT, NeXML. Application Programming Interfaces (API) are also available. A matrix based on media descriptors could be used as a pictorial identification tool (Fig. 2).

As-RaD System as a Design Model of the Network Automation Configuration System Based on the REST-API and Django Framework

2020 ◽  
pp. 291-298
Author(s):  
Adian Fatchur Rochim ◽  
Abda Rafi ◽  
Adnan Fauzi ◽  
Kurniawan Teguh Martono
Keyword(s):  
Information Technology ◽  
Application Programming Interface ◽  
Design Model ◽  
Automation System ◽  
Network Configuration ◽  
Web Based ◽  
Representational State Transfer ◽  
Application Programming ◽  
Rest Api ◽  
Python Programming

The use of information technology these days are very high. From business through education activities tend to use this technology most of the time. Information technology uses computer networks for integration and management data. To avoid business problems, the number of network devices installed requires a manageable network configuration for easier maintenance. Traditionally, each of network devices has to be manually configured by network administrators. This process takes time and inefficient. Network automation methods exist to overcome the repetitive process. Design model uses a web-based application for maintenance and automates networking tasks. In this research, the network automation system implemented and built a controller application that used REST API (Representational State Transfer Application Programming Interface) architecture and built by Django framework with Python programming language. The design modeled namely As-RaD System. The network devices used in this research are Cisco CSR1000V because it supports REST API communication to manage its network configuration and could be placed on the server either. The As-RaD System provides 75% faster performance than Paramiko and 92% than NAPALM.

scholarly journals Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Shawna Spoor ◽  
Connor Wytko ◽  
Brian Soto ◽  
Ming Chen ◽  
Abdullah Almsaeed ◽  
...  
Keyword(s):  
Workflow Management ◽  
Application Programming Interface ◽  
Scientific Workflow ◽  
Biological Databases ◽  
Web Based ◽  
Job Management ◽  
The Galaxy ◽  
Application Programming ◽  
Computational Resources ◽  
Programming Interface

Abstract Online biological databases housing genomics, genetic and breeding data can be constructed using the Tripal toolkit. Tripal is an open-source, internationally developed framework that implements FAIR data principles and is meant to ease the burden of constructing such websites for research communities. Use of a common, open framework improves the sustainability and manageability of such as site. Site developers can create extensions for their site and in turn share those extensions with others. One challenge that community databases often face is the need to provide tools for their users that analyze increasingly larger datasets using multiple software tools strung together in a scientific workflow on complicated computational resources. The Tripal Galaxy module, a ‘plug-in’ for Tripal, meets this need through integration of Tripal with the Galaxy Project workflow management system. Site developers can create workflows appropriate to the needs of their community using Galaxy and then share those for execution on their Tripal sites via automatically constructed, but configurable, web forms or using an application programming interface to power web-based analytical applications. The Tripal Galaxy module helps reduce duplication of effort by allowing site developers to spend time constructing workflows and building their applications rather than rebuilding infrastructure for job management of multi-step applications.

WIF4InL: Web-based integration framework for Indoor location

2016 ◽  
Vol 12 (1) ◽  
pp. 49-65 ◽  
Author(s):  
Long Niu ◽  
Sachio Saiki ◽  
Shinsuke Matsumoto ◽  
Masahide Nakamura
Keyword(s):  
Application Programming Interface ◽  
Common Data Model ◽  
Loose Coupling ◽  
Web Based ◽  
Integration Framework ◽  
Content Type ◽  
Positioning Systems ◽  
Indoor Location ◽  
Location Data ◽  
Application Programming

Purpose The purpose of this paper is to establish an application platform that addresses expensive development cost and effort of indoor location-aware application (InL-Apps) problems caused by tightly coupling between InL-App and indoor positioning systems (IPSs). Design/methodology/approach To achieve this purpose, in this paper, the authors proposes a Web-based integration framework called Web-based Integration Framework for Indoor Location (WIF4InL). With a common data model, WIF4InL integrates indoor location data obtained from heterogeneous IPS. It then provides application-neutral application programming interface (API) for various InL-Apps. Findings The authors integrate two different IPS (RedPin and BluePin) using WIF4InL and conduct a comparative study which is based on sufficiency of essential capabilities of location-dependent queries among three systems: RedPin, BluePin and WIF4InL. WIF4InL supports more capabilities for the location-dependent queries. Through the data and operation integration, WIF4InL even enriches the existing proprietary IPS. Originality/value As WIF4InL allows the loose coupling between IPS and InL-Apps, it significantly improves reusability of indoor location information and operation.

