| 1. |
- Feng, Shaohong, et al.
(författare)
-
Dense sampling of bird diversity increases power of comparative genomics
- 2020
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
-
Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
|
|
| 2. |
|
|
| 3. |
- Feyer, Stefan P., et al.
(författare)
-
2D, 2.5D, or 3D? : An Exploratory Study on Multilayer Network Visualisations in Virtual Reality
- 2024
-
Ingår i: IEEE Transactions on Visualization and Computer Graphics. - : IEEE. - 1077-2626 .- 1941-0506. ; 30:1, s. 469-479
-
Tidskriftsartikel (refereegranskat)abstract
- Relational information between different types of entities is often modelled by a multilayer network (MLN) - a network with subnetworks represented by layers. The layers of an MLN can be arranged in different ways in a visual representation, however, the impact of the arrangement on the readability of the network is an open question. Therefore, we studied this impact for several commonly occurring tasks related to MLN analysis. Additionally, layer arrangements with a dimensionality beyond 2D, which are common in this scenario, motivate the use of stereoscopic displays. We ran a human subject study utilising a Virtual Reality headset to evaluate 2D, 2.5D, and 3D layer arrangements. The study employs six analysis tasks that cover the spectrum of an MLN task taxonomy, from path finding and pattern identification to comparisons between and across layers. We found no clear overall winner. However, we explore the task-to-arrangement space and derive empirical-based recommendations on the effective use of 2D, 2.5D, and 3D layer arrangements for MLNs.
|
|
| 4. |
- Falk, Martin, et al.
(författare)
-
Atomistic Visualization of Mesoscopic Whole-Cell Simulations
- 2012
-
Ingår i: VCBM 12: Eurographics Workshop on Visual Computing for Biology and Medicine. - : The Eurographics Association. - 9783905674385 ; , s. 123-130
-
Konferensbidrag (refereegranskat)abstract
- Molecular visualizations are a principal tool for analyzing the results of biochemical simulations. With modern GPU ray casting approaches it is only possible to render several millions of atoms at interactive frame rates unless advanced acceleration methods are employed. But even simplified cell models of whole-cell simulations consist of at least several billion atoms. However, many instances of only a few different proteins occur in the intracellular environment, which is beneficial in order to fit the data into the graphics memory. One model is stored for each protein species and rendered once per instance. The proposed method exploits recent algorithmic advances for particle rendering and the repetitive nature of intracellular proteins to visualize dynamic results from mesoscopic simulations of cellular transport processes. We present two out-of-core optimizations for the interactive visualization of data sets composed of billions of atoms as well as details on the data preparation and the employed rendering techniques. Furthermore, we apply advanced shading methods to improve the image quality including methods to enhance depth and shape perception besides non-photorealistic rendering methods.
|
|
| 5. |
- Falk, Martin, et al.
(författare)
-
Atomistic Visualization of Mesoscopic Whole-Cell Simulations Using Ray-Casted Instancing
- 2013
-
Ingår i: Computer graphics forum (Print). - : Wiley. - 0167-7055 .- 1467-8659. ; 32:8, s. 195-206
-
Tidskriftsartikel (refereegranskat)abstract
- Molecular visualization is an important tool for analysing the results of biochemical simulations. With modern GPU ray casting approaches, it is only possible to render several million of atoms interactively unless advanced acceleration methods are employed. Whole-cell simulations consist of at least several billion atoms even for simplified cell models. However, many instances of only a few different proteins occur in the intracellular environment, which can be exploited to fit the data into the graphics memory. For each protein species, one model is stored and rendered once per instance. The proposed method exploits recent algorithmic advances for particle rendering and the repetitive nature of intracellular proteins to visualize dynamic results from mesoscopic simulations of cellular transport processes. We present two out-of-core optimizations for the interactive visualization of data sets composed of billions of atoms as well as details on the data preparation and the employed rendering techniques. Furthermore, we apply advanced shading methods to improve the image quality including methods to enhance depth and shape perception besides non-photorealistic rendering methods. We also show that the method can be used to render scenes that are composed of triangulated instances, not only implicit surfaces.
|
|
| 6. |
- Falk, Martin, et al.
