Difference between revisions of "Journal:Semantics for an integrative and immersive pipeline combining visualization and analysis of molecular data"
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|doi = [http://doi.org/10.1515/jib-2018-0004 10.1515/jib-2018-0004] | |doi = [http://doi.org/10.1515/jib-2018-0004 10.1515/jib-2018-0004] | ||
|issn = 1613-4516 | |issn = 1613-4516 | ||
|license = [ | |license = [https://creativecommons.org/licenses/by-nc-nd/4.0/ Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International] | ||
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==Abstract== | |||
The advances made in recent years in the field of structural biology significantly increased the throughput and complexity of data that scientists have to deal with. Combining and [[Data analysis|analyzing]] such heterogeneous amounts of data became a crucial time consumer in the daily tasks of scientists. However, only few efforts have been made to offer scientists an alternative to the standard compartmentalized tools they use to explore their data and that involve a regular back and forth between them. We propose here an integrated pipeline especially designed for immersive environments, promoting direct interactions on semantically linked 2D and 3D heterogeneous data, displayed in a common working space. The creation of a semantic definition describing the content and the context of a molecular scene leads to the creation of an intelligent system where data are (1) combined through pre-existing or inferred links present in our hierarchical definition of the concepts, (2) enriched with suitable and adaptive analyses proposed to the user with respect to the current task and (3) interactively presented in a unique working environment to be explored. | |||
'''Keywords''': virtual reality, semantics for interaction, structural biology | |||
==Introduction== | |||
Recent years have seen a profound change in the way structural biologists interact with their data. New techniques that try to capture the structure and dynamics of bio-molecules have reached an extraordinary high throughput of structural data.<ref name="ZhaoMature13">{{cite journal |title=Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics |journal=Nature |author=Zhao, G.; Perilla, J.R.; Yufenyuy, E.L. et al. |volume=497 |issue=7451 |pages=643–6 |year=2013 |doi=10.1038/nature12162 |pmid=23719463 |pmc=PMC3729984}}</ref><ref name="ZhangStructure17">{{cite journal |title=Structure of phycobilisome from the red alga Griffithsia pacifica |journal=Nature |author=Zhang, J.; Ma, J.; Liu, D. et al. |volume=551 |issue=7678 |pages=57–63 |year=2017 |doi=10.1038/nature24278 |pmid=29045394}}</ref> Scientists must try to combine and analyze data flows from different sources to draw their hypotheses and conclusions. However, despite this increasing complexity, they tend to rely mainly on compartmentalized tools to only [[Data visualization|visualize]] or analyze limited portions of their data. This situation leads to a constant back and forth between the different tools and their associated environments. Consequently, a significant amount of time is dedicated to the transformation of data to account for the heterogeneous input data types each tool is allowing. | |||
The need for platforms capable of handling the intricate data flow is then strong. In structural biology, the numerical simulation process is now able to deal with very large and heterogeneous molecular structures. These molecular assemblies may be composed of several million particles and consist of many different types of molecules, including a biologically realistic environment. This overall complexity raises the need to go beyond common visualization solutions and move towards integrated exploration systems where visualization and analysis can be merged. | |||
Immersive environments play an important role in this context, providing both a better comprehension of the three-dimensional structure of molecules, and offering new interaction techniques to reduce the number of data manipulations executed by the experts (see Figure 1). A few studies took advantage of recent developments in virtual reality to enhance some structural biology tasks. Visualization is the first and most obvious task that was improved through new adaptive stereoscopic screens and immersive environments, plunging experts into the very center of their molecules.