scholarly journals SugarDrawer: A Web-Based Database Search Tool with Editing Glycan Structures

Molecules ◽  
2021 ◽  
Vol 26 (23) ◽  
pp. 7149
Author(s):  
Shinichiro Tsuchiya ◽  
Masaaki Matsubara ◽  
Kiyoko F. Aoki-Kinoshita ◽  
Issaku Yamada
Keyword(s):  
Unique Feature ◽  
Database Search ◽  
Glycan Structure ◽  
Specific Information ◽  
Database Integration ◽  
Web Based ◽  
Research Fields ◽  
Attachment Sites ◽  
Structure Search ◽  
Search Tool

In life science fields, database integration is progressing and contributing to collaboration between different research fields, including the glycosciences. The integration of glycan databases has greatly progressed collaboration worldwide with the development of the international glycan structure repository, GlyTouCan. This trend has increased the need for a tool by which researchers in various fields can easily search glycan structures from integrated databases. We have developed a web-based glycan structure search tool, SugarDrawer, which supports the depiction of glycans including ambiguity, such as glycan fragments which contain underdetermined linkages, and a database search for glycans drawn on the canvas. This tool provides an easy editing feature for various glycan structures in just a few steps using template structures and pop-up windows which allow users to select specific information for each structure element. This tool has a unique feature for selecting possible attachment sites, which is defined in the Symbol Nomenclature for Glycans (SNFG). In addition, this tool can input and output glycans in WURCS and GlycoCT formats, which are the most commonly-used text formats for glycan structures.

scholarly journals The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases

Metabolites ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 113
Author(s):  
Julia Koblitz ◽  
Sabine Will ◽  
S. Riemer ◽  
Thomas Ulas ◽  
Meina Neumann-Schaal ◽  
...  
Keyword(s):  
Metabolic Networks ◽  
Point Of View ◽  
Use Cases ◽  
Mathematical Methods ◽  
State Behavior ◽  
Web Based ◽  
Research Fields ◽  
Balance Analysis ◽  
Metabolic Models ◽  
User Friendly

Genome-scale metabolic models are of high interest in a number of different research fields. Flux balance analysis (FBA) and other mathematical methods allow the prediction of the steady-state behavior of metabolic networks under different environmental conditions. However, many existing applications for flux optimizations do not provide a metabolite-centric view on fluxes. Metano is a standalone, open-source toolbox for the analysis and refinement of metabolic models. While flux distributions in metabolic networks are predominantly analyzed from a reaction-centric point of view, the Metano methods of split-ratio analysis and metabolite flux minimization also allow a metabolite-centric view on flux distributions. In addition, we present MMTB (Metano Modeling Toolbox), a web-based toolbox for metabolic modeling including a user-friendly interface to Metano methods. MMTB assists during bottom-up construction of metabolic models by integrating reaction and enzymatic annotation data from different databases. Furthermore, MMTB is especially designed for non-experienced users by providing an intuitive interface to the most commonly used modeling methods and offering novel visualizations. Additionally, MMTB allows users to upload their models, which can in turn be explored and analyzed by the community. We introduce MMTB by two use cases, involving a published model of Corynebacterium glutamicum and a newly created model of Phaeobacter inhibens.

scholarly journals Utilizing Context in Location-Aware Short-Range Wireless Communication

2010 ◽  
Vol 2010 ◽  
pp. 1-12 ◽  
Author(s):  
Vesa A. Korhonen ◽  
Ritva Pyykkönen
Keyword(s):  
Wireless Communication ◽  
Information Search ◽  
Short Range ◽  
Human Interaction ◽  
Preliminary Design ◽  
Data Filtering ◽  
Web Based ◽  
Communication Devices ◽  
Search Tool ◽  
Additional Value

