scholarly journals BigTop: A Three-Dimensional Virtual Reality tool for GWAS Visualization

2019 ◽  
Author(s):  
Samuel T. Westreich ◽  
Maria Nattestad ◽  
Christopher Meyer
Keyword(s):  
Virtual Reality ◽  
Association Studies ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Gene Location ◽  
P Value ◽  
Genome Wide Association Studies ◽  
Two Dimensional ◽  
Three Dimensional Representation ◽  
Manhattan Plot

AbstractBackgroundGenome-wide association studies (GWAS) are typically visualized using a two-dimensional Manhattan plot, displaying chromosomal location of SNPs along the x-axis and the negative log-10 of their p-value on the y-axis. This traditional plot provides a broad overview of the results, but offers little opportunity for interaction or expansion of specific regions, and is unable to show additional dimensions of the dataset.ResultsWe created BigTop, a visualization framework in virtual reality (VR), designed to render a Manhattan plot in three dimensions, wrapping the graph around the user in a simulated cylindrical room. BigTop uses the z-axis to display minor allele frequency of each SNP, allowing for the identification of allelic variants of genes. BigTop also offers additional interactivity, allowing users to select any individual SNP and receive expanded information, including SNP name, exact values, and gene location, if applicable. BigTop is built in JavaScript using the React and A-Frame frameworks, and can be rendered using commercially available VR headsets or in a two-dimensional web browser such as Google Chrome. Data is read into BigTop in JSON format, and can be provided as either JSON or a tab-separated text file.ConclusionsUsing additional dimensions and interactivity options offered through VR, we provide a new, interactive, three-dimensional representation of the traditional Manhattan plot for displaying and exploring GWAS data.

scholarly journals 2.5D Visualisation of Overlapping Biological Networks

2008 ◽  
Vol 5 (1) ◽  
pp. 77-93 ◽  
Author(s):  
David C.Y. Fung ◽  
Seok-Hee Hong ◽  
Dirk Koschützki ◽  
Falk Schreiber ◽  
Kai Xu
Keyword(s):  
Biological Networks ◽  
Metabolic Networks ◽  
Visual Analysis ◽  
Three Dimensional ◽  
Biological Data ◽  
Three Dimensions ◽  
Two Dimensional ◽  
Dimensional Representation ◽  
Three Dimensional Representation ◽  
Interconnected Networks

Abstract Biological data is often structured in the form of complex interconnected networks such as protein interaction and metabolic networks. In this paper, we investigate a new problem of visualising such overlapping biological networks. Two networks overlap if they share some nodes and edges. We present an approach for constructing visualisations of two overlapping networks, based on a restricted three dimensional representation. More specifically, we use three parallel two dimensional planes placed in three dimensions to represent overlapping networks: one for each network (the top and the bottom planes) and one for the overlapping part (in the middle plane).Our method aims to achieve both drawing aesthetics (or conventions) for each individual network, and highlighting the intersection part by them. Using three biological datasets, we evaluate our visualisation design with the aim to test whether overlapping networks can support the visual analysis of heterogeneous and yet interconnected networks.

Mine Impact Burial Prediction From One to Three Dimensions

2008 ◽  
Vol 62 (1) ◽  
Author(s):  
Peter C. Chu
Keyword(s):  
Three Dimensional ◽  
Time History ◽  
Three Dimensions ◽  
Vertical Position ◽  
Burial Depth ◽  
Prediction Errors ◽  
Two Dimensional ◽  
Dimensional Model ◽  
One Dimensional ◽  
Dimensional Models

The Navy’s mine impact burial prediction model creates a time history of a cylindrical or a noncylindrical mine as it falls through air, water, and sediment. The output of the model is the predicted mine trajectory in air and water columns, burial depth/orientation in sediment, as well as height, area, and volume protruding. Model inputs consist of parameters of environment, mine characteristics, and initial release. This paper reviews near three decades’ effort on model development from one to three dimensions: (1) one-dimensional models predict the vertical position of the mine’s center of mass (COM) with the assumption of constant falling angle, (2) two-dimensional models predict the COM position in the (x,z) plane and the rotation around the y-axis, and (3) three-dimensional models predict the COM position in the (x,y,z) space and the rotation around the x-, y-, and z-axes. These models are verified using the data collected from mine impact burial experiments. The one-dimensional model only solves one momentum equation (in the z-direction). It cannot predict the mine trajectory and burial depth well. The two-dimensional model restricts the mine motion in the (x,z) plane (which requires motionless for the environmental fluids) and uses incorrect drag coefficients and inaccurate sediment dynamics. The prediction errors are large in the mine trajectory and burial depth prediction (six to ten times larger than the observed depth in sand bottom of the Monterey Bay). The three-dimensional model predicts the trajectory and burial depth relatively well for cylindrical, near-cylindrical mines, and operational mines such as Manta and Rockan mines.

