scholarly journals GOAPhAR: An Integrative Discovery Tool for Annotation, Pathway Analysis

2009 ◽  
Vol 3 (1) ◽  
pp. 26-30 ◽  
Author(s):  
Mathur Sachin ◽  
Visvanathan Mahesh ◽  
Svojanovsky Stan ◽  
Yoo Byunggil ◽  
Srinivas Adagarla B. ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Protein Interactions ◽  
Microarray Data ◽  
Sources Of Information ◽  
Web Based ◽  
Gene Annotations ◽  
Functional Pathways ◽  
Microarray Datasets ◽  
User Friendly ◽  
The Web

We have developed the web based tool GOAPhAR (Gene Ontology, Annotations and Pathways for Array Research), that integrates information from disparate sources regarding gene annotations, protein annotations, identifiers associated with probe sets, functional pathways, protein interactions, Gene Ontology, publicly available microarray datasets and tools for statistically validating clusters in microarray data. Genes of interest can be input as Affymetrix probe identifiers, Genbank, or Unigene identifiers for human, mouse or rat genomes. Results are provided in a user friendly interface with hyperlinks to the sources of information. The tool is freely available at http://bioinformatics.kumc.edu/goaphar/.

Web-Based Responsive Mobile Learning (M-Learning) Design

2020 ◽  
pp. 301-317
Author(s):  
Alaattin Parlakkılıç
Keyword(s):  
Learning Styles ◽  
Instructional Strategies ◽  
Mobile Learning ◽  
Web Sites ◽  
Social Life ◽  
Solid Material ◽  
Web Based ◽  
Responsive Design ◽  
User Friendly ◽  
The Web

The mobile initiative is changing education and social life worldwide. The question is how to offer the same user-friendly, aesthetically pleasing mobile learning courses on different mobile devices. Developing effective web sites courses and content isn't only about creating a course with solid material. Managers and course authors are concerned about adapting different courses to a variety of learning styles and individual needs and keeping users interested and engaged. A good place to start is to organize thoughts and figure out exactly what is wanted to be included in the web sites course. Responsive design gives the ability to create a single m-learning course that automatically adapts to any browser or device. This allows the target audience to benefit from the courses without having to worry about screen size and resolution. In this chapter, m-learning is discussed in a responsive design context that can be used across platforms and offers the design of courses according to m-learning instructional strategies.

scholarly journals Mining Gene Ontology Data with AGENDA

2012 ◽  
Vol 6 ◽  
pp. BBI.S9101
Author(s):  
Guvanch Ovezmyradov ◽  
Qianhao Lu ◽  
Martin C. Göpfert
Keyword(s):  
Gene Ontology ◽  
Open Source ◽  
Genetic Information ◽  
Collaborative Effort ◽  
Controlled Vocabularies ◽  
Web Based ◽  
Commercial Use ◽  
Diverse Species ◽  
Go Terms ◽  
The Web

The Gene Ontology (GO) initiative is a collaborative effort that uses controlled vocabularies for annotating genetic information. We here present AGENDA (Application for mining Gene Ontology Data), a novel web-based tool for accessing the GO database. AGENDA allows the user to simultaneously retrieve and compare gene lists linked to different GO terms in diverse species using batch queries, facilitating comparative approaches to genetic information. The web-based application offers diverse search options and allows the user to bookmark, visualize, and download the results. AGENDA is an open source web-based application that is freely available for non-commercial use at the project homepage. URL: http://sourceforge.net/projects/bioagenda .

scholarly journals SHARING ON WEB 3D MODELS OF ANCIENT THEATRES. A METHODOLOGICAL WORKFLOW

2016 ◽  
Vol XLI-B2 ◽  
pp. 483-490 ◽  
Author(s):  
A. Scianna ◽  
M. La Guardia ◽  
M. L. Scaduto
Keyword(s):  
Methodological Approach ◽  
Three Dimensional ◽  
Spatial Models ◽  
3D Models ◽  
Web Based ◽  
Web 3D ◽  
The One ◽  
User Friendly ◽  
Geospatial Web Services ◽  
The Web

In the last few years, the need to share on the Web the knowledge of Cultural Heritage (CH) through navigable 3D models has increased. This need requires the availability of Web-based virtual reality systems and 3D WEBGIS. In order to make the information available to all stakeholders, these instruments should be powerful and at the same time very user-friendly. However, research and experiments carried out so far show that a standardized methodology doesn’t exist. All this is due both to complexity and dimensions of geometric models to be published, on the one hand, and to excessive costs of hardware and software tools, on the other. In light of this background, the paper describes a methodological approach for creating 3D models of CH, freely exportable on the Web, based on HTML5 and free and open source software. HTML5, supporting the WebGL standard, allows the exploration of 3D spatial models using most used Web browsers like Chrome, Firefox, Safari, Internet Explorer. The methodological workflow here described has been tested for the construction of a multimedia geo-spatial platform developed for three-dimensional exploration and documentation of the ancient theatres of Segesta and of Carthage, and the surrounding landscapes. The experimental application has allowed us to explore the potential and limitations of sharing on the Web of 3D CH models based on WebGL standard. Sharing capabilities could be extended defining suitable geospatial Web-services based on capabilities of HTML5 and WebGL technology.

