MultiNets: Web-Based Multilayer Network Visualization

Abstract Summary Visualizing a network provides a concise and practical understanding of the information it represents. Open-source web-based libraries help accelerate the creation of biologically based networks and their use. ccNetViz is an open-source, high speed and lightweight JavaScript library for visualization of large and complex networks. It implements customization and analytical features for easy network interpretation. These features include edge and node animations, which illustrate the flow of information through a network as well as node statistics. Properties can be defined a priori or dynamically imported from models and simulations. ccNetViz is thus a network visualization library particularly suited for systems biology. Availability and implementation The ccNetViz library, demos and documentation are freely available at http://helikarlab.github.io/ccNetViz/. Supplementary information Supplementary data are available at Bioinformatics online.

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

10.1101/102848 ◽

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]

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Cytoscape: the network visualization tool for GenomeSpace workflows

F1000Research ◽

10.12688/f1000research.4492.2 ◽

2014 ◽

Vol 3 ◽

pp. 151 ◽

Cited By ~ 69

Author(s):

Barry Demchak ◽

Tim Hull ◽

Michael Reich ◽

Ted Liefeld ◽

Michael Smoot ◽

...

Keyword(s):

User Experience ◽

Critical Analysis ◽

Genomic Analysis ◽

Network Visualization ◽

Visualization Tool ◽

Web Browser ◽

Web Based ◽

Data Flows ◽

Modern Genomic ◽

Selection Of

Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013.

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The BioCyc Metabolic Network Explorer

BMC Bioinformatics ◽

10.1186/s12859-021-04132-5 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Suzanne Paley ◽

Peter D. Karp

Keyword(s):

Metabolic Network ◽

Metabolic Networks ◽

Dynamic Control ◽

Software Tool ◽

Ease Of Use ◽

Network Visualization ◽

Software Suite ◽

Genome Database ◽

Web Based ◽

Visualization Tools

Abstract Background The Metabolic Network Explorer is a new addition to the BioCyc.org website and the Pathway Tools software suite that supports the interactive exploration of metabolic networks. Any metabolic network visualization tool must by necessity show only a subset of all possible metabolite connections, or the results will be visually overwhelming. Existing tools, even those that purport to show an organism’s full metabolic network, limit the set of displayed connections based on predefined pathways or other preselected criteria. We sought instead to provide a tool that would give the user dynamic control over which connections to follow. Results The Metabolic Network Explorer is an easy-to-use, web-based software tool that allows the user to specify a starting metabolite of interest and interactively explore its immediate metabolic neighborhood in either or both directions to any desired depth, letting the user select from the full set of connected reactions. Although, as for other tools, only a small portion of the metabolic network is visible at a time, that portion is selected by the user, based on the full reaction complement, and it is easy to switch among alternate paths of interest. The display is intuitive, customizable, and provides copious links to more detailed information pages. Conclusions The Metabolic Network Explorer fills a gap in the set of metabolic network visualization tools and complements other modes of exploration. Its primary strengths are its ease of use, diagrams that are intuitive to biologists, and its integration with the broader corpus of data provided by a BioCyc Pathway/Genome Database.

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The State of the Art in Multilayer Network Visualization

Computer Graphics Forum ◽

10.1111/cgf.13610 ◽

2019 ◽

Vol 38 (6) ◽

pp. 125-149 ◽

Cited By ~ 16

Author(s):

F. McGee ◽

M. Ghoniem ◽

G. Melançon ◽

B. Otjacques ◽

B. Pinaud

Keyword(s):

State Of The Art ◽

The State ◽

Network Visualization ◽

Multilayer Network

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Web-based metabolic network visualization with a zooming user interface

BMC Bioinformatics ◽

10.1186/1471-2105-12-176 ◽

2011 ◽

Vol 12 (1) ◽

Cited By ~ 23

Author(s):

Mario Latendresse ◽

Peter D Karp

Keyword(s):

User Interface ◽

Metabolic Network ◽

Network Visualization ◽

Web Based

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The PBL-Evaluator: a web-based tool for assessment in tutorials

Journal of Dental Education ◽

10.1002/j.0022-0337.1998.62.9.tb03231.x ◽

1998 ◽

Vol 62 (9) ◽

pp. 671-674

Author(s):

JF Chaves ◽

JA Chaves ◽

MS Lantz

Keyword(s):

Web Based

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Using Popular Mobile Devices in Voice Therapy

Perspectives on Voice and Voice Disorders ◽

10.1044/vvd23.3.82 ◽

2013 ◽

Vol 23 (3) ◽

pp. 82-87 ◽

Cited By ~ 1

Author(s):

Eva van Leer

Keyword(s):

Exercise Behavior ◽

Voice Therapy ◽

Pure Oxygen ◽

Mobile Platforms ◽

Self Monitoring ◽

Web Based ◽

Motivational Messages ◽

Related Information ◽

Health Related ◽

Tailored Approach

Mobile tools are increasingly available to help individuals monitor their progress toward health behavior goals. Commonly known commercial products for health and fitness self-monitoring include wearable devices such as the Fitbit© and Nike + Pedometer© that work independently or in conjunction with mobile platforms (e.g., smartphones, media players) as well as web-based interfaces. These tools track and graph exercise behavior, provide motivational messages, offer health-related information, and allow users to share their accomplishments via social media. Approximately 2 million software programs or “apps” have been designed for mobile platforms (Pure Oxygen Mobile, 2013), many of which are health-related. The development of mobile health devices and applications is advancing so quickly that the Food and Drug Administration issued a Guidance statement with the purpose of defining mobile medical applications and describing a tailored approach to their regulation.

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