PSVIII-10 Genome-wide CNV analysis unravels a deletion associated with parasite resistance in Florida native sheep

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 243-244
Author(s):  
Brittany N Diehl ◽  
Andres A Pech-Cervantes ◽  
Thomas H Terrill ◽  
Ibukun M Ogunade ◽  
Owen Rae ◽  
...  
Keyword(s):  
Copy Number ◽  
Association Studies ◽  
Chromosome 21 ◽  
Trend Test ◽  
P Value ◽  
Genome Wide Association Studies ◽  
Parasite Resistance ◽  
Association Testing ◽  
Genome Wide ◽  
Native Sheep

Abstract Florida Native sheep is an indigenous breed from Florida and expresses superior parasite resistance. Previous candidate and genome wide association studies with Florida Native sheep have identified single nucleotide polymorphisms with additive and non-additive effects associated with parasite resistance. However, the role of other potential DNA variants, such as copy number variants (CNVs), controlling this complex trait have not been evaluated. The objective of the present study was to investigate the importance of CNVs on resistance to natural Haemonchus contortus infections in Florida Native sheep. A total of 200 sheep were evaluated in the present study. Phenotypic records included fecal egg count (FEC, eggs/gram), FAMACHA score, and packed cell volume (PCV, %). Sheep were genotyped using the GGP Ovine 50K SNP chip. The copy number analysis was used to identify CNVs using the univariate method. A total of 170 animals with CNVs and phenotypic data were used for the association testing. Association tests were carried out using single linear regression and Principal Component Analysis (PCA) correction to identify CNVs associated with FEC, FAMACHA, and PCV. To confirm our results, a second association testing using the correlation-trend test with PCA correction was performed. Significant CNVs were detected when their adjusted p-value was < 0.05 after FDR correction. A deletion CNV in chromosome 21 was associated with FEC. This DNA variant was located in intron 2 of RAB3IL gene and overlapped a QTL associated with changes in eosinophil number. Our study demonstrated for the first time that CNVs could be potentially involved with parasite resistance in this heritage sheep breed.

Immersion, interactivity and three-dimensionality: virtual reality documentation of media art installations

2021 ◽  
Author(s):  
Kira A. Brown
Keyword(s):  
Virtual Reality ◽  
Case Studies ◽  
Three Dimensional ◽  
Research Paper ◽  
Sensory Experience ◽  
Three Dimensions ◽  
Media Art ◽  
Essential Information ◽  
Art Installation ◽  
High Level

This research paper explores the possibilities for virtual reality (VR) documentation of media art installations. Based on an analysis of the characteristics of media art, and a survey of current documentation strategies, this paper investigates the viability of three-dimensional documentation. Four cross-disciplinary case studies are presented and analysed to demonstrate that VR documentation provides an immersive and richer reconstruction of a media art installation in three dimensions. In addition, the interactive components can be simulated within the VR environment, offering the possibility for curators and visitors to virtually re-experience the artwork. The case studies show that, although the creation of VR documentation can be costly and time-consuming, and currently requires a high-level of expertise, it can be a useful addition to established documentation strategies by providing essential information about the visual aspects of the artwork, its environment and the user’s multi-sensory experience.

Monkey superior colliculus represents rapid eye movements in a two-dimensional motor map

1993 ◽  
Vol 69 (3) ◽  
pp. 965-979 ◽  
Author(s):  
K. Hepp ◽  
A. J. Van Opstal ◽  
D. Straumann ◽  
B. J. Hess ◽  
V. Henn
Keyword(s):  
Eye Movements ◽  
Superior Colliculus ◽  
Degrees Of Freedom ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Eye Position ◽  
Two Dimensional ◽  
Vestibular Nystagmus ◽  
Rapid Eye Movements ◽  
Q Model

