A parallel and sensitive software tool for methylation analysis on multicore platforms.
Abstract 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 bis…
Providing Full Awareness to Distributed Virtual Environments Based on Peer-to-Peer Architectures
In recent years, large scale distributed virtual environments (DVEs) have become a major trend in distributed applications, mainly due to the enormous popularity of multiplayer online games in the entertainment industry. Since architectures based on networked servers seems to be not scalable enough to support massively multiplayer applications, peer-to-peer (P2P) architectures have been proposed as an efficient and truly scalable solution for this kind of systems. However, the main challenge of P2P architectures consists of providing each avatar with updated information about which other avatars are its neighbors. We have denoted this problem as the awareness problem. Although some proposal…
A Comparison Study of Modern Heuristics for Solving the Partitioning Problem in Distributed Virtual Environment Systems
Fast Internet connections and the widespread use of high performance graphic cards are making Distributed Virtual Environment (DVE) systems very common nowadays. However, there are several key issues in these systems that should still be improved in order to design a scalable and cost-effective system. One of these key issues is the partitioning problem. This problem consists of efficiently assigning clients (3-D avatars) to the servers in the system. In this paper, we present a comparison study of different modern heuristics for solving the partitioning problem in DVE systems, as an alternative to the ad-hoc heuristic proposed in the literature. Performance evaluation results show that som…
Improving topological mapping on NoCs
Networks-on-Chip (NoCs) have been proposed as an efficient solution to the complex communications on System-on-chip (SoCs). The design flow of network-on-chip (NoCs) include several key issues, and one of them is the decision of where cores have to be topologically mapped. This thesis proposes a new approach to the topological mapping strategy for NoCs. Concretely, we propose a new topological mapping technique for regular and irregular NoC platforms and its application for optimizing application specific NoC based on distributed and source routing.
A nested virtualization tool for information technology practical education
Background A common problem of some information technology courses is the difficulty of providing practical exercises. Although different approaches have been followed to solve this problem, it is still an open issue, specially in security and computer network courses. Results This paper proposes NETinVM, a tool based on nested virtualization that includes a fully functional lab, comprising several computers and networks, in a single virtual machine. It also analyzes and evaluates how it has been used in different teaching environments. Conclusions The results show that this tool makes it possible to perform demos, labs and practical exercises, greatly appreciated by the students, that woul…
A comparison study of evolutive algorithms for solving the partitioning problem in distributed virtual environment systems
Fast Internet connections and the widespread use of high performance graphic cards are making Distributed Virtual Environment (DVE) systems very common nowadays. However, there are several key issues in these systems that should still be improved in order to design a scalable and cost-effective system. One of these key issues is the partitioning problem. This problem consists of efficiently assigning clients (3D avatars) to the servers in the system. In this paper, we present a comparison study of different modern heuristics for solving the partitioning problem in DVE systems, as an alternative to the ad hoc heuristic proposed in the literature. Performance evaluation results show that some…
A GPU-Based Multi-agent System for Real-Time Simulations
The huge number of cores existing in current Graphics Processor Units (GPUs) provides these devices with computing capabilities that can be exploited by distributed applications. In particular, these capabilites have been used in crowd simulations for enhancing the crowd rendering, and even for simulating continuum crowds. However, GPUs have not been used for simulating large crowds of complex agents, since these simulations require distributed architectures that can support huge amounts of agents. In this paper, we propose a GPU-based multi-agent system for crowd simulation. Concretely, we propose the use of an on-board GPU to implement one of the main tasks that a distributed server for c…
The Quality of Service Issue in Virtual Environments
Networked virtual environments (NVEs) have become a major trend in distributed computing, mainly due to the enormous popularity of multi-player online games in the entertainment industry. Nowadays, NVE systems are considered as the supporting technology for many networked and virtual organizations (NVO) (Singhal & Zyda, 1999), especially to those classified within the field of computer supported cooperative work (CSCW), where networked computer can be seen as a standard to provide the technological means to support the team design (Ott & Nastansky, 1997). These highly interactive systems simulate a virtual world where multiple users share the same scenario. The system renders the im…
Improving the performance of CAR systems based on mobile phones
