Mariano Pérez

Virtual reality for driving simulation

In this paper, the authors describe the data structure necessary to provide real time simulation and visualization of complex environments and situations. Through the SIRCA project, the development of driving oriented simulators, using Virtual Reality (VR) and evaluating it in comparison with convention technologies, has taken place. Focus is on some of the algorithms and data structure required to provide real time simulation of the complex urban environment and its visualization under the conditions of VR devices.

Terrain data compression using wavelet-tiled pyramids for online 3D terrain visualization

Last years have witnessed the widespread use of online terrain visualization applications. However, the significant improvements achieved in sensing technologies have allowed an increasing size of the terrain databases. These increasing sizes represent a serious drawback when terrain data must be transmitted and rendered at interactive rates. In this paper, we propose a novel wavelet-tiled pyramid for compressing terrain data that replaces the traditional multiresolution pyramid usually used in wavelet compression schemes. The new wavelet-tiled pyramid modifies the wavelet analysis and synthesis processes, allowing an efficient transmission and reconstruction of terrain data in those applications based on multiresolution tiled pyramids. A comparative performance evaluation with the currently existing techniques shows that the proposed scheme obtains a better compression ratio of the terrain data, reducing the storage space and transmission bandwidth required, and achieving a better visual quality of the virtual terrain reconstructed after data decompression.

A parallel and sensitive software tool for methylation analysis on multicore platforms

Motivation: DNA methylation analysis suffers from very long processing time, as the advent of Next-Generation Sequencers has shifted the bottleneck of genomic studies from the sequencers that obtain the DNA samples to the software that performs the analysis of these samples. The existing software for methylation analysis does not seem to scale efficiently neither with the size of the dataset nor with the length of the reads to be analyzed. As it is expected that the sequencers will provide longer and longer reads in the near future, efficient and scalable methylation software should be developed. Results: We present a new software tool, called HPG-Methyl, which efficiently maps bisulphite sequencing reads on DNA, analyzing DNA methylation. The strategy used by this software consists of leveraging the speed of the Burrows–Wheeler Transform to map a large number of DNA fragments (reads) rapidly, as well as the accuracy of the Smith–Waterman algorithm, which is exclusively employed to deal with the most ambiguous and shortest reads. Experimental results on platforms with Intel multicore processors show that HPG-Methyl significantly outperforms in both execution time and sensitivity state-of-the-art software such as Bismark, BS-Seeker or BSMAP, particularly for long bisulphite reads. Availability and implementation: Software in the form of C libraries and functions, together with instructions to compile and execute this software. Available by sftp to anonymous@clariano.uv.es (password ‘anonymous’). Contact: juan.orduna@uv.es or jdopazo@cipf.es

Efficient coding of quadtree nodes

In this paper an alternative non-pointer quadtree node codification to manage geographical spatial data is presented. New codification is based on a variable sequence of z-ordered base four digits. Memory requirements of the new codification are lower than previous codifications, and in particular lower than FD codification, the most commonly used in linear quadtrees. Furthermore, z-ordering makes compatible new codification with most of the algorithms developed for FD.

Visualization of Large Terrain Using Non-restricted Quadtree Triangulations

This paper presents a set of new techniques oriented towards the real-time visualization of large terrains. These techniques are mainly focused on semi-regular triangulations of non-restricted quadtree terrain representations. Despite the fact that the paper shows that triangulations based on non-restricted quadtrees are as simple and efficient as those based on restricted quadtrees, the new triangulations avoid discontinuity problems among the boundaries of different patches without the need for tree balancing and extra triangles addition. Another important feature of the proposed triangulation is that it incorporates an efficient method for building triangle strips and triangle fans for the efficient rendering of the final triangle mesh.

Real time graphics and virtual reality for driving simulation in urban environments

This paper presents a method to manage an urban environment complex database, making use of hierarchical elision techniques over a spatial connectivity network. It also shows how to adapt and refine traffic microsimulation algorithms to provide visual quality in a local area.

Combining displacement mapping methods on the GPU for real-time terrain visualization

Real-time terrain visualization plays an important role in multiple popular applications. In these applications, displacement mapping algorithms (both per-vertex and per-pixel methods) can be used to improve the accuracy and performance of terrain rendering. Per-vertex methods are usually implemented by means of hardware tessellation, and per-pixel techniques, such as parallax mapping, apply changes at the pixel level using the fragment shader. However, parallax mapping has not still been used in real-time terrain visualization applications due to different reasons. In this paper, we propose a comparison study of different combinations of per-vertex and per-pixel methods. The performance evaluation results reveal that any of the implemented schemes improve the performance of terrain rendering, with respect to the performance yielded by the exclusive use of hardware tessellation. These results validate the proposed schemes as efficient alternatives for real-time terrain visualization applications.

Improving hybrid distributed architectures for interactive terrain visualization

Interactive 3D terrain visualization plays an important role in multiple networked applications like virtual worlds visualization, multiplayer games or distributed simulators. Since the client/server architecture has obvious scalability limitations, different peer-to-peer schemes have been proposed as trade-off solutions that yield good robustness, availability and scalability for this kind of systems. In this paper, we propose a new hybrid distributed architecture that significantly improves the scalability and performance of the existing proposals. The proposed scheme redesigns the relationships between the different elements of a hybrid architecture, modifies the information shared by each client with its neighboring peers and varies the messages exchanged among them, providing a larger number of users with a fluid navigation experience over a large virtual terrain.

A new parallel pipeline for DNA methylation analysis of long reads datasets

BackgroundDNA methylation is an important mechanism of epigenetic regulation in development and disease. New generation sequencers allow genome-wide measurements of the methylation status by reading short stretches of the DNA sequence (Methyl-seq). Several software tools for methylation analysis have been proposed over recent years. However, the current trend is that the new sequencers and the ones expected for an upcoming future yield sequences of increasing length, making these software tools inefficient and obsolete.ResultsIn this paper, we propose a new software based on a strategy for methylation analysis of Methyl-seq sequencing data that requires much shorter execution times while yielding a better level of sensitivity, particularly for datasets composed of long reads. This strategy can be exported to other methylation, DNA and RNA analysis tools.ConclusionsThe developed software tool achieves execution times one order of magnitude shorter than the existing tools, while yielding equal sensitivity for short reads and even better sensitivity for long reads.

Adding Synthetic Detail to Natural Terrain Using a Wavelet Approach

Terrain representation is a basic topic in the field of interactive graphics. The amount of data required for good quality terrain representation offers an important challenge to developers of such systems. For users of these applications the accuracy of geographical data is less important than their natural visual appearance. This makes it possible to mantain a limited geographical data base for the system and to extend it generating synthetic data.In this paper we combine fractal and wavelet theories to provide extra data which keeps the natural essence of actual information available. The new levels of detail(LOD) for the terrain are obtained applying an inverse Wavelet Transform (WT) to a set of values randomly generated, maintaining statistical properties coherence with original geographical data.