Morphological evidence for paraphyly of Holopothrips Hood (Thysanoptera: Phlaeothripidae), a Neotropical genus of gall-inducing thrips

2021 ◽  
pp. 1-24
Author(s):  
Mariana F. Lindner ◽  
Augusto Ferrari ◽  
Adriano Cavalleri
Keyword(s):  
Phylogenetic Analysis ◽  
Host Plants ◽  
Morphological Diversity ◽  
Morphological Characters ◽  
Bootstrap Support ◽  
Morphological Evidence ◽  
Diverse Group ◽  
The Matrix ◽  
Internal Relations ◽  
Evolutionary Story

Abstract Holopothrips is a diverse group of thrips associated to galls in the Neotropics, with a variety of host plants and wide morphological diversity. Relationships to other Neotropical groups have been proposed, but are still untested, and the monophyly of the genus remains doubtful. Here, we perform a phylogenetic analysis of Holopothrips, based on morphological characters. A total of 87 species were included in the matrix and eight analyses were carried out, but all of them failed to recover Holopothrips as a monophyletic grouping. Bremer and Bootstrap support values were low, and the topologies varied among all analyses, with uncertain internal relations for the ingroup. These results indicate that the relationships for Holopothrips species, and the proposed related genera, are more complex than previously reported; and morphological characters may not be enough to recover the evolutionary story within this group. We also discuss the influences of different character coding, continuous characters and weighting schemes in our results.

Open Innovation through Customers

2014 ◽  
pp. 335-374
Author(s):  
Barbara Aquilani ◽  
Tindara Abbate
Keyword(s):  
Literature Review ◽  
Open Innovation ◽  
Paradigm Shift ◽  
Review Process ◽  
Organizational Changes ◽  
Hybrid Mode ◽  
Web Based ◽  
Organizational Issues ◽  
Areas Of Interest

This chapter aims at analyzing how firms can successfully embrace an Open Innovation (OI) process through customers, involving them, individually or in communities, in the co-creation of ideas, knowledge, products, services, processes, putting into action and integrating their creativity with firms' resources. Three main areas of interest are analyzed through a literature review process, to create a framework able to show the challenges organizations have to meet simultaneously externally (i.e. consumerism) and internally (i.e. organizational changes) in this shift of the innovation paradigm: consumerism features and challenges, OI approach and web-based platforms, and organizational issues involved in the OI paradigm shift. This chapter affords consumerism and OI approach, while the next, which is the sequel of this one, discusses OI platforms and organizational changes as well as the resulting framework. Four contributions distinguish this study: (i) the link between consumerism and OI; (ii) the focus on customers as a source of external innovation; (iii) the identification of alternative ways to access OI with customers and their features; (iv) the disclosure of a “hybrid” mode to develop OI through customers.

Web 2.0 in Governance

2016 ◽  
pp. 1674-1696
Author(s):  
Lefkothea Spiliotopoulou ◽  
Yannis Charalabidis
Keyword(s):  
Social Media ◽  
Web 2.0 ◽  
Opinion Mining ◽  
Policy Formulation ◽  
Web Based ◽  
Policy Makers ◽  
Web 3.0 ◽  
Significant Research ◽  
Application Programming ◽  
Programming Interfaces

There has been significant research in the private sector towards systematic exploitation of the emerging Web 2.0/Web 3.0 and social media paradigms. However, not much has been achieved with regards to the embodiment of similar technologies. Currently, governments and organizations are making considerable efforts, trying to enhance citizens' participation in decision-making and policy-formulation processes. This chapter presents a novel policy analysis framework, proposing a Web-based platform that enables publishing content and micro-applications to multiple Web 2.0 social media and collecting citizens' interactions (e.g. comments, ratings) with efficient use of Application Programming Interfaces (APIs) of these media. Citizens' opinions and interactions can then be processed through different techniques or methods (Web analytics, opinion mining, simulation modeling) in order to use the extracted conclusions as support to government decision and policy makers.

scholarly journals The MINOUWApp: a web-based tool in support of by-catch and discards management

2020 ◽  
Vol 192 (12) ◽  
Author(s):  
Lorenzo D’Andrea ◽  
Aida Campos ◽  
Karim Erzini ◽  
Paulo Fonseca ◽  
Simone Franceschini ◽  
...  
Keyword(s):  
Management Strategies ◽  
Fishing Effort ◽  
Negative Effects ◽  
Web Based ◽  
Management Plans ◽  
By Catch ◽  
Selection Of Species ◽  
Areas Of Interest ◽  
Ecosystem Based Fisheries Management ◽  
Selection Of

