scholarly journals HiGlass: Web-based Visual Exploration and Analysis of Genome Interaction Maps

2017 ◽  
Author(s):  
Peter Kerpedjiev ◽  
Nezar Abdennur ◽  
Fritz Lekschas ◽  
Chuck McCallum ◽  
Kasper Dinkla ◽  
...  
Keyword(s):  
Open Source ◽  
Visual Exploration ◽  
Visualization Tool ◽  
Data Types ◽  
Experimental Conditions ◽  
Web Based ◽  
Web Technologies ◽  
Link Type

AbstractWe present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D genomic tracks, allowing users to combine various data types, synchronize multiple visualization modalities, and share fully customizable views with others. We demonstrate its utility in exploring different experimental conditions, comparing the results of analyses, and creating interactive snapshots to share with collaborators and the broader public. HiGlass is accessible online athttp://higlass.ioand is also available as a containerized application that can be run on any platform.

scholarly journals LandScape: a web application for interactive genomic summary visualization

2019 ◽  
Author(s):  
Wenlong Jia ◽  
Hechen Li ◽  
Shiying Li ◽  
Shuaicheng Li
Keyword(s):  
Genetic Information ◽  
Web Application ◽  
Genomic Research ◽  
File Format ◽  
Data Types ◽  
Web Based ◽  
Link Type ◽  
Level Data ◽  
Real Time Visualization ◽  
Information Landscape

ABSTRACTSummaryVisualizing integrated-level data from genomic research remains a challenge, as it requires sufficient coding skills and experience. Here, we present LandScapeoviz, a web-based application for interactive and real-time visualization of summarized genetic information. LandScape utilizes a well-designed file format that is capable of handling various data types, and offers a series of built-in functions to customize the appearance, explore results, and export high-quality diagrams that are available for publication.Availability and implementationLandScape is deployed at bio.oviz.org/demo-project/analyses/landscape for online use. Documentation and demo data are freely available on this website and GitHub (github.com/Nobel-Justin/Oviz-Bio-demo)[email protected]

scholarly journals CrosstalkNet: mining large-scale bipartite co-expression networks to characterize epi-stroma crosstalk

2017 ◽  
Author(s):  
Venkata Manem ◽  
George Adam ◽  
Tina Gruosso ◽  
Mathieu Gigoux ◽  
Nicholas Bertos ◽  
...  
Keyword(s):  
Stromal Cells ◽  
Large Scale ◽  
Network Visualization ◽  
Visualization Tool ◽  
Biological Processes ◽  
Web Based ◽  
Link Type ◽  
A Cell ◽  
Large Scale Networks ◽  
User Friendly

ABSTRACTBackground:Over the last several years, we have witnessed the metamorphosis of network biology from being a mere representation of molecular interactions to models enabling inference of complex biological processes. Networks provide promising tools to elucidate intercellular interactions that contribute to the functioning of key biological pathways in a cell. However, the exploration of these large-scale networks remains a challenge due to their high-dimensionality.Results:CrosstalkNet is a user friendly, web-based network visualization tool to retrieve and mine interactions in large-scale bipartite co-expression networks. In this study, we discuss the use of gene co-expression networks to explore the rewiring of interactions between tumor epithelial and stromal cells. We show how CrosstalkNet can be used to efficiently visualize, mine, and interpret large co-expression networks representing the crosstalk occurring between the tumour and its microenvironment.Conclusion:CrosstalkNet serves as a tool to assist biologists and clinicians in exploring complex, large interaction graphs to obtain insights into the biological processes that govern the tumor epithelial-stromal crosstalk. A comprehensive tutorial along with case studies are provided with the application.Availability:The web-based application is available at the following location: http://epistroma.pmgenomics.ca/app/. The code is open-source and freely available from http://github.com/bhklab/EpiStroma-webapp.Contact:[email protected]

Web-Based Data Visualization Platform for MATSim

2020 ◽  
Vol 2674 (10) ◽  
pp. 124-133
Author(s):  
Billy Charlton ◽  
Janek Laudan
Keyword(s):  
User Interface ◽  
Open Source ◽  
Data Visualization ◽  
Aggregate Level ◽  
Web Based ◽  
Client Server ◽  
Web Technologies ◽  
Front End ◽  
Advanced User ◽  
Simulation Results