<ref name="vanDamImmersive00">{{cite journal |title=Immersive VR for scientific visualization: A progress report |journal=IEEE Computer Graphics and Applications |author=van Dam, A.; Forsberg, A.S.; Laidlaw, D.H. et al. |volume=20 |issue=6 |pages=26–52 |year=2000 |doi=10.1109/38.888006}}</ref><ref name="StoneImmersive10">{{cite journal |title=Immersive molecular visualization and interactive modeling with commodity hardware |journal=Proceedings of the 6th International Conference on Advances in Visual Computing |author=Stone. J.E.; Kohlmeyer, A.; Vandivort, K.L.; Schulten, K. |pages=382–93 |year=2010 |doi=10.1007/978-3-642-17274-8_38}}</ref><ref name="ODonoghueVisual10">{{cite journal |title=Visualization of macromolecular structures |journal=Nature Methods |author=O'Donoghue, S.I.; Goodsell, D.S.; Frangakis, A.S. et al. |volume=7 |issue=3 Suppl. |pages=S42–55 |year=2010 |doi=10.1038/nmeth.1427 |pmid=20195256}}</ref><ref name="HirstMolec14">{{cite journal |title=Molecular simulations and visualization: Introduction and overview |journal=Faraday Discussions |author=Hirst, J.D.; Glowacki, D.R.; Baaden, M. et al. |volume=169 |pages=9–22 |year=2014 |doi=10.1039/c4fd90024c |pmid=25285906}}</ref><ref name="GoddardUCSF18">{{cite journal |title=UCSF ChimeraX: Meeting modern challenges in visualization and analysis |journal=Protein Science |author=Goddard, T.D., Huang, C.C.; Meng, E.C. et al. |volume=27 |issue=1 |pages=14–25 |year=2018 |doi=10.1002/pro.3235 |pmid=28710774 |pmc=PMC5734306}}</ref> Structure manipulations during specific docking experiments have been improved thanks to the use of haptic devices and audio feedback to drive a simulation.<ref name="FéreyMulti09">{{cite journal |title=Multisensory VR interaction for protein-docking in the CoRSAIRe project |journal=Virtual Reality |author=Férey, N.; Nelson, J.; Martin, C. et al. |volume=13 |pages=273 |year=2009 |doi=10.1007/s10055-009-0136-z}}</ref> However, if 3D objects can rather easily be represented and manipulated in such environments, the integration of analytical values (energies, distance to reference, etc.)—2D by nature—leads to a certain complexity and is not a solved problem yet. As a consequence, no specific development has been made to set up an immersive platform where the expert could manipulate data coming from different sources to accelerate and improve the development of new hypotheses. | |||
==References== | ==References== | ||
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==Notes== | ==Notes== | ||
This presentation is faithful to the original, with only a few minor changes to presentation. Some grammar and punctuation was cleaned up to improve readability. In some cases important information was missing from the references, and that information was added. | This presentation is faithful to the original, with only a few minor changes to presentation. Some grammar and punctuation was cleaned up to improve readability. In some cases important information was missing from the references, and that information was added. Nothing else was changed in accordance with the NoDerivatives portion of the license. | ||
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Revision as of 00:05, 5 March 2019
| Full article title | Semantics for an integrative and immersive pipeline combining visualization and analysis of molecular data |
|---|---|
| Journal | Journal of Integrative Bioinformatics |
| Author(s) | Trellet, Mikael; Férey, Nicolas; Flotyński, Jakub; Baaden, Marc; Bourdot, Patrick |
| Author affiliation(s) | Bijvoet Center for Biomolecular Research, Université Paris Sud, Poznań Univ. of Economics and Business, Laboratoire de Biochimie Théorique |
| Primary contact | Email: m dot e dot trellet at uu dot nl |
| Year published | 2018 |
| Volume and issue | 15(2) |
| Page(s) | 20180004 |
| DOI | 10.1515/jib-2018-0004 |
| ISSN | 1613-4516 |
| Distribution license | Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International |
| Website | https://www.degruyter.com/view/j/jib.2018.15.issue-2/jib-2018-0004/jib-2018-0004.xml |
| Download | https://www.degruyter.com/downloadpdf/j/jib.2018.15.issue-2/jib-2018-0004/jib-2018-0004.xml (PDF) |
Abstract
The advances made in recent years in the field of structural biology significantly increased the throughput and complexity of data that scientists have to deal with. Combining and analyzing such heterogeneous amounts of data became a crucial time consumer in the daily tasks of scientists. However, only few efforts have been made to offer scientists an alternative to the standard compartmentalized tools they use to explore their data and that involve a regular back and forth between them. We propose here an integrated pipeline especially designed for immersive environments, promoting direct interactions on semantically linked 2D and 3D heterogeneous data, displayed in a common working space. The creation of a semantic definition describing the content and the context of a molecular scene leads to the creation of an intelligent system where data are (1) combined through pre-existing or inferred links present in our hierarchical definition of the concepts, (2) enriched with suitable and adaptive analyses proposed to the user with respect to the current task and (3) interactively presented in a unique working environment to be explored.
