Data Visualization Web Application Research Articles

Report and Application of a Tool Compound Data Set.

Small molecule tool compounds have enabled profound advances in life science research. These chemicals are potent, cell active, and selective, and, thus, are suitable for interrogating biological processes. For these chemicals to be useful they must be correctly characterized and researchers must be aware of them. We mined the ChEMBL bioactivity database to identify high quality tool compounds in an unbiased way. We identified 407 best-in-class compounds for 278 protein targets, and these are reported in an annotated data set. Additionally, we developed informatics functions and a web application for data visualization and automated pharmacological hypothesis generation. These functions were used to predict inhibitors of the Chromobox Protein Homologue 5 (CBX5) mediated gene repression pathway that currently lacks appropriate inhibitors. The predictions were subsequently validated by a highly specific cell based assay, revealing new chemical modulators of CBX5-mediated heterochromatin formation. This data set and associated functions will help researchers make the best use of these valuable compounds.

Abstract C03: Disparitome-Miner: A data visualization web-application for ‘gene-of-interest’ in health disparities

Abstract Attempting to understand the gene-environment interactions that lead to disease is the basis of modern molecular medicine. DNA microarray technology has provided vast quantities of new data for building up these models. Unfortunately the vast majority of studies using this technology consist of samples from populations of European ancestry. To understand the gene-environment interactions that contribute to racial and ethnic health disparities data from studies with samples from diverse populations must be analyzed. Currently, this data is limited and hard to access. The few studies that use samples from diverse populations are lost among the millions of published microarray datasets. To address this issue we have developed Disparitome-Miner, a microarray database and web-based data-mining platform that will serve as a tool for facilitating discovery from published transcriptomic datasets. To date, Disparitome-Miner contains 18 microarray datasets consisting of samples from diverse patient populations. Differential expression analyses comparing tissue samples from healthy and disease states in multiple ancestry backgrounds are provided. Transcriptomic microarray data is analyzed and visualized interactively through Shiny Server, an open-source package for web-based R applications. Our hope is that Disparitome-Miner allows life scientists without advanced statistical training to evaluate their gene-of-interest for a role in the gene-environment interactions that contribute to racial and ethnic health disparities. This web-app can provide help in hypothesis-generation and facilitate further investigation into health disparities. Citation Format: Aasakiran Madamanchi, David Cappel, Chaitanya Madamanchi, Roman Covarrubias, John Micheal Thomson. Disparitome-Miner: A data visualization web-application for ‘gene-of-interest’ in health disparities. [abstract]. In: Proceedings of the Sixth AACR Conference: The Science of Cancer Health Disparities; Dec 6–9, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2014;23(11 Suppl):Abstract nr C03. doi:10.1158/1538-7755.DISP13-C03

LIT: transcription, annotation, search and visualization tools for the Lexicon of the Italian Television

LIT (Lexicon of the Italian Television) is a project conceived by the Accademia della Crusca, the leading research institution on the Italian language, in collaboration with CLIEO (Center for theoretical and historical Linguistics: Italian, European and Oriental languages), with the aim of studying frequencies of the Italian vocabulary used in television. Approximately 170 hours of random television recordings acquired from the national broadcaster RAI (Italian Radio Television) during the year 2006 have been used to create the corpus of transcriptions. The principal outcome of the project is the design and implementation of an interactive system which combines a web-based video transcription and annotation tool, a full featured search engine, and a web application for data visualization with text-video syncing. Furthermore, the project is currently under deployment as a module of the larger national research funding FIRB 2009 VIVIT (Fondo di Investimento per la Ricerca di Base, Vivi l'Italiano), which will integrate its achievements and results within a semantic web infrastructure.

Usage of Web Applications for Monitoring of Geothermal Systems

This paper deals with a description of a unique system for borehole temperature measurement, and its consequent Web application for data visualization based on OPC communication and FTP access. There are some short descriptions of the Big Research Polygon (BRP), and the Small Research Polygon (SRP) - main parts of the largest heating system with heat pumps in the Czech Republic. They serve not only for scientific and education purposes, but also for problem of renewable energy resources. Each of these boreholes contains some temperature sensors (analogue, digital) connected to some PLC/PAC systems for data acquisition, data processing, and their saving to a measurement file. A Web application uses possibility of dynamic HTML pages created in PHP programming language. Current version of this application reshapes measurement data (from boreholes and heat pumps) into some general tables in dependence on borehole competency, and heat pump parameters, such as mass-flow, density, or volume-flow. In the future it is planned to use MS SQL database system.