Browsing by Subject "Data visualization"

Now showing 1 - 6 of 6

Open Access
The BioPAX community standard for pathway data sharing
(Nature Publishing Group, 2010-09) Demir, Emek; Cary, M. P.; Paley, S.; Fukuda, K.; Lemer, C.; Vastrik, I.; Wu, G.; D'Eustachio, P.; Schaefer, C.; Luciano, J.; Schacherer, F.; Martinez-Flores, I.; Hu, Z.; Jimenez-Jacinto, V.; Joshi-Tope, G.; Kandasamy, K.; Lopez-Fuentes, A. C.; Mi, H.; Pichler, E.; Rodchenkov, I.; Splendiani, A.; Tkachev, S.; Zucker, J.; Gopinath, G.; Rajasimha, H.; Ramakrishnan, R.; Shah, I.; Syed, M.; Anwar, N.; Babur, Özgün; Blinov, M.; Brauner, E.; Corwin, D.; Donaldson, S.; Gibbons, F.; Goldberg, R.; Hornbeck, P.; Luna, A.; Murray-Rust, P.; Neumann, E.; Reubenacker, O.; Samwald, M.; Iersel, Martijn van; Wimalaratne, S.; Allen, K.; Braun, B.; Whirl-Carrillo, M.; Cheung, Kei-Hoi; Dahlquist, K.; Finney, A.; Gillespie, M.; Glass, E.; Gong, L.; Haw, R.; Honig, M.; Hubaut, O.; Kane, D.; Krupa, S.; Kutmon, M.; Leonard, J.; Marks, D.; Merberg, D.; Petri, V.; Pico, A.; Ravenscroft, D.; Ren, L.; Shah, N.; Sunshine, M.; Tang R.; Whaley, R.; Letovksy, S.; Buetow, K. H.; Rzhetsky, A.; Schachter, V.; Sobral, B. S.; Doğrusöz, Uğur; McWeeney, S.; Aladjem, M.; Birney, E.; Collado-Vides, J.; Goto, S.; Hucka, M.; Novère, Nicolas Le; Maltsev, N.; Pandey, A.; Thomas, P.; Wingender, E.; Karp, P. D.; Sander, C.; Bader, G. D.
Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery. © 2010 Nature America, Inc. All rights reserved.
Open Access
Comparison of two image-space subdivision algorithms for direct volume rendering on distributed-memory multicomputers
(Springer, 1995-08) Tanin, Egemen; Kurç, Tahsin M.; Aykanat, Cevdet; Özgüç, Bülent
Direct Volume Rendering (DVR) is a powerful technique for visualizing volumetric data sets. However, it involves intensive computations. In addition, most of the volumetric data sets consist of large number of 3D sampling points. Therefore, visualization of such data sets also requires large computer memory space. Hence, DVR is a good candidate for parallelization on distributed-memory multicomputers. In this work, image-space parallelization of Raycasting based DVR for unstructured grids on distributed-memory multicomputers is presented and discussed. In order to visualize unstructured volumetric datasets where grid points of the dataset are irregularly distributed over the 3D space, the underlying algorithms should resolve the point location and view sort problems of the 3D grid points. In this paper, these problems are solved using a Scanline Z-buffer based algorithm. Two image space subdivision heuristics, namely horizontal and recursive rectangular subdivision heuristics, are utilized to distribute the computations evenly among the processors in the rendering phase. The horizontal subdivision algorithm divides the image space into horizontal bands composed of consecutive scanlines. In the recursive subdivision algorithm, the image space is divided into rectangular subregions recursively. The experimental performance evaluation of the horizontal and recursive subdivision algorithms on an IBM SP2 system are presented and discussed. © Springer-Verlag Berlin Heidelberg 1996.
Open Access
Development of a shiny application for comparative transcriptomics and differential gene expression analysis
(2022-09) Leka, Ronaldo
RNA sequencing has proven to be an effective technique for divulging information about the transcriptome in molecular biology research. Compared to microarrays and early methods of cDNA sequencing, high-throughput RNA sequencing has better resolution, low background noise, a higher range to quantify gene expression, and relatively lower cost. The development of sequencing technique has led to the development of tools for analyzing the high volume of data that is generated. Statistical methods for normalizing, filtering, performing exploratory and differential analysis, and other functional analyses based on RNA sequencing count data have made RNA sequencing one of the most popular techniques in genomics. To help facilitate the use of such statistical tools, web applications developed in R using the shiny package offer an advantageous environment where researchers can use a graphical interface to give inputs and instructions to the underlying server-side libraries that analyze and generate results in tables and plots. This thesis presents a new tool that has been developed for exploratory analysis, data normalization and filtering, differential gene expression analysis (DGEA), correlation analysis, principal component analysis, and functional analysis such as over-representation analysis and gene set enrichment analysis. When compared to other available applications, this new application offers the ability to run multiple methods for DGEA and compare results between them, leading to the output of gene sets that are discovered as DEGs in multiple tests. Here I present the features of this application in detail where I aim to improve upon the applications that are available in the literature. An example dataset from our lab was also investigated by this RNA-seq tool leading to a better understanding of Mineralocorticoid Receptor (MR) signaling in breast cancer.
Open Access
Optical reconstruction of transparent objects with phase-only SLMs
(Optical Society of American (OSA), 2013) Stoykova, E.; Yaraş F.; Yontem, A.Ö.; Kang H.; Onural L.; Hamel P.; Delacrétaz, Y.; Bergoënd I.; Arfire, C.; Depeursinge, C.
Three approaches for visualization of transparent micro-objects from holographic data using phase-only SLMs are described. The objects are silicon micro-lenses captured in the near infrared by means of digital holographic microscopy and a simulated weakly refracting 3D object with size in the micrometer range. In the first method, profilometric/tomographic data are retrieved from captured holograms and converted into a 3D point cloud which allows for computer generation of multi-view phase holograms using Rayleigh-Sommerfeld formulation. In the second method, the microlens is computationally placed in front of a textured object to simulate the image of the textured data as seen through the lens. In the third method, direct optical reconstruction of the micrometer object through a digital lens by modifying the phase with the Gerchberg-Saxton algorithm is achieved. © 2013 Optical Society of America.
Open Access
Procedural visualization of knitwear and woven cloth
(Pergamon Press, 2007-11) Durupınar, F.; Güdükbay, Uğur
In this paper, a procedural method for the visualization of knitted and woven fabrics is presented. The proposed method is compatible with a mass-spring model and makes use of the regular warp-weft structure of the cloth. The visualization parameters for the loops and threads are easily mapped to the animated mass-spring model. The simulation idea underlying both knitted and woven fabrics is similar as we represent both structures in 3D. As the proposed method is simple and practical, we can achieve near real-time rendering performance with good visual quality. © 2007 Elsevier Ltd. All rights reserved.
Open Access
A virtual garment design and simulation system
(IEEE, 2007-07) Durupınar, Funda; Güdükbay, Uğur
In this paper, a 3D graphics environment for virtual garment design and simulation is presented. The proposed system enables the three dimensional construction of a garment from its cloth panels, for which the underlying structure is a mass-spring model. The garment construction process is performed through automatic pattern generation, posterior correction, and seaming. Afterwards, it is possible to do fitting on virtual mannequins as if in a real life tailor's workshop. The system provides the users with the flexibility to design their own garment patterns and make changes on the garment even after the dressing of the model. Furthermore, rendering alternatives for the visualization of knitted and woven fabric are presented. © 2007 IEEE.