We discuss how a short-range wireless communication service implemented for modern mobile communication devices can provide additional value for both the consumer and the service/product provider. When used as an information search tool, such systems allow services and products being promoted at the location they are available. For the customer, it may provide a “digitally augmented vision”, an enhanced view to the current environment. With data filtering and search rules, this may provide a self-manageable context, where the user's own personal environment and preferences to the features available in the current surroundings cooperate with a direct connection to the web-based social media. A preliminary design for such service is provided. The conclusion is that the method can generate additional revenue to the company and please the customers' buying process. In addition to the marketing, the principles described here are also applicable to other forms of human interaction.

scholarly journals Web-Based Search Tool for Visualizing Instrument Performance Using the Triple Knockout (TKO) Proteome Standard

2018 ◽  
Vol 18 (2) ◽  
pp. 687-693 ◽  
Author(s):  
Jeremy P. Gygi ◽  
Qing Yu ◽  
Jose Navarrete-Perea ◽  
Ramin Rad ◽  
Steven P. Gygi ◽  
...  
Keyword(s):  
Web Based ◽  
Instrument Performance ◽  
Search Tool

scholarly journals A Sample Book Of Late 20th And Early 21st Century Expired Silver Gelatin Photographic Papers

2021 ◽  
Author(s):  
Joanne R. Guillemette
Keyword(s):  
21St Century ◽  
Specific Information ◽  
Educational Tool ◽  
Web Based ◽  
Early 21St Century ◽  
Visual Identification ◽  
Hands On ◽  
Long Term Preservation

In this applied thesis project, a sample booklet of various expired silver gelatin papers is created. Specific information on the use of expired photographic papers by contemporary photographers is discussed as well as insights from collection caretakers (collection managers/archivists/conservators) on the possible implications that printing with expired silver gelatin papers may have for the long-term preservation of photographic works. The major contribution of this thesis is to create and gain a better understanding of tools that can be used in the characterisation and identification of expired silver gelatin papers. It is also to demonstrate that a tactile tool such as the sample booklet can assist in identifying various deterioration events. I feel that it is important to have a hands-on source that can be used independently or collectively with other sources such as web-based visual identification tools. The booklet will be useful as an educational tool for students, collection care takers, as well as professionals in the photographic field.

scholarly journals THE URBIS PROJECT: IDENTIFICATION AND CHARACTERIZATION OF POTENTIAL URBAN DEVELOPMENT AREAS AS A WEB-BASED SERVICE

2016 ◽  
Vol XLI-B4 ◽  
pp. 227-233
Author(s):  
Nina Manzke ◽  
Martin Kada ◽  
Thomas Kastler ◽  
Shaojuan Xu ◽  
Norbert de Lange ◽  
...  
Keyword(s):  
Urban Areas ◽  
Landscape Fragmentation ◽  
Urban Land ◽  
End Users ◽  
Information Services ◽  
Urban Land Use ◽  
Specific Information ◽  
Remotely Sensed Data ◽  
Web Based ◽  
Site Specific

Urban sprawl and the related landscape fragmentation is a Europe-wide challenge in the context of sustainable urban planning. The URBan land recycling Information services for Sustainable cities (URBIS) project aims for the development, implementation, and validation of web-based information services for urban vacant land in European functional urban areas in order to provide end-users with site specific characteristics and to facilitate the identification and evaluation of potential development areas. The URBIS services are developed based on open geospatial data. In particular, the Copernicus Urban Atlas thematic layers serve as the main data source for an initial inventory of sites. In combination with remotely sensed data like SPOT5 images and ancillary datasets like OpenStreetMap, detailed site specific information is extracted. Services are defined for three main categories: i) baseline services, which comprise an initial inventory and typology of urban land, ii) update services, which provide a regular inventory update as well as an analysis of urban land use dynamics and changes, and iii) thematic services, which deliver specific information tailored to end-users' needs.