1. Although the eye has three rotational degrees of freedom, eye positions, during fixations, saccades, and smooth pursuit, with the head stationary and upright, are constrained to a plane by ListingR's law. We investigated whether Listing's law for rapid eye movements is implemented at the level of the deeper layers of the superior colliculus (SC). 2. In three alert rhesus monkeys we tested whether the saccadic motor map of the SC is two dimensional, representing oculocentric target vectors (the vector or V-model), or three dimensional, representing the coordinates of the rotation of the eye from initial to final position (the quaternion or Q-model). 3. Monkeys made spontaneous saccadic eye movements both in the light and in the dark. They were also rotated about various axes to evoke quick phases of vestibular nystagmus, which have three degrees of freedom. Eye positions were measured in three dimensions with the magnetic search coil technique. 4. While the monkey made spontaneous eye movements, we electrically stimulated the deeper layers of the SC and elicited saccades from a wide range of initial positions. According to the Q-model, the torsional component of eye position after stimulation should be uniquely related to saccade onset position. However, stimulation at 110 sites induced no eye torsion, in line with the prediction of the V-model. 5. Activity of saccade-related burst neurons in the deeper layers of the SC was analyzed during rapid eye movements in three dimensions. No systematic eye-position dependence of the movement fields, as predicted by the Q-model, could be detected for these cells. Instead, the data fitted closely the predictions made by the V-model. 6. In two monkeys, both SC were reversibly inactivated by symmetrical bilateral injections of muscimol. The frequency of spontaneous saccades in the light decreased dramatically. Although the remaining spontaneous saccades were slow, Listing's law was still obeyed, both during fixations and saccadic gaze shifts. In the dark, vestibularly elicited fast phases of nystagmus could still be generated in three dimensions. Although the fastest quick phases of horizontal and vertical nystagmus were slower by about a factor of 1.5, those of torsional quick phases were unaffected. 7. On the basis of the electrical stimulation data and the properties revealed by the movement field analysis, we conclude that the collicular motor map is two dimensional. The reversible inactivation results suggest that the SC is not the site where three-dimensional fast phases of vestibular nystagmus are generated.(ABSTRACT TRUNCATED AT 400 WORDS)

scholarly journals A system for generating virtual seeds

1998 ◽  
Vol 55 (spe) ◽  
pp. 39-45 ◽  
Author(s):  
Y. Sako ◽  
K. Fujimura ◽  
M.B. McDonald ◽  
D. James
Keyword(s):  
Three Dimensional ◽  
Promising Method ◽  
Two Dimensional ◽  
Dimensional Representation ◽  
Accurate Identification ◽  
Computer Screen ◽  
Three Dimensional Objects ◽  
Three Dimensional Representation ◽  
Quicktime Vr

Seed analysts need to identify seeds, and seed catalogs are used as a reference to accomplish this task. Conventional seed catalogs supply two-dimensional photographs and hand-drawn diagrams. In this study, a new, three-dimensional representation of seeds is developed to supplement these traditional photographs and drawings. QuickTime VR is a promising method for viewing three-dimensional objects on a computer screen. It permits manipulation of an object by rotating and viewing it from any pre-specified angle at an interactive speed, allowing the viewer the sense of examining a hand-held object. In this study, QuickTime VR object movies of seeds were created as interactive "movies" of seeds that can be rotated and scaled to give the viewer the sensation of examining actual seeds. This approach allows the examination of virtual seeds from any angle, permitting more accurate identification of seeds by seed analysts.

scholarly journals Physiological State and Learning Ability of Students in Normal and Virtual Reality Conditions: Complexity-Based Analysis (Preprint)

2020 ◽  
Author(s):  
Mohammad H Babini ◽  
Vladimir V Kulish ◽  
Hamidreza Namazi
Keyword(s):  
Virtual Reality ◽  
Fractal Theory ◽  
Physiological State ◽  
Three Dimensional ◽  
Physiological Signals ◽  
Learning Ability ◽  
Two Dimensional ◽  
Reality Condition ◽  
Computer Mediated ◽  
Dimensional Condition

