research-article

Remote visualization of dynamic molecular data using WebGL

Authors:

Finian Mwalongo,

Michael Becher,

Thomas ErtlAuthors Info & Claims

Web3D '15: Proceedings of the 20th International Conference on 3D Web Technology

Pages 115 - 122

https://doi.org/10.1145/2775292.2775307

Published: 18 June 2015 Publication History

Abstract

Visualization of dynamic data from molecular dynamics simulations is crucial for understanding the functioning of molecules. Many existing visualization tools have mainly focused on supporting a single user working on a desktop computer. Technical advancements in browser features increase the potential for the development of web-based collaborative visualization tools. Although web-based molecular viewers already exist, their support for dynamic molecular data at interactive rates is lacking. To address this gap, we present an efficient web application for visualization of dynamic molecular data using WebGL that exploits HTML5 technologies like WebSockets and Web Workers. We demonstrate the feasibility to visualize large dynamic molecular data in the browser at interactive frame rates. Moreover, the application can be employed for remote simulation monitoring on mobile devices. Our approach allows scientists at arbitrary locations to concurrently visually analyze the same data. The interactive parametrization of the visualization can be shared among multiple clients, providing the basis for collaborative research.

References

[1]

Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. 2000. The protein data bank. Nucleic Acids Research 28, 1, 235--242.

[2]

Blinn, J. F. 1977. Models of light reflection for computer synthesized pictures. In Proceedings of the 4th Annual Conference on Computer Graphics and Interactive Techniques, ACM, New York, NY, USA, SIGGRAPH '77, 192--198.

Digital Library

[3]

Callieri, M., Andrei, R. M., Di Benedetto, M., Zoppè, M., and Scopigno, R. 2010. Visualization methods for molecular studies on the web platform. In Web3D 2010. 15th Conference on 3D Web technology, web3d consortium.

Digital Library

[4]

Doulamis, N., Chronis, E., Miaoulis, G., and Plemenos, D. 2010. Personalized view selection of 3d molecular proteins. In Intelligent Computer Graphics 2010, D. Plemenos and G. Miaoulis, Eds., vol. 321 of Studies in Computational Intelligence. Springer Berlin Heidelberg, 211--227.

[5]

Fette, I., and Melnikov, A., 2011. The WebSocket Protocol. http://www.rfc-editor.org/info/rfc6455. Online; accessed 09.03.2015.

[6]

Fielding, R. T. 2000. Architectural Styles and the Design of Network-based Software Architectures. PhD thesis, University of California, Irvine. AAI9980887.

Digital Library

[7]

Grottel, S., Krone, M., Scharnowski, K., and Ertl, T. 2012. Object-Space Ambient Occlusion for Molecular Dynamics. In IEEE Pacific Visualization Symposium, IEEE, 209--216.

Digital Library

[8]

Grottel, S., Krone, M., Mller, C., Reina, G., and Ertl, T. 2015. MegaMol - A Prototyping Framework for Particlebased Visualization. IEEE Transactions on Visualization and Computer Graphics 21, 2, 201--214.

[9]

Gumhold, S. 2003. Splatting illuminated ellipsoids with depth correction. In Proceedings of the Vision, Modeling, and Visualization Conference 2003 (VMV 2003), 245--252.

[10]

Hongjian Li, Kwong-Sak Leung, T. N., and Wong, M.-H. 2014. iview: an interactive webgl visualizer for protein-ligand complex. BMC Bioinformatics 15, 56.

[11]

Humphrey, W., Dalke, A., and Schulten, K. 1996. VMD -- Visual Molecular Dynamics. Journal of Molecular Graphics 14, 33--38.

[12]

Jmol, 2009. Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/. {Online; accessed 10.03.2015}.

[13]

JSmol, 2013. JSmol: JavaScript-Based Molecular Viewer From Jmol. http://sourceforge.net/projects/jsmol/. {Online; accessed 10.03.2015}.

[14]

JSmolWiki, 2015. Jmol Wiki: JSmol pros and cons. http://wiki.jmol.org/index.php/JSmol_pros_and_cons. {Online; accessed 10.03.2015}.

[15]

Kajalin, V. 2009. Screen-Space Ambient Occlusion. In ShaderX7: Advanced Rendering Techniques, W. Engel, Ed. Charles River Media, 413--424.