There are many tools available for analyzing MATSim transport simulation results, both open-source and commercial. This research builds a new open-source visualization platform for MATSim outputs that is entirely web-based. After initial experiments with many different web technologies, a client-server platform design emerges which leverages the advanced user interface capabilities of modern browsers on the front-end, and relies on back-end server processing for more processor-intensive tasks. The initial platform is now operational and includes several aggregate-level visualizations including origin–destination flows, transit supply, and emissions levels as well as a fully disaggregate traffic animation visualization. These visualizations are general enough to be useful for various projects. Further work is needed to make them more compelling and the platform more useful for practitioners.

scholarly journals NASQAR: A web-based platform for high-throughput sequencing data analysis and visualization

2019 ◽  
Author(s):  
Ayman Yousif ◽  
Nizar Drou ◽  
Jillian Rowe ◽  
Mohammed Khalfan ◽  
Kristin C Gunsalus
Keyword(s):  
New York ◽  
Data Analysis ◽  
Open Source ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Web Applications ◽  
Rna Seq ◽  
Sequencing Data ◽  
Web Based ◽  
Link Type

AbstractBackgroundAs high-throughput sequencing applications continue to evolve, the rapid growth in quantity and variety of sequence-based data calls for the development of new software libraries and tools for data analysis and visualization. Often, effective use of these tools requires computational skills beyond those of many researchers. To ease this computational barrier, we have created a dynamic web-based platform, NASQAR (Nucleic Acid SeQuence Analysis Resource).ResultsNASQAR offers a collection of custom and publicly available open-source web applications that make extensive use of a variety of R packages to provide interactive data analysis and visualization. The platform is publicly accessible at http://nasqar.abudhabi.nyu.edu/. Open-source code is on GitHub at https://github.com/nasqar/NASQAR, and the system is also available as a Docker image at https://hub.docker.com/r/aymanm/nasqarall. NASQAR is a collaboration between the core bioinformatics teams of the NYU Abu Dhabi and NYU New York Centers for Genomics and Systems Biology.ConclusionsNASQAR empowers non-programming experts with a versatile and intuitive toolbox to easily and efficiently explore, analyze, and visualize their Transcriptomics data interactively. Popular tools for a variety of applications are currently available, including Transcriptome Data Preprocessing, RNA-seq Analysis (including Single-cell RNA-seq), Metagenomics, and Gene Enrichment.

scholarly journals META-pipe Authorization service

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 32
Author(s):  
Inge Alexander Raknes ◽  
Lars Ailo Bongo
Keyword(s):  
Data Analysis ◽  
Open Source ◽  
Service Providers ◽  
Storage System ◽  
Web Based ◽  
Single Sign On ◽  
Link Type ◽  
Metagenomics Data ◽  
Access To Data

We describe the design, implementation, and use of the META-pipe Authorization service. META-pipe is a complete workflow for the analysis of marine metagenomics data. We will provide META-pipe as a web based data analysis service for ELIXIR users. We have integrated our Authorization service with the ELIXIR Authorization and Authentication Infrastructure (AAI) that allows single sign-on to services across the ELIXIR infrastructure. We use the Authorization service to authorize access to data on the META-pipe storage system and jobs in the META-pipe job queue. Our Authorization server was among the first SAML2 service providers  that integrated with ELIXIR AAI. The code is open source at: https://gitlab.com/uit-sfb/AuthService2.

scholarly journals PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization

2017 ◽  
Author(s):  
Łukasz Kreft ◽  
Alexander Botzki ◽  
Frederik Coppens ◽  
Klaas Vandepoele ◽  
Michiel Van Bel
Keyword(s):  
Phylogenetic Tree ◽  
Functional Genomics ◽  
Open Source ◽  
Web Sites ◽  
Phylogenetic Trees ◽  
Biological Data ◽  
Web Technologies ◽  
Link Type ◽  
Current Implementation ◽  
Tree Viewer