(författare)
-
Interactive GPU-based Visualization of Large Dynamic Particle Data
- 2016
-
Bok (refereegranskat)abstract
- Prevalent types of data in scientific visualization are volumetric data, vector field data, and particle-based data. Particle data typically originates from measurements and simulations in various fields, such as life sciences or physics. The particles are often visualized directly, that is, by simple representants like spheres. Interactive rendering facilitates the exploration and visual analysis of the data. With increasing data set sizes in terms of particle numbers, interactive high-quality visualization is a challenging task. This is especially true for dynamic data or abstract representations that are based on the raw particle data.This book covers direct particle visualization using simple glyphs as well as abstractions that are application-driven such as clustering and aggregation. It targets visualization researchers and developers who are interested in visualization techniques for large, dynamic particle-based data. Its explanations focus on GPU-accelerated algorithms for high-performance rendering and data processing that run in real-time on modern desktop hardware. Consequently, the implementation of said algorithms and the required data structures to make use of the capabilities of modern graphics APIs are discussed in detail. Furthermore, it covers GPU-accelerated methods for the generation of application-dependent abstract representations. This includes various representations commonly used in application areas such as structural biology, systems biology, thermodynamics, and astrophysics.
|
|
| 7. |
- Kozlíková, Barbora, et al.
(författare)
-
Visualization of Molecular Structure: The State of the Art
- 2015
-
Ingår i: Eurographics Conference on Visualization (EuroVis) - STARs. - : Eurographics - European Association for Computer Graphics.
-
Konferensbidrag (refereegranskat)abstract
- Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The report concludes with an outlook on promising and important research topics to enable further success in advancing the knowledge about interaction of molecular structures.
|
|
| 8. |
- Krone, Michael, et al.
(författare)
-
Interactive Exploration of Protein Cavities
- 2011
-
Ingår i: Computer graphics forum (Print). - : Blackhorse Publishing. - 0167-7055 .- 1467-8659. ; 30:3, s. 673-682
-
Tidskriftsartikel (refereegranskat)abstract
- We present a novel application for the interactive exploration of cavities within proteins in dynamic data sets. Inside a protein, cavities can often be found close to the active center. Therefore, when analyzing a molecular dynamics simulation trajectory it is of great interest to find these cavities and determine if such a cavity opens up to the environment, making the binding site accessible to the surrounding substrate. Our user-driven approach enables expert users to select a certain cavity and track its evolution over time. The user is supported by different visualizations of the extracted cavity to facilitate the analysis. The boundary of the protein and its cavities is obtained by means of volume ray casting, where the volume is computed in real-time for each frame, therefore allowing the examination of time-dependent data sets. A fast, partial segmentation of the volume is applied to obtain the selected cavity and trace it over time. Domain experts found our method useful when they applied it exemplarily on two trajectories of lipases from Rhizomucor miehei and Candida antarctica. In both data sets cavities near the active center were easily identified and tracked over time until they reached the surface and formed an open substrate channel.
|
|
| 9. |
- Reina, Guido, et al.
(författare)
-
The moving target of visualization software for an increasingly complex world
- 2020
-
Ingår i: Computers & graphics. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0097-8493 .- 1873-7684. ; 87, s. 12-29
-
Tidskriftsartikel (refereegranskat)abstract
- Visualization has evolved into a mature scientific field and it has also become widely accepted as a standard approach in diverse fields, including physics, life sciences, and business intelligence. However, despite its successful development, there are still many open research questions that require customized implementations in order to explore and establish concepts, and to perform experiments and take measurements. Many methods and tools have been developed and published but most are stand-alone prototypes and have not reached a mature state that can be used in a reliable manner by collaborating domain scientists or a wider audience. In this study, we discuss the challenges, solutions, and open research questions that affect the development of sophisticated, relevant, and novel scientific visualization solutions with minimum overheads. We summarize and discuss the results of a recent National Institute of Informatics Shonan seminar on these topics. (C) 2020 Elsevier Ltd. All rights reserved.
|
|
| 10. |
- Wijayatunga, Priyantha, 1967-, et al.
(författare)
-
Discussion on the meeting on 'Data visualization'
- 2019
-
Ingår i: Journal of the Royal Statistical Society. - UK : Royal Statistical Society. - 0964-1998 .- 1467-985X. ; 182:2, s. 433-441
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Visualizing both conditional and marginal associations in contingency tables by using simple diagrams is discussed
|
|
