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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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Volume 13, Issue 4

Issues

Web-based hybrid-dimensional Visualization and Exploration of Cytological Localization Scenarios

Gökhan Kovanci
  • Bio-/Medical Informatics Department, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Mehmood Ghaffar
  • Bio-/Medical Informatics Department, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Björn Sommer
  • Corresponding author
  • Computational Life Sciences, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
  • Faculty of Information Technology, Monash University, 20 Research Way, 3800 Melbourne, Australia
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2017-04-20 | DOI: https://doi.org/10.1515/jib-2016-298

Summary

The CELLmicrocosmos 4.2 PathwayIntegration (CmPI) is a tool which provides hybriddimensional visualization and analysis of intracellular protein and gene localizations in the context of a virtual 3D environment. This tool is developed based on Java/Java3D/JOGL and provides a standalone application compatible to all relevant operating systems. However, it requires Java and the local installation of the software. Here we present the prototype of an alternative web-based visualization approach, using Three.js and D3.js. In this way it is possible to visualize and explore CmPI-generated localization scenarios including networks mapped to 3D cell components by just providing a URL to a collaboration partner. This publication describes the integration of the different technologies - Three.js, D3.js and PHP - as well as an application case: a localization scenario of the citrate cycle. The CmPI web viewer is available at: http://CmPIweb.CELLmicrocosmos.org.

About the article

Published Online: 2017-04-20

Published in Print: 2016-10-01


Citation Information: Journal of Integrative Bioinformatics, Volume 13, Issue 4, Pages 47–58, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2016-298.

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© 2016 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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[1]
Stephen Jia Wang, Björn Sommer, Wenlong Cheng, Falk Schreiber, and Yih-Kuen Jan
PLOS ONE, 2018, Volume 13, Number 6, Page e0195670

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