[16]

Khronos, 2011. WebGL 1.0 specification. http://www.khronos.org/registry/webgl/specs/latest/1.0/. {Online; accessed 09.03.2015}.

[17]

Khronos, 2011. WebGL Security. https://www.khronos.org/webgl/security/. {Online; accessed 13.03.2015}.

[18]

Khronos, 2013. Typed Array Specification. http://www.khronos.org/registry/typedarray/specs/latest/. Online; accessed 09.03.2015.

[19]

Khronos, 2014. WebGL OES_element_index_uint Khronos Ratified Extension Specification. https://www.khronos.org/registry/webgl/extensions/OES_element_index_uint/. Online; accessed 09.03.2015.

[20]

Khronos, 2015. OpenGL ES 3.1 Specification. https://www.khronos.org/registry/gles/specs/3.1/es_spec_3.1.pdf. {Online; accessed 13.03.2015}.

[21]

Libwebsockets, 2011. Libwebsockets: C Websockets Library (Version 1.3). https://libwebsockets.org/trac/libwebsockets. {Online; accessed 10.03.2015}.

[22]

Lindow, N., Baum, D., and Hege, H.-C. 2012. Interactive rendering of materials and biological structures on atomic and nanoscopic scale. Computer Graphics Forum 31, 3, 1325--1334.

Digital Library

[23]

Mwalongo, F., Krone, M., Karch, G., Becher, M., Reina, G., and Ertl, T. 2014. Visualization of Molecular Structures using State-of-the-Art Techniques in WebGL. In International Conference on 3D Web Technology, ACM, vol. 19, 133--141.

Digital Library

[24]

Pettit, J.-B., and Marioni, J. C. 2013. bioweb3d: an online webgl 3d data visualisation tool. BMC Bioinformatics 14, 185.

[25]

Saito, T., and Takahashi, T. 1990. Comprehensible Rendering of 3-D Shapes. Computer Graphics (Proc. SIGGRAPH 1990) 24, 4, 197--206.

Digital Library

[26]

Schrödinger, LLC, 2010. The PyMOL molecular graphics system, version 1.3r1. http://www.pymol.org/. {Online; accessed 13.03.2015}.

[27]

Tarini, M., Cignoni, P., and Montani, C. 2006. Ambient occlusion and edge cueing for enhancing real time molecular visualization. IEEE Transactions on Visualization and Computer Graphics 12, 5, 1237--1244.

Digital Library

[28]

W3C, 2012. Web Workers: W3C Candidate Recommendation. http://www.w3.org/TR/workers/. {Online; accessed 09.03.2015}.

[29]

W3C, 2013. File API. http://www.w3.org/TR/FileAPI/. {Online; accessed 10.03.2015}.

Cited By

Papp GKunkli R(2019)TabularVis: An Interactive Relationship Visualization Tool Supported by Optimization and Search AlgorithmsComputer Vision, Imaging and Computer Graphics Theory and Applications10.1007/978-3-030-26756-8_8(167-192)Online publication date: 24-Jul-2019
https://doi.org/10.1007/978-3-030-26756-8_8
Mwalongo FKrone MReina GErtl TWeiskopf DBeck FDachsbacher CSadlo F(2018)Web-based volume rendering using progressive importance-based data transferProceedings of the Conference on Vision, Modeling, and Visualization10.2312/vmv.20181264(147-154)Online publication date: 10-Oct-2018
https://dl.acm.org/doi/10.2312/vmv.20181264
Abriata L(2017)Web Apps Come of Age for Molecular SciencesInformatics10.3390/informatics40300284:3(28)Online publication date: 24-Aug-2017
https://doi.org/10.3390/informatics4030028
Show More Cited By

Index Terms

Remote visualization of dynamic molecular data using WebGL
1. Applied computing
  1. Life and medical sciences
2. Computing methodologies
  1. Computer graphics
    1. Graphics systems and interfaces
      1. Graphics file formats
    2. Rendering
      1. Ray tracing

Recommendations

Visualization of molecular structures using state-of-the-art techniques in WebGL
Web3D '14: Proceedings of the 19th International ACM Conference on 3D Web Technologies

The potential of web browsers as a platform for remote visualization has long been recognized. One of the motivations behind remote visualization has mainly been large data that cannot be easily transferred to the client. Further impeding factors for ...
Visualization Mosaics for Multivariate Visual Exploration

We present a new model for creating composite visualizations of multidimensional data sets using simple visual representations such as point charts, scatterplots and parallel coordinates as components. Each visual representation is contained in a tile, ...
A cloud-enabled remote visualization tool for time-varying climate data analytics

The ever-growing time-varying climate datasets pose challenges for efficient analytics using the current desktop-based or generic remote visualization tools. We present a tightly-coupled scalable cloud-enabled remote visualization tool that exploits the ...