Restful Web Service and Web-Based Data Visualization for Environmental Monitoring

2015 ◽  
Vol 3 (1) ◽  
pp. 75-94 ◽  
Author(s):  
Sungchul Lee ◽  
Ju-Yeon Jo ◽  
Yoohwan Kim
Keyword(s):  
Web Service ◽  
Data Visualization ◽  
Water Environment ◽  
Environmental Data ◽  
Renewable Energy Resources ◽  
Service Architecture ◽  
Web Based ◽  
Research Fields ◽  
Restful Web Service ◽  
Rest Api

The Nevada Solar Energy-Water-Environment Nexus project collects a large amount of environmental data from a variety of sensors such as soil, atmosphere, biology, and ecology. Mostly, the environmental data is related to a development of renewable energy resources in the Nexus project. The environmental data can have an impact on other research fields if it can easily be shared with other researchers, students, teachers, and general users. Therefore, Nevada Climate Change Portal (NCCP) site was created for Nexus project with a purpose of sharing such data. However, there are some challenges to address in utilizing such data, collecting the data, and sharing the data among the users. In this research, the authors propose Extended Web Service Architecture for solving these challenges. The authors implement Arduino instead of CR1000 as a collector due to its cost effectiveness. The authors also use REST API to overcome the limitations of Arduino. Moreover, the authors experiment with popular Web-based data visualization tools such as Google Chart, Flex, OFC, and D3 to visualize NCCP data.

scholarly journals JUMP: A Tag-based Database Search Tool for Peptide Identification with High Sensitivity and Accuracy

2014 ◽  
Vol 13 (12) ◽  
pp. 3663-3673 ◽  
Author(s):  
Xusheng Wang ◽  
Yuxin Li ◽  
Zhiping Wu ◽  
Hong Wang ◽  
Haiyan Tan ◽  
...  
Keyword(s):  
Peptide Identification ◽  
High Sensitivity ◽  
Database Search ◽  
Search Tool

Pathogenicity of mutation analyzer (PathoMAN): A fast automation of germline genomic variant curation in clinical sequencing.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 1529-1529
Author(s):  
Vijai Joseph ◽  
Vignesh Ravichandran ◽  
Kenneth Offit
Keyword(s):  
Specific Information ◽  
Web Based ◽  
Clinical Sequencing ◽  
Bioinformatic Tools ◽  
Manual Curation ◽  
Lack Of Information ◽  
Public Resources ◽  
Uncertain Significance ◽  
Patients At Risk ◽  
Genomic Variant

1529 Background: A challenge in clinical oncology is interpretation of multiplexed gene sequencing of patients at risk. The plethora of variants to be curated for pathogenicity or actionability poses a growing burden for cancer care professionals. Current guidelines by the ACMG requires the aggregation of multiple lines of genomic data evidences from diverse resources. A computational tool that automates, provide uniformity and significantly speed the interpretive process is thus necessary. Methods: The Pathogenicity of Mutation Analyzer (PathoMAN), is a tool that automates germline genomic variant curation from clinical sequencing based on ACMG guidelines. PathoMAN aggregates multiple tracks of genomic, protein and disease specific information from public sources such as ClinVar, ExAC, UniProt, 1000 genomes, dbNSFP and locus specific databases. Variant specific and gene specific annotations are used to classify variants to model the ACMG rubric. We analyzed 2500 manually curated and classified, high quality variants in 180 genes from 3 large, published studies to quantify the performance of PathoMAN; analyzing 242 pathogenic/likely pathogenic (P/LP), 1272 benign/likely benign (B/LB) and 1261 variants of uncertain significance (VUS). We report the summary of PathoMAN classifications in four categories contrasted against the manual curation. Results: PathoMan achieves an average of 75% concordance and 1.5% discordance for P/LP mutations and 60% and 0.1% for B/LB variants. PathoMAN is able to resolve 12% of reported VUS as either P/LP or B/LB. It loses resolution to classify 25% of P/LP and B/LB variants due to lack of information and due to inconsistencies in available data from public resources. Conclusions: PathoMAN provides a breakthrough in rapid classification of genetic variants by generation of robust models using a knowledgebase of diverse genetic data. It is easily accessible, web-based resource that allows the community to rapidly test a large number of variants for pathogenicity. Such bioinformatic tools are essential to reduce manual workload of a domain level experts. We propose, a new nosology for the 5 ACMG classes to facilitate better reporting to ClinVar.

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