scholarly journals BioGraph: a web application and a graph database for querying and analyzing bioinformatics resources

2018 ◽  
Vol 12 (S5) ◽  
Author(s):  
Antonio Messina ◽  
Antonino Fiannaca ◽  
Laura La Paglia ◽  
Massimo La Rosa ◽  
Alfonso Urso
Keyword(s):  
Web Application ◽  
Graph Database

scholarly journals Advantages of using graph databases to explore chromatin conformation capture experiments

2021 ◽  
Vol 22 (S2) ◽  
Author(s):  
Daniele D’Agostino ◽  
Pietro Liò ◽  
Marco Aldinucci ◽  
Ivan Merelli
Keyword(s):  
Web Application ◽  
High Throughput Sequencing ◽  
Cell Types ◽  
Graph Database ◽  
Graph Databases ◽  
Sources Of Information ◽  
Chromosome Conformation ◽  
Wide Scale ◽  
User Friendly ◽  
Different Cell Types

Abstract Background High-throughput sequencing Chromosome Conformation Capture (Hi-C) allows the study of DNA interactions and 3D chromosome folding at the genome-wide scale. Usually, these data are represented as matrices describing the binary contacts among the different chromosome regions. On the other hand, a graph-based representation can be advantageous to describe the complex topology achieved by the DNA in the nucleus of eukaryotic cells. Methods Here we discuss the use of a graph database for storing and analysing data achieved by performing Hi-C experiments. The main issue is the size of the produced data and, working with a graph-based representation, the consequent necessity of adequately managing a large number of edges (contacts) connecting nodes (genes), which represents the sources of information. For this, currently available graph visualisation tools and libraries fall short with Hi-C data. The use of graph databases, instead, supports both the analysis and the visualisation of the spatial pattern present in Hi-C data, in particular for comparing different experiments or for re-mapping omics data in a space-aware context efficiently. In particular, the possibility of describing graphs through statistical indicators and, even more, the capability of correlating them through statistical distributions allows highlighting similarities and differences among different Hi-C experiments, in different cell conditions or different cell types. Results These concepts have been implemented in NeoHiC, an open-source and user-friendly web application for the progressive visualisation and analysis of Hi-C networks based on the use of the Neo4j graph database (version 3.5). Conclusion With the accumulation of more experiments, the tool will provide invaluable support to compare neighbours of genes across experiments and conditions, helping in highlighting changes in functional domains and identifying new co-organised genomic compartments.

scholarly journals NGLMS-CR: A Web-Based Clerical Review Tool

2020 ◽  
Vol 5 (5) ◽  
Author(s):  
James Farrow ◽  
Miro Palfy
Keyword(s):  
Web Application ◽  
Ad Hoc ◽  
Multiple Birth ◽  
Graph Database ◽  
Sensitive Data ◽  
Web Based ◽  
Time Activity ◽  
Gender Information ◽  
Other Information ◽  
Birth Records

Native applications often require special permissions to install and update which may not always be available in secure/controlled sensitive-data environments. Deploying new features can be time-consuming and introduce delays. The Next Generation Linkage System Clerical Review tool (NGLMS-CR) is a configurable web application which side-steps these issues. The NGLMS-CR allows rapid response to changing project requirements. Objectives and ApproachWe wanted a lightweight platform-independent tool to run in any modern web-browser. This avoids a need for special administrative privileges and allows rapid deployment/update. The NGLMS-CR communicates via a simple RESTful protocol to a server managing user-permissions, workflows and review data. Data is stored in a relational or graph database. The NGLMS-CR does not require a graph database. Users see various workpools (collections of records) and work through these at their own pace. Different workpools may be configured for different requirements, e.g. clusters requiring special expertise, clusters requiring higher data security, overly-large clusters &c. Custom workflows are built around workpools. Individual clusters can have customisable status indicators displayed to highlight integrity checks and other information, e.g. a cluster containing multiple birth records or containing records with inconsistent gender information. The tool also promotes ergonomic and health objectives as well as collecting metrics about review activity. The review session tracks reviewer engagement and gives feedback on the situation so far: how long has been spent reviewing; how long activity has been undertaken without a break. The user is given visual warnings when sessions extend beyond a set time. Activity is logged and metrics regarding throughput/accuracy collated for analysis.ResultsIn real-time manual clerical review tasks the customisable nature of the NGLMS-CR has proven important. Changes are immediately visible to users and workflow and status icons changes available with no delay while software is ‘rolled out’. Conclusion / ImplicationsUncoupling review from any particular linkage system enables flexibility in project administration. A web-based review application may run on any system and requires minimal administrative permissions. This facilitates deployment in sensitive environments. Customisable workflow allows quick creation of ad hoc projects/tasks, even mid-project as new situations are discovered. Customisable cluster integrity checks allows cluster- and project-sensitive feedback to be rapidly deployed to aid review. By being flexible and independent the NGLMS-CR can supplement and complement existing linkage and review processes.

