scholarly journals Enhancements in Functionality of the Interactive Visual Explorer for ATLAS Computing Metadata

2020 ◽  
Vol 245 ◽  
pp. 05032
Author(s):  
M.A. Grigorieva ◽  
A.A. Alekseev ◽  
A.A. Artamonov ◽  
T.P. Galkin ◽  
D.V. Grin ◽  
...  
Keyword(s):  
Data Storage ◽  
Visual Analytics ◽  
Visual Analysis ◽  
Clustering Algorithms ◽  
Level Of Detail ◽  
Web Based ◽  
Atlas Experiment ◽  
Monitoring Tools ◽  
Preparation Stage ◽  
Interactive Visual Analysis

The development of the Interactive Visual Explorer (InVEx), a visual analytics tool for the computing metadata of the ATLAS experiment at LHC, includes research of various approaches for data handling both on server and client sides. InVEx is implemented as a web-based application which aims at the enhancing of analytical and visualization capabilities of the existing monitoring tools and facilitates the process of data analysis with the interactivity and human supervision. The current work is focused on the architecture enhancements of the InVEx application. First, we will describe the user-manageable data preparation stage for cluster analysis. Then, the Level-of-Detail approach for the interactive visual analysis will be presented. It starts with the low detailing, when all data records are grouped (by clustering algorithms or by categories) and aggregated. We provide users with means to look deeply into this data, incrementally increasing the level of detail. Finally, we demonstrate the development of data storage backend for InVEx, which is adapted for the Level-of-Detail method to keep all stages of data derivation sequence.

scholarly journals Panomicon: A web-based environment for interactive, visual analysis of multi-omics data

Heliyon ◽  
2020 ◽  
Vol 6 (8) ◽  
pp. e04618
Author(s):  
Rodolfo S. Allendes Osorio ◽  
Johan T. Nyström-Persson ◽  
Yosui Nojima ◽  
Yuji Kosugi ◽  
Kenji Mizuguchi ◽  
...  
Keyword(s):  
Visual Analysis ◽  
Omics Data ◽  
Web Based ◽  
Interactive Visual Analysis

The Scalable Reasoning System: Lightweight Visualization for Distributed Analytics

2009 ◽  
Vol 8 (1) ◽  
pp. 71-84 ◽  
Author(s):  
William Pike ◽  
Joe Bruce ◽  
Bob Baddeley ◽  
Daniel Best ◽  
Lyndsey Franklin ◽  
...  
Keyword(s):  
Law Enforcement ◽  
Visual Analytics ◽  
Visual Analysis ◽  
Web Based ◽  
Reasoning Strategies ◽  
Reasoning System ◽  
Mobile Interfaces ◽  
Service Oriented ◽  
Distributed Analytics

A central challenge in visual analytics is the creation of accessible, widely distributable analysis applications that bring the benefits of visual discovery to as broad a user base as possible. Moreover, to support the role of visualization in the knowledge creation process, it is advantageous to allow users to describe the reasoning strategies they employ while interacting with analytic environments. We introduce an application suite called the scalable reasoning system (SRS), which provides web-based and mobile interfaces for visual analysis. The service-oriented analytic framework that underlies SRS provides a platform for deploying pervasive visual analytic environments across an enterprise. SRS represents a ‘lightweight’ approach to visual analytics whereby thin client analytic applications can be rapidly deployed in a platform-agnostic fashion. Client applications support multiple coordinated views while giving analysts the ability to record evidence, assumptions, hypotheses and other reasoning artifacts. We describe the capabilities of SRS in the context of a real-world deployment at a regional law enforcement organization.

scholarly journals BioViz Connect: Web application linking CyVerse science gateway resources to genomic visualization in the Integrated Genome Browser

2020 ◽  
Author(s):  
Nowlan H Freese ◽  
Karthik Raveendran ◽  
Chaitanya Kintali ◽  
Srishti Tiwari ◽  
Pawan Bole ◽  
...  
Keyword(s):  
Visual Analytics ◽  
Web Application ◽  
Visual Analysis ◽  
Genomic Data ◽  
Application Programming Interface ◽  
Genome Browser ◽  
Rna Seq ◽  
Web Based ◽  
Science Gateways ◽  
Application Programming

