Towards a hybrid user interface for the visual exploration of large biomolecular networks using virtual reality
Biomolecular networks, including genome-scale metabolic models (GSMMs), assemble the knowledge regarding the biological processes that happen inside specific organisms in a way that allows for analysis, simulation, and exploration. With the increasing availability of genome annotations and the devel...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
De Gruyter
2022-10-01
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| Series: | Journal of Integrative Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1515/jib-2022-0034 |
| _version_ | 1827387545671958528 |
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| author | Aichem Michael Klein Karsten Czauderna Tobias Garkov Dimitar Zhao Jinxin Li Jian Schreiber Falk |
| author_facet | Aichem Michael Klein Karsten Czauderna Tobias Garkov Dimitar Zhao Jinxin Li Jian Schreiber Falk |
| author_sort | Aichem Michael |
| collection | DOAJ |
| description | Biomolecular networks, including genome-scale metabolic models (GSMMs), assemble the knowledge regarding the biological processes that happen inside specific organisms in a way that allows for analysis, simulation, and exploration. With the increasing availability of genome annotations and the development of powerful reconstruction tools, biomolecular networks continue to grow ever larger. While visual exploration can facilitate the understanding of such networks, the network sizes represent a major challenge for current visualisation systems. Building on promising results from the area of immersive analytics, which among others deals with the potential of immersive visualisation for data analysis, we present a concept for a hybrid user interface that combines a classical desktop environment with a virtual reality environment for the visual exploration of large biomolecular networks and corresponding data. We present system requirements and design considerations, describe a resulting concept, an envisioned technical realisation, and a systems biology usage scenario. Finally, we discuss remaining challenges. |
| first_indexed | 2024-03-08T16:03:47Z |
| format | Article |
| id | doaj.art-a9c6c014e0b14dad9c63a79cf2639669 |
| institution | Directory Open Access Journal |
| issn | 1613-4516 |
| language | English |
| last_indexed | 2024-03-08T16:03:47Z |
| publishDate | 2022-10-01 |
| publisher | De Gruyter |
| record_format | Article |
| series | Journal of Integrative Bioinformatics |
| spelling | doaj.art-a9c6c014e0b14dad9c63a79cf26396692024-01-08T09:53:35ZengDe GruyterJournal of Integrative Bioinformatics1613-45162022-10-0119417410610.1515/jib-2022-0034Towards a hybrid user interface for the visual exploration of large biomolecular networks using virtual realityAichem Michael0Klein Karsten1Czauderna Tobias2Garkov Dimitar3Zhao Jinxin4Li Jian5Schreiber Falk6Department of Computer and Information Science, University of Konstanz, Konstanz, GermanyDepartment of Computer and Information Science, University of Konstanz, Konstanz, GermanyFaculty of Applied Computer Sciences & Biosciences, University of Applied Sciences Mittweida, Mittweida, GermanyDepartment of Computer and Information Science, University of Konstanz, Konstanz, GermanyInfection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, AustraliaInfection Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, AustraliaDepartment of Computer and Information Science, University of Konstanz, Konstanz, GermanyBiomolecular networks, including genome-scale metabolic models (GSMMs), assemble the knowledge regarding the biological processes that happen inside specific organisms in a way that allows for analysis, simulation, and exploration. With the increasing availability of genome annotations and the development of powerful reconstruction tools, biomolecular networks continue to grow ever larger. While visual exploration can facilitate the understanding of such networks, the network sizes represent a major challenge for current visualisation systems. Building on promising results from the area of immersive analytics, which among others deals with the potential of immersive visualisation for data analysis, we present a concept for a hybrid user interface that combines a classical desktop environment with a virtual reality environment for the visual exploration of large biomolecular networks and corresponding data. We present system requirements and design considerations, describe a resulting concept, an envisioned technical realisation, and a systems biology usage scenario. Finally, we discuss remaining challenges.https://doi.org/10.1515/jib-2022-0034hybrid user interfacesimmersive analyticsmetabolic network modelssystems biologyvirtual reality |
| spellingShingle | Aichem Michael Klein Karsten Czauderna Tobias Garkov Dimitar Zhao Jinxin Li Jian Schreiber Falk Towards a hybrid user interface for the visual exploration of large biomolecular networks using virtual reality Journal of Integrative Bioinformatics hybrid user interfaces immersive analytics metabolic network models systems biology virtual reality |
| title | Towards a hybrid user interface for the visual exploration of large biomolecular networks using virtual reality |
| title_full | Towards a hybrid user interface for the visual exploration of large biomolecular networks using virtual reality |
| title_fullStr | Towards a hybrid user interface for the visual exploration of large biomolecular networks using virtual reality |
| title_full_unstemmed | Towards a hybrid user interface for the visual exploration of large biomolecular networks using virtual reality |
| title_short | Towards a hybrid user interface for the visual exploration of large biomolecular networks using virtual reality |
| title_sort | towards a hybrid user interface for the visual exploration of large biomolecular networks using virtual reality |
| topic | hybrid user interfaces immersive analytics metabolic network models systems biology virtual reality |
| url | https://doi.org/10.1515/jib-2022-0034 |
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