Collaborative Augmented Reality (CAR) systems allow multiple users to share a real work environment including computer-generated images in real time. Currently, the hardware features of most mobile phones makes them a natural platform for CAR systems. However, the wide variety of these hardware features can have important effects on the performance of the mobile CAR applications. This thesis proposes a performance characterization and improvement of CAR systems based on mobile phones. The research results, at the time of writing this paper, shows that a CAR system using mobile phones as clients and with a single server can support up to one thousand clients while providing interactive respo…
Performance improvements of real-time crowd simulations
The current challenge for crowd simulations is the design and development of a scalable system that is capable of simulating the individual behavior of millions of complex agents populating large scale virtual worlds with a good frame rate. In order to overcome this challenge, this thesis proposes different improvements for crowd simulations. Concretely, we propose a distributed software architecture that can take advantage of the existing distributed and multi-core architectures. In turn, the use of these distributed architectures requires partitioning strategies and workload balancing techniques for distributed crowd simulations. Also, these architectures allow the use of GPUs not only fo…
HPG-HMapper: A DNA hydroxymethylation analysis tool
DNA methylation (mC) and hydroxymethylation (hmC) can significantly affect the normal human development, as well as health and disease status. hmC studies require not only specific treatment of DNA, but also software tools for their analysis. However, there are no software tools capable of analyzing DNA hmC currently. In this article, we propose HPG-HMapper, a parallel software tool for analyzing the DNA hmC data obtained by ten-eleven translocation–assisted bisulfite sequencing. This tool takes as input data the output files of mC aligner tools, and it yields mC maps and the accounting of methylated and hydroxymethylated bases on each chromosome. The design of this tool includes the consi…
A new AR authoring tool using depth maps for industrial procedures
Several augmented reality systems have been proposed for different target fields such as medical, cultural heritage and military. However, most of the current AR authoring tools are actually programming interfaces that are exclusively suitable for programmers. In this paper, we propose an AR authoring tool which provides advanced visual effect, such as occlusion or media contents. This tool allows non-programming users to develop low-cost AR applications, specially oriented to on-site assembly and maintenance/repair tasks. A new 3D edition interface is proposed, using photos and Kinect depth information to improve 3D scenes composition. In order to validate our AR authoring tool, two evalua…
On the Characterization of Distributed Virtual Environment Systems
Distributed Virtual Environment systems have experienced a spectacular growth last years. One of the key issues in the design of scalable and cost-effective DVE systems is the partitioning problem. This problem consists of efficiently assigning clients (3-D avatars) to the servers in the system, and some techniques have been already proposed for solving it.
MARL-Ped+Hitmap: Towards Improving Agent-Based Simulations with Distributed Arrays
Multi-agent systems allow the modelling of complex, heterogeneous, and distributed systems in a realistic way. MARL-Ped is a multi-agent system tool, based on the MPI standard, for the simulation of different scenarios of pedestrians who autonomously learn the best behavior by Reinforcement Learning. MARL-Ped uses one MPI process for each agent by design, with a fixed fine-grain granularity. This requirement limits the performance of the simulations for a restricted number of processors that is lesser than the number of agents. On the other hand, Hitmap is a library to ease the programming of parallel applications based on distributed arrays. It includes abstractions for the automatic parti…
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 applic…
Tuning Java to Run Interactive Multiagent Simulations over Jason
Java-based simulation environments are currently used by many multiagent systems (MAS), since they mainly provide portability as well as an interesting reduction of the development cost. However, this kind of MAS are rarely considered when developing interactive applications with time response constraints. This paper analyses the performance provided by Jason, a well-known Java-based MAS platform, as a suitable framework for developing interactive multiagent simulations. We show how to tune both the heap size and the garbage collection of the Java Virtual Machine in order to achieve a good performance while executing a simple locomotion benchmark based on crowd simulations. Furthermore, the…
An Easy-to-Use AR Authoring Tool for Industrial Applications
Augmented Reality (AR) applications have been emerged last years as a valuable tool for saving significant costs in maintenance and process control tasks in industry. This trend has been stimulated by the appearance of authoring tools that allow the fast and easy development of AR applications. However, most of current AR authoring tools are actually programming interfaces that are exclusively suitable for programmers, and they do not provide advanced visual effects such as occlusion or object collision detection.