BACKGROUND Education and learning are the most important goals of all universities. For this purpose, lecturers use various tools to grab the attention of students and improve their learning ability. Virtual reality refers to the subjective sensory experience of being immersed in a computer-mediated world, and has recently been implemented in learning environments. OBJECTIVE The aim of this study was to analyze the effect of a virtual reality condition on students’ learning ability and physiological state. METHODS Students were shown 6 sets of videos (3 videos in a two-dimensional condition and 3 videos in a three-dimensional condition), and their learning ability was analyzed based on a subsequent questionnaire. In addition, we analyzed the reaction of the brain and facial muscles of the students during both the two-dimensional and three-dimensional viewing conditions and used fractal theory to investigate their attention to the videos. RESULTS The learning ability of students was increased in the three-dimensional condition compared to that in the two-dimensional condition. In addition, analysis of physiological signals showed that students paid more attention to the three-dimensional videos. CONCLUSIONS A virtual reality condition has a greater effect on enhancing the learning ability of students. The analytical approach of this study can be further extended to evaluate other physiological signals of subjects in a virtual reality condition.

scholarly journals Boosting GWAS using biological networks: A study on susceptibility to familial breast cancer

2021 ◽  
Vol 17 (3) ◽  
pp. e1008819
Author(s):  
Héctor Climente-González ◽  
Christine Lonjou ◽  
Fabienne Lesueur ◽  
Dominique Stoppa-Lyonnet ◽  
Nadine Andrieu ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cancer Progression ◽  
Biological Networks ◽  
Familial Breast Cancer ◽  
Association Studies ◽  
P Value ◽  
Genome Wide Association Studies ◽  
Functional Relationships ◽  
Network Methods ◽  
The Impact

Genome-wide association studies (GWAS) explore the genetic causes of complex diseases. However, classical approaches ignore the biological context of the genetic variants and genes under study. To address this shortcoming, one can use biological networks, which model functional relationships, to search for functionally related susceptibility loci. Many such network methods exist, each arising from different mathematical frameworks, pre-processing steps, and assumptions about the network properties of the susceptibility mechanism. Unsurprisingly, this results in disparate solutions. To explore how to exploit these heterogeneous approaches, we selected six network methods and applied them to GENESIS, a nationwide French study on familial breast cancer. First, we verified that network methods recovered more interpretable results than a standard GWAS. We addressed the heterogeneity of their solutions by studying their overlap, computing what we called the consensus. The key gene in this consensus solution was COPS5, a gene related to multiple cancer hallmarks. Another issue we observed was that network methods were unstable, selecting very different genes on different subsamples of GENESIS. Therefore, we proposed a stable consensus solution formed by the 68 genes most consistently selected across multiple subsamples. This solution was also enriched in genes known to be associated with breast cancer susceptibility (BLM, CASP8, CASP10, DNAJC1, FGFR2, MRPS30, and SLC4A7, P-value = 3 × 10−4). The most connected gene was CUL3, a regulator of several genes linked to cancer progression. Lastly, we evaluated the biases of each method and the impact of their parameters on the outcome. In general, network methods preferred highly connected genes, even after random rewirings that stripped the connections of any biological meaning. In conclusion, we present the advantages of network-guided GWAS, characterize their shortcomings, and provide strategies to address them. To compute the consensus networks, implementations of all six methods are available at https://github.com/hclimente/gwas-tools.

scholarly journals Development and assessment of CootVR, a virtual reality computer program for model building

2021 ◽  
Vol 77 (1) ◽  
pp. 19-27
Author(s):  
Hamish Todd ◽  
Paul Emsley
Keyword(s):  
Virtual Reality ◽  
Computer Program ◽  
Model Building ◽  
Three Dimensional ◽  
Specific Model ◽  
Three Dimensions ◽  
Biological Macromolecules ◽  
Data Set ◽  
X Ray Crystallography ◽  
Order Of Magnitude

Biological macromolecules have complex three-dimensional shapes that are experimentally examined using X-ray crystallography and electron cryo-microscopy. Interpreting the data that these methods yield involves building 3D atomic models. With almost every data set, some portion of the time put into creating these models must be spent manually modifying the model in order to make it consistent with the data; this is difficult and time-consuming, in part because the data are `blurry' in three dimensions. This paper describes the design and assessment of CootVR (available at http://hamishtodd1.github.io/cvr), a prototype computer program for performing this task in virtual reality, allowing structural biologists to build molecular models into cryo-EM and crystallographic data using their hands. CootVR was timed against Coot for a very specific model-building task, and was found to give an order-of-magnitude speedup for this task. A from-scratch model build using CootVR was also attempted; from this experience it is concluded that currently CootVR does not give a speedup over Coot overall.

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