Comments

Please enable JavaScript to view thecomments powered by Disqus.

Information & Contributors

Information

Published In

cover image ACM Conferences

Web3D '15: Proceedings of the 20th International Conference on 3D Web Technology

June 2015

274 pages

ISBN:9781450336475

DOI:10.1145/2775292

Program Chairs:
Jinyuan Jia
TongJi University, China
,
Felix Hamza-Lup
Armstrong State University
,
Tobias Schreck
Graz University of Technology, Austria

Copyright © 2015 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than the author(s) must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected].

Sponsors

SIGGRAPH: ACM Special Interest Group on Computer Graphics and Interactive Techniques

Publisher

Association for Computing Machinery

New York, NY, United States

Publication History

Published: 18 June 2015

Permissions

Request permissions for this article.

Request Permissions

Check for updates

Author Tags

Qualifiers

Research-article

Funding Sources

German Academic Exchange Service (DAAD)
German Research Foundation (DFG)

Conference

Web3D '15

Sponsor:

SIGGRAPH

Web3D '15: The 20th International Conference on Web3D Technology

June 18 - 21, 2015

Crete, Heraklion, Greece

Acceptance Rates

Overall Acceptance Rate 27 of 71 submissions, 38%

Contributors

Other Metrics

View Article Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

6
Total Citations
View Citations
310
Total Downloads

Downloads (Last 12 months)7
Downloads (Last 6 weeks)0

Reflects downloads up to 26 Sep 2024

Other Metrics

View Author Metrics

Citations

Cited By

Papp GKunkli R(2019)TabularVis: An Interactive Relationship Visualization Tool Supported by Optimization and Search AlgorithmsComputer Vision, Imaging and Computer Graphics Theory and Applications10.1007/978-3-030-26756-8_8(167-192)Online publication date: 24-Jul-2019
https://doi.org/10.1007/978-3-030-26756-8_8
Mwalongo FKrone MReina GErtl TWeiskopf DBeck FDachsbacher CSadlo F(2018)Web-based volume rendering using progressive importance-based data transferProceedings of the Conference on Vision, Modeling, and Visualization10.2312/vmv.20181264(147-154)Online publication date: 10-Oct-2018
https://dl.acm.org/doi/10.2312/vmv.20181264
Abriata L(2017)Web Apps Come of Age for Molecular SciencesInformatics10.3390/informatics40300284:3(28)Online publication date: 24-Aug-2017
https://doi.org/10.3390/informatics4030028
Mwalongo FKrone MReina GErtl T(2016)State-of-the-Art Report in Web-based VisualizationComputer Graphics Forum10.5555/3071534.307158935:3(553-575)Online publication date: 1-Jun-2016
https://dl.acm.org/doi/10.5555/3071534.3071589
Kozlíková BKrone MFalk MLindow NBaaden MBaum DViola IParulek JHege H(2016)Visualization of Biomolecular Structures: State of the Art RevisitedComputer Graphics Forum10.1111/cgf.1307236:8(178-204)Online publication date: 18-Nov-2016
https://doi.org/10.1111/cgf.13072
Mwalongo FKrone MReina GErtl T(2016)State‐of‐the‐Art Report in Web‐based VisualizationComputer Graphics Forum10.1111/cgf.1292935:3(553-575)Online publication date: 4-Jul-2016
https://doi.org/10.1111/cgf.12929

View Options

Get Access

Login options

Check if you have access through your login credentials or your institution to get full access on this article.

Full Access

Get this Publication

View options

PDF

View or Download as a PDF file.

eReader

View online with eReader.

Media

Figures

Other

Tables

View Table of Contents