Keywords: virtual reality, semantics for interaction, structural biology
Introduction
Recent years have seen a profound change in the way structural biologists interact with their data. New techniques that try to capture the structure and dynamics of bio-molecules have reached an extraordinary high throughput of structural data.[1][2] Scientists must try to combine and analyze data flows from different sources to draw their hypotheses and conclusions. However, despite this increasing complexity, they tend to rely mainly on compartmentalized tools to only visualize or analyze limited portions of their data. This situation leads to a constant back and forth between the different tools and their associated environments. Consequently, a significant amount of time is dedicated to the transformation of data to account for the heterogeneous input data types each tool is allowing.
The need for platforms capable of handling the intricate data flow is then strong. In structural biology, the numerical simulation process is now able to deal with very large and heterogeneous molecular structures. These molecular assemblies may be composed of several million particles and consist of many different types of molecules, including a biologically realistic environment. This overall complexity raises the need to go beyond common visualization solutions and move towards integrated exploration systems where visualization and analysis can be merged.
Immersive environments play an important role in this context, providing both a better comprehension of the three-dimensional structure of molecules, and offering new interaction techniques to reduce the number of data manipulations executed by the experts (see Figure 1). A few studies took advantage of recent developments in virtual reality to enhance some structural biology tasks. Visualization is the first and most obvious task that was improved through new adaptive stereoscopic screens and immersive environments, plunging experts into the very center of their molecules.[3][4][5][6][7] Structure manipulations during specific docking experiments have been improved thanks to the use of haptic devices and audio feedback to drive a simulation.[8] However, if 3D objects can rather easily be represented and manipulated in such environments, the integration of analytical values (energies, distance to reference, etc.)—2D by nature—leads to a certain complexity and is not a solved problem yet. As a consequence, no specific development has been made to set up an immersive platform where the expert could manipulate data coming from different sources to accelerate and improve the development of new hypotheses.
References
- ↑ Zhao, G.; Perilla, J.R.; Yufenyuy, E.L. et al. (2013). "Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics". Nature 497 (7451): 643–6. doi:10.1038/nature12162. PMC PMC3729984. PMID 23719463. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3729984.
- ↑ Zhang, J.; Ma, J.; Liu, D. et al. (2017). "Structure of phycobilisome from the red alga Griffithsia pacifica". Nature 551 (7678): 57–63. doi:10.1038/nature24278. PMID 29045394.
- ↑ van Dam, A.; Forsberg, A.S.; Laidlaw, D.H. et al. (2000). "Immersive VR for scientific visualization: A progress report". IEEE Computer Graphics and Applications 20 (6): 26–52. doi:10.1109/38.888006.
- ↑ Stone. J.E.; Kohlmeyer, A.; Vandivort, K.L.; Schulten, K. (2010). "Immersive molecular visualization and interactive modeling with commodity hardware". Proceedings of the 6th International Conference on Advances in Visual Computing: 382–93. doi:10.1007/978-3-642-17274-8_38.
- ↑ O'Donoghue, S.I.; Goodsell, D.S.; Frangakis, A.S. et al. (2010). "Visualization of macromolecular structures". Nature Methods 7 (3 Suppl.): S42–55. doi:10.1038/nmeth.1427. PMID 20195256.
- ↑ Hirst, J.D.; Glowacki, D.R.; Baaden, M. et al. (2014). "Molecular simulations and visualization: Introduction and overview". Faraday Discussions 169: 9–22. doi:10.1039/c4fd90024c. PMID 25285906.
- ↑ Goddard, T.D., Huang, C.C.; Meng, E.C. et al. (2018). "UCSF ChimeraX: Meeting modern challenges in visualization and analysis". Protein Science 27 (1): 14–25. doi:10.1002/pro.3235. PMC PMC5734306. PMID 28710774. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734306.
- ↑ Férey, N.; Nelson, J.; Martin, C. et al. (2009). "Multisensory VR interaction for protein-docking in the CoRSAIRe project". Virtual Reality 13: 273. doi:10.1007/s10055-009-0136-z.
Notes
This presentation is faithful to the original, with only a few minor changes to presentation. Some grammar and punctuation was cleaned up to improve readability. In some cases important information was missing from the references, and that information was added. Nothing else was changed in accordance with the NoDerivatives portion of the license.