scholarly journals SHARING ON WEB 3D MODELS OF ANCIENT THEATRES. A METHODOLOGICAL WORKFLOW

2016 ◽  
Vol XLI-B2 ◽  
pp. 483-490 ◽  
Author(s):  
A. Scianna ◽  
M. La Guardia ◽  
M. L. Scaduto
Keyword(s):  
Methodological Approach ◽  
Three Dimensional ◽  
Spatial Models ◽  
3D Models ◽  
Web Based ◽  
Web 3D ◽  
The One ◽  
User Friendly ◽  
Geospatial Web Services ◽  
The Web

In the last few years, the need to share on the Web the knowledge of Cultural Heritage (CH) through navigable 3D models has increased. This need requires the availability of Web-based virtual reality systems and 3D WEBGIS. In order to make the information available to all stakeholders, these instruments should be powerful and at the same time very user-friendly. However, research and experiments carried out so far show that a standardized methodology doesn’t exist. All this is due both to complexity and dimensions of geometric models to be published, on the one hand, and to excessive costs of hardware and software tools, on the other. In light of this background, the paper describes a methodological approach for creating 3D models of CH, freely exportable on the Web, based on HTML5 and free and open source software. HTML5, supporting the WebGL standard, allows the exploration of 3D spatial models using most used Web browsers like Chrome, Firefox, Safari, Internet Explorer. The methodological workflow here described has been tested for the construction of a multimedia geo-spatial platform developed for three-dimensional exploration and documentation of the ancient theatres of Segesta and of Carthage, and the surrounding landscapes. The experimental application has allowed us to explore the potential and limitations of sharing on the Web of 3D CH models based on WebGL standard. Sharing capabilities could be extended defining suitable geospatial Web-services based on capabilities of HTML5 and WebGL technology.

scholarly journals TACITuS: transcriptomic data collector, integrator, and selector on big data platform

2019 ◽  
Vol 20 (S9) ◽  
Author(s):  
Salvatore Alaimo ◽  
Antonio Di Maria ◽  
Dennis Shasha ◽  
Alfredo Ferro ◽  
Alfredo Pulvirenti
Keyword(s):  
High Throughput ◽  
Rna Seq ◽  
Web Based ◽  
Large Bandwidth ◽  
Specific Analysis ◽  
Galaxy Environment ◽  
Public Repositories ◽  
Microarray Datasets ◽  
User Friendly ◽  
Ngs Data

Abstract Background Several large public repositories of microarray datasets and RNA-seq data are available. Two prominent examples include ArrayExpress and NCBI GEO. Unfortunately, there is no easy way to import and manipulate data from such resources, because the data is stored in large files, requiring large bandwidth to download and special purpose data manipulation tools to extract subsets relevant for the specific analysis. Results TACITuS is a web-based system that supports rapid query access to high-throughput microarray and NGS repositories. The system is equipped with modules capable of managing large files, storing them in a cloud environment and extracting subsets of data in an easy and efficient way. The system also supports the ability to import data into Galaxy for further analysis. Conclusions TACITuS automates most of the pre-processing needed to analyze high-throughput microarray and NGS data from large publicly-available repositories. The system implements several modules to manage large files in an easy and efficient way. Furthermore, it is capable deal with Galaxy environment allowing users to analyze data through a user-friendly interface.

scholarly journals Distributed aggregation of heterogeneous Web-based Fine Art Information: enabling multi-source accessibility and curation

2015 ◽  
Vol 30 (2) ◽  
pp. 220-236 ◽  
Author(s):  
Frances Buchanan ◽  
Niccolo Capanni ◽  
Horacio González-Vélez
Keyword(s):  
Web Application ◽  
Web Applications ◽  
Information Service ◽  
Application Programming Interface ◽  
Fine Art ◽  
Public Access ◽  
Distributed Data ◽  
Sources Of Information ◽  
Web Based ◽  
The Web

AbstractThe sources of information on the Web relating to Fine Art and in particular to Fine Artists are numerous, heterogeneous and distributed. Data relating to the biographies of an artist, images of their artworks, location of the artworks and exhibition reviews invariably reside in distinct and seemingly unrelated, or at least unlinked, sources. While communication and exchange exists, there is a great deal of independence between major repositories, such as museum, often owing to their ownership or heritage. This increases the individuality in the repository’s own processes and dissemination. It is currently necessary to browse through numerous different websites to obtain information about any one artist, and at this time there is little aggregation of Fine Art Information. This is in contrast to the domain of books and music, where the aggregation and re-grouping of information (usually by author or artist/band name) has become the norm. A Museum API (Application Programming Interface), however, is a tool that can facilitate a similar information service for the domain of Fine Art, by allowing the retrieval and aggregation of Web-based Fine Art Information, whilst at the same time increasing public access to the content of a museum’s collection. In this paper, we present the case for a pragmatic solution to the problems of heterogeneity and distribution of Fine Art Data and this is the first step towards the comprehensive re-presentation of Fine Art Information in a more ‘artist-centric’ way, via accessible Web applications. This paper examines the domain of Fine Art Information on the Web, putting forward the case for more Web services such as generic Museum APIs, highlighting this via a prototype Web application known as the ArtBridge. The generic Museum API is the standardisation mechanism to enable interfacing with specific Museum APIs.