AbstractCurrent fishing practices often do not allow adequate selection of species or sizes of fish, resulting in unwanted catches, subsequently discarded, with the consequent negative effects on both marine communities and fisheries profitability. The cross-analysis of density patches of potential unwanted catches and distribution of fishing effort can support the identification of spatial-temporal hot-spots in which the fishing pressure should be reduced to limit the amount of discards. The MinouwApp represents a technological and methodological framework to bring different, and structurally complex, sources of georeferenced data together into a simple visual interface aiming to interactively explore temporal ranges and areas of interest. The objective is to improve the understanding of fisheries dynamics, including discards, thus contributing to the implementation of discard management plans in a context of participative, ecosystem-based fisheries management strategies.

scholarly journals Genetic Diversity Based on ISSR Markers of Apple Genotypes in Ardahan/Turkey

2018 ◽  
Vol 10 (4) ◽  
pp. 554-558
Author(s):  
Emre SEVİNDİK ◽  
Hüseyin UYSAL ◽  
Zehra Tuğba MURATHAN
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genetic Distance ◽  
Uv Light ◽  
Genetic Relationships ◽  
Issr Markers ◽  
Genetic Distances ◽  
The Matrix ◽  
Commercial Kits ◽  
Issr Primers

Within the present study, it was conducted a genetic diversity analysis using ISSR markers for some apple genotypes grown in Ardahan region, Turkey. Total genomic DNA (gDNA) isolation from apple leaves was performed using commercial kits. Five ISSR primers were used to determine the genetic diversity among the genotypes studied. Polymerase Chain Reaction (PCR) was performed with all gDNA samples to produce bands to score. PCR products were run in agarose gel and visualized under UV light. Bands on the gels were scored as “1”, while no bands at the corresponding positions were scored as “0”, to generate the matrix file. Five ISSR primers produced a total of 35 bands, and 20 of them were polymorphic. The polymorphic bands rated approximately 57%. Phylogenetic relationships and genetic distances between the genotypes were calculated by using the PAUP [Phylogenetic Analysis Using Parsimony (and Other Methods)] program.  According to the PAUP data, the closest genetic distance was 0.03704 between ‘Kaburga’ and ‘Japon Apple’ genotypes, while the furthest genetic distance was 0.48148 between ‘Karanfil Apple’ and ‘Sisli Uruset’. The phylogenetic analysis obtained using UPGMA algorithm produced a phylogenetic tree with two clades. The results suggest that ISSR markers are useful tools for determining genetic relationships among apple genotypes.

Monitoring oral anti-cancer therapy adherence in cancer patients using web based application guided communication compared with nurse counseling in a community cancer center.

2017 ◽  
Vol 35 (5_suppl) ◽  
pp. 88-88
Author(s):  
Milana V. Dolezal ◽  
Vivian Leong ◽  
Rajesh Behl
Keyword(s):  
Cancer Therapy ◽  
Cancer Patients ◽  
Effective Communication ◽  
Smart Device ◽  
Cancer Center ◽  
Free Text ◽  
Communication Tools ◽  
Web Based ◽  
Electronic Alerts ◽  
Anti Cancer

88 Background: Smart phone web based applications (apps) can be effective communication tools for monitoring compliance and increasing adherence to oral anti-cancer therapy in the outpatient setting. Methods: Cancer patients age 18-90 treated with various oral anti-cancer therapies were recruited to this prospective, 3 month observational trial at our large community cancer center to determine feasibility of using an app for oral anti-cancer therapy compliance. Enrolled patients are randomized to either Arm 1 App arm and nurse counseling or Arm 2 nurse counseling only. The free apps MyMeds and Medisafe incorporate medication reminders and record doses. Patients complete the validated RAND 36- item quality of life (QOL) questionnaire and a free text feedback. Results: 91 patients were screened between 11/2015 to 9/2016 (45 declined enrollment due to various factors). 46 patients were randomized with 25 to Arm 1 and 21 to Arm 2. Demographics included 10 men (various tumor types but mostly multiple myeloma) and 36 women; 22 with breast cancer. MyMeds app lacked the necessary real-time communication so patients were switched to the MediSafe app which features email alerts. 15 patients have completed the study through Month 3. Four patients on Arm 1 missing their monthly visit or were non-compliant with the app. 23 patients remain active in the study. Differences are a higher QOL score in Arm 1 vs Arm 2 in measured domains of Energy/Fatigue (56% in Arm 1 compared to 44% for Arm 2) and Pain (72% in Arm 1 compared to 58% in Arm 2). Patients randomized to the app found the electronic alerts very helpful. Conclusions: Our limited pilot study demonstrated the potential of smart device apps as effective communication tools for improving patients’ adherence to oral anti-cancer therapy and QOL. Ultimately, convenient ways to monitor patients’ compliance with anti-cancer therapy will impact survival and facilitate provider-patient communication.

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