AbstractMotivation:Comparative and evolutionary studies utilise phylogenetic trees to analyse and visualise biological data. Recently, several web-based tools for the display, manipulation, and annotation of phylogenetic trees, such as iTOL and Evolview, have released updates to be compatible with the latest web technologies. While those web tools operate an open server access model with a multitude of registered users, a feature-rich open source solution using current web technologies is not available.Results:Here, we present an extension of the widely used PhyloXML standard with several new options to accommodate functional genomics or annotation datasets for advanced visualization. Furthermore, PhyD3 has been developed as a lightweight tool using the JavaScript library D3.js to achieve a state-of-the-art phylogenetic tree visualisation in the web browser, with support for advanced annotations. The current implementation is open source, easily adaptable and easy to implement in third parties’ web sites.Availability:More information about PhyD3 itself, installation procedures, and implementation links are available at http://phyd3.bits.vib.be and at http://github.com/vibbits/phyd3/.Contact:[email protected]

scholarly journals META-pipe Authorization service

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 32 ◽  
Author(s):  
Inge Alexander Raknes ◽  
Lars Ailo Bongo
Keyword(s):  
Data Analysis ◽  
Open Source ◽  
Storage System ◽  
Web Based ◽  
Single Sign On ◽  
Link Type ◽  
Metagenomics Data ◽  
Access To Data

We describe the design, implementation, and use of the META-pipe Authorization service. META-pipe is a complete workflow for the analysis of marine metagenomics data. We will provide META-pipe as a web based data analysis service for ELIXIR users. We have integrated our Authorization service with the ELIXIR Authorization and Authentication Infrastructure (AAI) that allows single sign-on to services across the ELIXIR infrastructure. We use the Authorization service to authorize access to data on the META-pipe storage system and jobs in the META-pipe job queue. Our Authorization server was among the first services that integrated with ELIXIR AAI. The code is open source at: https://gitlab.com/uit-sfb/AuthService2.

scholarly journals BPG: Seamless, Automated and Interactive Visualization of Scientific Data

2017 ◽  
Author(s):  
Christine P’ng ◽  
Jeffrey Green ◽  
Lauren C. Chong ◽  
Daryl Waggott ◽  
Stephenie D. Prokopec ◽  
...  
Keyword(s):  
Open Source ◽  
Interactive Visualization ◽  
Scientific Data ◽  
High Dimensional ◽  
Seamless Integration ◽  
Web Based ◽  
Link Type ◽  
Interactive Tool ◽  
High Dimensional Datasets ◽  
Publication Quality

AbstractWe introduce BPG, an easy-to-use framework for generating publication-quality, highly-customizable plots in the R statistical environment. This open-source package includes novel methods of displaying high-dimensional datasets and facilitates generation of complex multi-panel figures, making it ideal for complex datasets. A web-based interactive tool allows online figure customization, from which R code can be downloaded for seamless integration with computational pipelines. BPG is available at http://labs.oicr.on.ca/boutros-lab/software/bpg

scholarly journals GiraFFe Browse: A lightweight web based tool for inspecting GFF and FASTA data

2018 ◽  
Author(s):  
Owen Garland ◽  
Amanda Clare ◽  
Wayne Aubrey
Keyword(s):  
Escherichia Coli ◽  
Software Engineering ◽  
Open Source ◽  
Fasta File ◽  
Web Based ◽  
Link Type ◽  
European Nucleotide Archive ◽  
Specialist Knowledge ◽  
Engineering Practices ◽  
User Friendly

AbstractSummaryGiraFFe Browse is a tool aimed at making GFF and FASTA data more useful and accessible to researchers. Existing solutions are large in scope and difficult to maintain without specialist knowledge of computer systems. GiraFFe Browse is a lightweight alternative, built using modern software engineering practices with a focus on being developer and user friendly.Availability and implementationGiraFFe Browse is open source (GPL) software that is available from the Github repository: https://github.com/bag-man/giraffe-browseDemo versionAn example installation of the application is available at http://giraffe.owen.cymru, using a GFF and FASTA file of Escherichia coli from the European Nucleotide [email protected]

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