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.

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 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.

The Sahara

2017 ◽  
Author(s):  
Barbara E. Barich
Keyword(s):  
Human Body ◽  
Manufacturing Process ◽  
Three Dimensional ◽  
Two Dimensional ◽  
Dimensional Representation ◽  
Three Dimensional Representation ◽  
The Difference ◽  
Symbolic Content ◽  
The Relationship

This chapter discusses the collection of objects, in clay and stone, from various pastoral Saharan sites whose original core area lay between Libya (Tadrart Acacus) and Algeria (Tassili- n-Ajjer). The chapter starts from the general theme of the relationship between the figurines and the subjects they represent, and the difference between two-dimensional and three-dimensional representation. It goes on to discuss the manufacturing process of the clay specimens (dating from between 7000 and 4000 years ago) and the significance of the changes introduced by the Neolithic. Most of the items studied fall into the category of zoomorphic figurines, with only two anthropomorphic examples, and find in the depiction of cattle their most striking subject. These representations possess an evident symbolic content which must be framed within the pastoral ideology of the Saharan Neolithic. In the anthropomorphic figurines the representation of the human body also plays the role of recapturing the sense of wholeness.

Multimedia technology-assisted stereo geometry teaching

2021 ◽  
pp. 002072092098468
Author(s):  
Yu Wang
Keyword(s):  
Three Dimensional ◽  
Three Dimensions ◽  
Multimedia Technology ◽  
Traditional Teaching ◽  
Dimensional Representation ◽  
Three Dimensional Representation ◽  
Education Community ◽  
The Media ◽  
Network Platform ◽  
Control Interaction

Multimedia technology makes our life more stereoscopic and intuitive. Graphic images and animations are the most important part of multimedia information expression. It makes our visual effects of three-dimensional representation of things more vivid, like the plane and three-dimensional we usually see. As with the picture, modern multimedia technology transforms our lives into three dimensions, integration, control, interaction and interaction. For the vivid three-dimensional representation of three-dimensional geometric figures in teaching, not only is it limited to the geometric composition of a piece of chalk, but more with the wide application of multimedia technology, multimedia-assisted teaching, especially multimedia-assisted three-dimensional geometric figure teaching is playing more and more The important role, through the aid of multimedia, has cultivated students’ spatial abstract thinking ability and ability to understand graphics and theorems. As multimedia becomes more and more concerned by the education community, this paper is about the question of why multimedia technology should be used to assist the teaching and application of solid geometry applications, and how to apply multimedia technology to achieve the maximum value of the teaching effect of stereo geometry. A lot of experimental research has been carried out. Through experiments, we have built a more complete multimedia assistant teaching system, which is beneficial for students to acquire new knowledge on the Internet. The multimedia technology-assisted three-dimensional geometric method is more conducive to mobilizing the enthusiasm and initiative of students than the traditional method. The biggest innovation of this paper is to use the indispensable advantages of traditional teaching to discount the media to the network platform. To some extent, the research in this paper enhances the guiding significance of interactive research to the actual development work.

ON THE "CROSSROAD AREA–SADDLE AREA" AND "CROSSROAD AREA–SPRING AREA" TRANSITIONS

1991 ◽  
Vol 01 (03) ◽  
pp. 641-655 ◽  
Author(s):  
C. MIRA ◽  
J. P. CARCASSÈS
Keyword(s):  
Three Dimensional ◽  
Parameter Plane ◽  
Flip Bifurcation ◽  
Two Dimensional ◽  
Cusp Point ◽  
Dimensional Representation ◽  
One Dimensional ◽  
Transition Mechanism ◽  
Three Dimensional Representation ◽  
Spring Area

Let T be a one-dimensional or two-dimensional map. The three considered areas are related to three different configurations of fold and flip bifurcation curves, centred at a cusp point of a fold curve in the T parameter plane (b, c). The two transitions studied here occur via a codimension-three bifurcation defined in each case, when varying a third parameter a. The transition "mechanism," from an area type to another one, is given with a three-dimensional representation describing the sheet configuration of the parameter plane.

Navigating through a volumetric world does not imply needing a full three-dimensional representation

2013 ◽  
Vol 36 (5) ◽  
pp. 547-548
Author(s):  
Claus-Christian Carbon ◽  
Vera M. Hesslinger
Keyword(s):  
Three Dimensional ◽  
Specific Situation ◽  
Two Dimensional ◽  
Dimensional Representation ◽  
Physical Conditions ◽  
Three Dimensional Representation ◽  
The World ◽  
Elevation Data ◽  
Individual Needs

AbstractJeffery et al. extensively and thoroughly describe how different species navigate through a three-dimensional environment. Undeniably, the world offers numerous three-dimensional opportunities. However, we argue that for most navigation tasks a two-dimensional representation is nevertheless sufficient, as physical conditions and limitations such as gravity, thermoclines, or layers of earth encountered in a specific situation provide the very elevation data the navigating individual needs.

Revealing gross three-dimensional structure in the SEM

1987 ◽  
Vol 45 ◽  
pp. 656-657
Author(s):  
Sterling P. Newberry
Keyword(s):  
Freeze Drying ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Small Object ◽  
Final Solution ◽  
Dimensional Representation ◽  
X Ray ◽  
Three Dimensional Representation ◽  
Freeze Dried ◽  
Critical Point Drying

The beautiful three dimensional representation of small object surfaces by the SEM leads one to search for ways to open up the sample and look inside. Could this be the answer to a better microscopy for gross biological 3-D structure? We know from X-Ray microscope images that Freeze Drying and Critical Point Drying give promise of adequately preserving gross structure. Can we slice such preparations open for SEM inspection? In general these preparations crush more readily than they slice. Russell and Dagihlian got around the problem by “deembedding” a section before imaging. This some what defeats the advantages of direct dry preparation, thus we are reluctant to accept it as the final solution to our problem. Alternatively, consider fig 1 wherein a freeze dried onion root has a window cut in its surface by a micromanipulator during observation in the SEM.

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