iCAVE: an open source tool for visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D

Abstract Visualizations of biomolecular networks assist in systems-level data exploration in many cellular processes. Data generated from high-throughput experiments increasingly inform these networks, yet current tools do not adequately scale with concomitant increase in their size and complexity....

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Veröffentlicht in:Gigascience 2017-08, Vol.6 (8), p.1-13
Hauptverfasser: Liluashvili, Vaja, Kalayci, Selim, Fluder, Eugene, Wilson, Manda, Gabow, Aaron, Gümüş, Zeynep H.
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container_end_page 13
container_issue 8
container_start_page 1
container_title Gigascience
container_volume 6
creator Liluashvili, Vaja
Kalayci, Selim
Fluder, Eugene
Wilson, Manda
Gabow, Aaron
Gümüş, Zeynep H.
description Abstract Visualizations of biomolecular networks assist in systems-level data exploration in many cellular processes. Data generated from high-throughput experiments increasingly inform these networks, yet current tools do not adequately scale with concomitant increase in their size and complexity. We present an open source software platform, interactome-CAVE (iCAVE), for visualizing large and complex biomolecular interaction networks in 3D. Users can explore networks (i) in 3D using a desktop, (ii) in stereoscopic 3D using 3D-vision glasses and a desktop, or (iii) in immersive 3D within a CAVE environment. iCAVE introduces 3D extensions of known 2D network layout, clustering, and edge-bundling algorithms, as well as new 3D network layout algorithms. Furthermore, users can simultaneously query several built-in databases within iCAVE for network generation or visualize their own networks (e.g., disease, drug, protein, metabolite). iCAVE has modular structure that allows rapid development by addition of algorithms, datasets, or features without affecting other parts of the code. Overall, iCAVE is the first freely available open source tool that enables 3D (optionally stereoscopic or immersive) visualizations of complex, dense, or multi-layered biomolecular networks. While primarily designed for researchers utilizing biomolecular networks, iCAVE can assist researchers in any field.
doi_str_mv 10.1093/gigascience/gix054
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Data generated from high-throughput experiments increasingly inform these networks, yet current tools do not adequately scale with concomitant increase in their size and complexity. We present an open source software platform, interactome-CAVE (iCAVE), for visualizing large and complex biomolecular interaction networks in 3D. Users can explore networks (i) in 3D using a desktop, (ii) in stereoscopic 3D using 3D-vision glasses and a desktop, or (iii) in immersive 3D within a CAVE environment. iCAVE introduces 3D extensions of known 2D network layout, clustering, and edge-bundling algorithms, as well as new 3D network layout algorithms. Furthermore, users can simultaneously query several built-in databases within iCAVE for network generation or visualize their own networks (e.g., disease, drug, protein, metabolite). iCAVE has modular structure that allows rapid development by addition of algorithms, datasets, or features without affecting other parts of the code. 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subjects Algorithms
Animals
Cellular communication
Clustering
Complexity
Computational Biology - methods
Databases, Factual
Gene Regulatory Networks
Humans
Layouts
Metabolic Networks and Pathways
Metabolites
Modular structures
Multilayers
Networks
Open source software
Protein Interaction Maps
Signal Transduction
Software
Stereoscopy
Technical Note
User-Computer Interface
title iCAVE: an open source tool for visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D
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