scholarly journals A SEMANTIC GRAPH DATABASE FOR BIM-GIS INTEGRATED INFORMATION MODEL FOR AN INTELLIGENT URBAN MOBILITY WEB APPLICATION

2018 ◽  
Vol IV-4 ◽  
pp. 89-96 ◽  
Author(s):  
A.-H. Hor ◽  
G. Sohn ◽  
P. Claudio ◽  
M. Jadidi ◽  
A. Afnan
Keyword(s):  
Web Application ◽  
Architectural Design ◽  
Data Extraction ◽  
Semantic Integration ◽  
Graph Database ◽  
Graph Databases ◽  
Urban Mobility ◽  
Real World Data ◽  
Semantic Web Technologies ◽  
Rdf Data

<p><strong>Abstract.</strong> Over the recent years, the usage of semantic web technologies and Resources Description Framework (RDF) data models have been notably increased in many fields. Multiple systems are using RDF data to describe information resources and semantic associations. RDF data plays a very important role in advanced information retrieval, and graphs are efficient ways to visualize and represent real world data by providing solutions to many real-time scenarios that can be simulated and implemented using graph databases, and efficiently query graphs with multiple attributes representing different domains of knowledge. Given that graph databases are schema less with efficient storage for semi-structured data, they can provide fast and deep traversals instead of slow RDBMS SQL based joins allowing Atomicity, Consistency, Isolation and durability (ACID) transactions with rollback support, and by utilizing mathematics of graph they can enormous potential for fast data extraction and storage of information in the form of nodes and relationships. In this paper, we are presenting an architectural design with complete implementation of BIM-GIS integrated RDF graph database. The proposed integration approach is composed of four main phases: ontological BIM and GIS model’s construction, mapping and semantic integration using interoperable data formats, then an import into a graph database with querying and filtering capabilities. The workflows and transformations of IFC and CityGML schemas into object graph databases model are developed and applied to an intelligent urban mobility web application on a game engine platform validate the integration methodology.</p>

Practical Approach towards Charitable Giving via Interactive Web Application for Online Philanthropy

2017 ◽  
Author(s):  
Saurabh Mahajan ◽  
Pranati Paidipat ◽  
Rasika Khangarle ◽  
Mona Mulchandani
Keyword(s):  
Web Application ◽  
Charitable Giving ◽  
Practical Approach

ANALYZING AND IMPROVING WEB APPLICATION QUALITY USING DESIGN PATTERNS

2012 ◽  
Vol 2 (2) ◽  
pp. 112-116
Author(s):  
Shikha Bhatia ◽  
Mr. Harshpreet Singh
Keyword(s):  
Web Application ◽  
Design Pattern ◽  
Design Patterns ◽  
Web Applications ◽  
Past Research ◽  
Software Systems ◽  
Interactive Software ◽  
Web Based ◽  
Software Application ◽  
Execution Speed

With the mounting demand of web applications, a number of issues allied to its quality have came in existence. In the meadow of web applications, it is very thorny to develop high quality web applications. A design pattern is a general repeatable solution to a generally stirring problem in software design. It should be noted that design pattern is not a finished product that can be directly transformed into source code. Rather design pattern is a depiction or template that describes how to find solution of a problem that can be used in many different situations. Past research has shown that design patterns greatly improved the execution speed of a software application. Design pattern are classified as creational design patterns, structural design pattern, behavioral design pattern, etc. MVC design pattern is very productive for architecting interactive software systems and web applications. This design pattern is partition-independent, because it is expressed in terms of an interactive application running in a single address space. We will design and analyze an algorithm by using MVC approach to improve the performance of web based application. The objective of our study will be to reduce one of the major object oriented features i.e. coupling between model and view segments of web based application. The implementation for the same will be done in by using .NET framework.

Sign in / Sign up

Export Citation Format

Share Document