scholarly journals PINAWeb: A web-based tool for the comparison of Protein-Protein Interaction Networks Aligners

2021 ◽  
Author(s):  
A. Alcalá ◽  
G. Riera ◽  
I. García ◽  
R. Alberich ◽  
M. Llabrés
Keyword(s):  
Protein Interaction ◽  
Protein Interactions ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Protein Protein Interactions ◽  
Considerable Effort ◽  
Web Based ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Networks ◽  
User Friendly

AbstractMotivationSeveral protein-protein interaction networks (PPIN) aligners have been developed during the last 15 years. One of their goals is to help the functional annotation of proteins and the prediction of protein-protein interactions. A correct aligner must preserve the network’s topology as well as the biological coherence. However, this is a trade-off that is hard to achieve. In addition, most aligners require a considerable effort to use in practice and many researchers must choose an aligner without the opportunity to previously compare the performance of different aligners.ResultsWe developed PINAWeb, a user-friendly web-based tool to obtain and compare the results produced by the aligners: AligNet, HubAlign, L-GRAAL, PINALOG and SPINAL. PPINs can be uploaded either from the STRING database or from a user database. The source code of PINAWeb is freely available on GitHub to enable researchers to add other aligners, network databases or alignment score metrics. In addition, PINAWeb provides a report with the analysis for every alignment in terms of topological and functional information scores, as well as the visualization of the alignments’ comparison (agreement/differences) when more than one aligner are considered.Availabilityhttps://bioinfo.uib.es/~recerca/PINAWeb

scholarly journals Xeno-miRNet: a comprehensive database and analytics platform to explore xeno-miRNAs and their potential targets

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5650 ◽  
Author(s):  
Yannan Fan ◽  
Maria Habib ◽  
Jianguo Xia
Keyword(s):  
Host Species ◽  
Species Interactions ◽  
Web Application ◽  
Potential Functions ◽  
Circulation System ◽  
Multiple Sources ◽  
Web Based ◽  
User Friendly ◽  
The Web ◽  
Computational Predictions

Xeno-miRNAs are microRNAs originating from exogenous species detected in host biofluids. A growing number of studies have suggested that many of these xeno-miRNAs may be involved in cross-species interactions and manipulations. To date, hundreds of xeno-miRNAs have been reported in different hosts at various abundance levels. Based on computational predictions, many more miRNAs could be potentially transferred to human circulation system. There is a clear need for bioinformatics resources and tools dedicated to xeno-miRNA annotations and their potential functions. To address this need, we have systematically curated xeno-miRNAs from multiple sources, performed target predictions using well-established algorithms, and developed a user-friendly web-based tool—Xeno-miRNet—to allow researchers to search and explore xeno-miRNAs and their potential targets within different host species. Xeno-miRNet currently contains 1,702 (including both detected and predicted) xeno-miRNAs from 54 species and 98,053 potential gene targets in six hosts. The web application is freely available at http://xeno.mirnet.ca.

scholarly journals EXTRACTING HUMAN BEHAVIORAL PATTERNS BY MINING GEO-SOCIAL NETWORKS

2014 ◽  
Vol XL-2/W3 ◽  
pp. 115-120
Author(s):  
M. Forghani ◽  
F. Karimipour
Keyword(s):  
Social Networks ◽  
Data Analysis ◽  
Location Information ◽  
Sources Of Information ◽  
Web Based ◽  
Travel Experience ◽  
Information Layer ◽  
Over Time ◽  
The Web ◽  
Category Usage

Accessibility of positioning technologies such as GPS offer the opportunity to store one’s travel experience and publish it on the web. Using this feature in web-based social networks and considering location information shared by users as a bridge connecting the users’ network to location information layer leads to the formation of Geo-Social Networks. The availability of large amounts of geographical and social data on these networks provides rich sources of information that can be utilized for studying human behavior through data analysis in a spatial-temporal-social context. This paper attempts to investigate the behavior of around 1150 users of Foursquare network by making use of their check-ins. The authors analyzed the metadata associated with the whereabouts of the users, with an emphasis on the type of places, to uncover patterns across different temporal and geographical scales for venue category usage. The authors found five groups of meaningful patterns that can explore region characteristics and recognize a number of major crowd behaviors that recur over time and space.

Sign in / Sign up

Export Citation Format

Share Document