AbstractBackgroundVisualization of genomic data is a key step in validating methods and results. Web-based science gateways such as CyVerse provide storage and analysis tools for genomic data but often lack visualization capability. Desktop visualization tools like Integrated Genome Browser (IGB) enable highly interactive data visualization but are difficult to deploy in science gateways. Developing ways for gateways to interoperate with pre-existing external tools like IGB would enhance their value to users.ResultsWe developed BioViz Connect, a new web application that connects CyVerse and IGB using the CyVerse Terrain Application Programming Interface (API). Using BioViz Connect, users can (i) stream their CyVerse data to IGB for visualization, (ii) add IGB specific metadata such as genome version and track appearance to CyVerse data, and (iii) run compute-intensive visual analytics functions to create new visualizations for IGB. To demonstrate BioViz Connect, we present an example visual analysis of RNA-Seq data from Arabidopsis thaliana plants undergoing heat and desiccation stresses. The example shows how researchers can seamlessly analyze and visualize their CyVerse data in IGB. BioViz Connect is accessible from https://bioviz.org.ConclusionsBioViz Connect demonstrates a new way to integrate science gateways with desktop applications using APIs.

scholarly journals Interactive analysis of Long-read RNA isoforms with Iso-Seq Browser

2017 ◽  
Author(s):  
Jingyuan Hu ◽  
Prech Uapinyoying ◽  
Jeremy Goecks
Keyword(s):  
Rna Sequencing ◽  
Visual Analytics ◽  
Visual Analysis ◽  
Sequencing Data ◽  
Web Based ◽  
Interactive Analysis ◽  
Pacific Biosciences ◽  
Long Read ◽  
Gene Transcripts ◽  
Gene Isoforms

AbstractBackgroundLong-read RNA sequencing, such as Pacific Biosciences’ Iso-Seq method, enables generation of sequencing reads that are 10 kilobases or even longer. These reads are ideal for discovering splice junctions and resolving full-length gene transcripts without time-consuming and error-prone techniques such as transcript assembly and junction inference.ResultsIso-Seq Browser is a Web-based visual analytics tool for long-read RNA sequencing data produced by Pacific Biosciences’ isoform sequencing (Iso-Seq) techniques. Key features of the Iso-Seq Browser are: 1) an exon-only web-based interface with zooming and exon highlighting for exploring reference gene transcripts and novel gene isoforms, 2) automated grouping of transcripts and isoforms by similarity, 3) many customization features for data exploration and creating publication ready figures, and 4) exporting selected isoforms into fasta files for further analysis. Iso-Seq Browser is written in Python using several scientific libraries. The application and analyses described in this paper are freely available to both academic and commercial users at https://github.com/goeckslab/isoseq-browserConclusionsIso-Seq Browser enables interactive genome-wide visual analysis of long RNA sequence reads. Through visualization, highlighting, clustering, and filtering of gene isoforms, ISB makes it simple to identify novel isoforms and novel isoform features such as exons, introns and untranslated regions.

scholarly journals Visual Analysis of Biomarkers Reveals Differences in Lipid Profiles and Liver Enzymes before and after Gastric Sleeve and Bypass

Obesity Facts ◽  
2021 ◽  
pp. 1-11
Author(s):  
Marijn Marthe Georgine van Berckel ◽  
Saskia L.M. van Loon ◽  
Arjen-Kars Boer ◽  
Volkher Scharnhorst ◽  
Simon W. Nienhuijs
Keyword(s):  
Bariatric Surgery ◽  
Visual Analytics ◽  
Biochemical Markers ◽  
Visual Analysis ◽  
Large Population ◽  
High Volume ◽  
Cholesterol Concentration ◽  
Health State ◽  
Data Set ◽  
Before And After

<b><i>Introduction:</i></b> Bariatric surgery results in both intentional and unintentional metabolic changes. In a high-volume bariatric center, extensive laboratory panels are used to monitor these changes pre- and postoperatively. Consecutive measurements of relevant biochemical markers allow exploration of the health state of bariatric patients and comparison of different patient groups. <b><i>Objective:</i></b> The objective of this study is to compare biomarker distributions over time between 2 common bariatric procedures, i.e., sleeve gastrectomy (SG) and gastric bypass (RYGB), using visual analytics. <b><i>Methods:</i></b> Both pre- and postsurgical (6, 12, and 24 months) data of all patients who underwent primary bariatric surgery were collected retrospectively. The distribution and evolution of different biochemical markers were compared before and after surgery using asymmetric beanplots in order to evaluate the effect of primary SG and RYGB. A beanplot is an alternative to the boxplot that allows an easy and thorough visual comparison of univariate data. <b><i>Results:</i></b> In total, 1,237 patients (659 SG and 578 RYGB) were included. The sleeve and bypass groups were comparable in terms of age and the prevalence of comorbidities. The mean presurgical BMI and the percentage of males were higher in the sleeve group. The effect of surgery on lowering of glycated hemoglobin was similar for both surgery types. After RYGB surgery, the decrease in the cholesterol concentration was larger than after SG. The enzymatic activity of aspartate aminotransferase, alanine aminotransferase, and alkaline phosphate in sleeve patients was higher presurgically but lower postsurgically compared to bypass values. <b><i>Conclusions:</i></b> Beanplots allow intuitive visualization of population distributions. Analysis of this large population-based data set using beanplots suggests comparable efficacies of both types of surgery in reducing diabetes. RYGB surgery reduced dyslipidemia more effectively than SG. The trend toward a larger decrease in liver enzyme activities following SG is a subject for further investigation.

scholarly journals Sequoia: an interactive visual analytics platform for interpretation and feature extraction from nanopore sequencing datasets

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ratanond Koonchanok ◽  
Swapna Vidhur Daulatabad ◽  
Quoseena Mir ◽  
Khairi Reda ◽  
Sarath Chandra Janga
Keyword(s):  
Single Molecule ◽  
Visual Analytics ◽  
Visual Analysis ◽  
Direct Sequencing ◽  
Visual Exploration ◽  
Nanopore Sequencing ◽  
Sequencing Data ◽  
Rna Sequences ◽  
Sequencing Technologies ◽  
Signal Features

Abstract Background Direct-sequencing technologies, such as Oxford Nanopore’s, are delivering long RNA reads with great efficacy and convenience. These technologies afford an ability to detect post-transcriptional modifications at a single-molecule resolution, promising new insights into the functional roles of RNA. However, realizing this potential requires new tools to analyze and explore this type of data. Result Here, we present Sequoia, a visual analytics tool that allows users to interactively explore nanopore sequences. Sequoia combines a Python-based backend with a multi-view visualization interface, enabling users to import raw nanopore sequencing data in a Fast5 format, cluster sequences based on electric-current similarities, and drill-down onto signals to identify properties of interest. We demonstrate the application of Sequoia by generating and analyzing ~ 500k reads from direct RNA sequencing data of human HeLa cell line. We focus on comparing signal features from m6A and m5C RNA modifications as the first step towards building automated classifiers. We show how, through iterative visual exploration and tuning of dimensionality reduction parameters, we can separate modified RNA sequences from their unmodified counterparts. We also document new, qualitative signal signatures that characterize these modifications from otherwise normal RNA bases, which we were able to discover from the visualization. Conclusions Sequoia’s interactive features complement existing computational approaches in nanopore-based RNA workflows. The insights gleaned through visual analysis should help users in developing rationales, hypotheses, and insights into the dynamic nature of RNA. Sequoia is available at https://github.com/dnonatar/Sequoia.

scholarly journals Fraud Audit Based on Visual Analysis: A Process Mining Approach

2021 ◽  
Vol 11 (11) ◽  
pp. 4751
Author(s):  
Jorge-Félix Rodríguez-Quintero ◽  
Alexander Sánchez-Díaz ◽  
Leonel Iriarte-Navarro ◽  
Alejandro Maté ◽  
Manuel Marco-Such ◽  
...  
Keyword(s):  
Visual Analytics ◽  
Visual Analysis ◽  
Process Mining ◽  
Fraud Detection ◽  
Financial Sector ◽  
Contextual Analysis ◽  
Use Case ◽  
Hotel Management ◽  
Domain Iii ◽  
Audit Approach

Among the knowledge areas in which process mining has had an impact, the audit domain is particularly striking. Traditionally, audits seek evidence in a data sample that allows making inferences about a population. Mistakes are usually committed when generalizing the results and anomalies; therefore, they appear in unprocessed sets; however, there are some efforts to address these limitations using process-mining-based approaches for fraud detection. To the best of our knowledge, no fraud audit method exists that combines process mining techniques and visual analytics to identify relevant patterns. This paper presents a fraud audit approach based on the combination of process mining techniques and visual analytics. The main advantages are: (i) a method is included that guides the use of the visual capabilities of process mining to detect fraud data patterns during an audit; (ii) the approach can be generalized to any business domain; (iii) well-known process mining techniques are used (dotted chart, trace alignment, fuzzy miner…). The techniques were selected by a group of experts and were extended to enable filtering for contextual analysis, to handle levels of process abstraction, and to facilitate implementation in the area of fraud audits. Based on the proposed approach, we developed a software solution that is currently being used in the financial sector as well as in the telecommunications and hospitality sectors. Finally, for demonstration purposes, we present a real hotel management use case in which we detected suspected fraud behaviors, thus validating the effectiveness of the approach.

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