A genetic approach for adding QoS to distributed virtual environments
Distributed virtual environment (DVE) systems have been designed last years as a set of distributed servers. These systems allow a large number of remote users to share a single 3D virtual scene. In order to provide quality of service in a DVE system, clients should be properly assigned to servers taking into account system throughput and system latency. The latter one is composed of both network and computational delays. This highly complex problem is known as the quality of service (QoS) problem. In this paper, we study the implementation of a genetic algorithm (GA) for solving the QoS problem in DVE systems. Performance evaluation results show that, due to its ability of both finding goo…
A Comparison Study of Metaheuristic Techniques for Providing QoS to Avatars in DVE Systems
Network-server architecture has become a de-facto standard for Distributed Virtual Environment (DVE) systems. In these systems, a large set of remote users share a 3D virtual scene. In order to design scalable DVE systems, different approaches have been proposed to maintain the DVE system working under its saturation point, maximizing system throughput. Also, in order to provide quality of service to avatars in a DVE systems, avatars should be assigned to servers taking into account, among other factors, system throughput and system latency. This highly complex problem is called quality of service (QoS) problem in DVE systems. This paper proposes two different approaches for solving the QoS…
M-GRASP: A GRASP With Memory for Latency-Aware Partitioning Methods in DVE Systems
A necessary condition for providing quality of service to distributed virtual environments (DVEs) is to provide a system response below a maximum threshold to the client computers. In this sense, latency-aware partitioning methods try to provide response times below the threshold to the maximum number of client computers as possible. These partitioning methods should find an assignment of clients to servers that optimizes system throughput, system latency, and partitioning efficiency. In this paper, we present a new algorithm based on greedy randomized adaptive search procedure with memory for finding the best solutions as possible to this problem. We take into account several different alt…
Sociable Behaviors in Virtual Worlds
When simulating three-dimensional environments populated by virtual humanoids, immersion requires the simulation of consistent social behaviors to keep the attention of the user/s while displaying realistic scenes. However, intelligent virtual actors still lack a kind of collective or social intelligence necessary to reinforce the roles they are playing in the simulated environment (e.g. a waiter, a guide, etc). Decision making for virtual agents has been traditionally modeled under self interested assumptions, which are not suitable for social multi-agent domains. Instead, artificial society models should be introduced to provide virtual actors with socially acceptable decisions, which are…
Workload Characterization in Multiplayer Online Games
In recent years, distributed virtual environments (DVEs) have become a major trend in distributed applications, mainly due to the enormous popularity of multiplayer online games in the entertainment industry. Although the workload generated by avatars in a DVE system has already been characterized, the special features of multiplayer online games make these applications to require a particular workload characterization. This paper presents the workload characterization of multiplayer online games. This characterization is based on real traces, and it shows that the movement patterns of avatars used to develop optimization techniques for DVE systems can be extrapolated to First Person Shooti…
Ensuring the performance and scalability of peer-to-peer distributed virtual environments
Large scale distributed virtual environments (DVEs) have become a major trend in distributed applications. Peer-to-peer (P2P) architectures have been proposed as an efficient and truly scalable solution for these kinds of systems. However, in order to design efficient P2P DVEs these systems must be characterized, measuring the impact of different client behavior on system performance. This paper presents the experimental characterization of P2P DVEs. The results show that the saturation of a given client has an exclusive effect on the surrounding clients in the virtual world, having no noticeable effect at all on the rest of clients. Nevertheless, the interactions among clients that can tak…
A new approach for the visualization of DNA methylation results
A multi-objective strategy for concurrent mapping and routing in networks on chip
The design flow of network-on-chip (NoCs) include several key issues. Among other parameters, the decision of where cores have to be topologically mapped and also the routing algorithm represent two highly correlated design problems that must be carefully solved for any given application in order to optimize several different performance metrics. The strong correlation between the different parameters often makes that the optimization of a given performance metric has a negative effect on a different performance metric. In this paper we propose a new strategy that simultaneously refines the mapping and the routing function to determine the Pareto optimal configurations which optimize averag…
A scalable multiagent system architecture for interactive applications
Interactive applications like crowd simulations need to properly render the virtual world while simulating the interaction of thousands of agents at the same time. The computational workload generated by these two tasks highly increases with the number of the simulated agents, requiring a scalable design of the multiagent system. In this paper, we present, in an unified manner, a distributed multiagent system architecture that can manage large crowds of autonomous agents at interactive rates while rendering multiple views of the virtual world being simulated. This architecture consists of a distributed multiagent system and a complementary distributed visualization subsystem. We also presen…
A distributed visualization system for crowd simulations1
The visualization system of large-scale crowd simulations should scale up with both the number of visuals views of the virtual world and the number of agents displayed in each visual. Otherwise, we could have large scale crowd simulations where only a small percentage of the population is displayed. Several approaches have been proposed in order to efficiently render crowds of animated characters. However, these approaches either render crowds animated with simple behaviors or they can only support a few hundreds of user-driven entities. In this paper, we propose a distributed visualization system for large crowds of autonomous agents that allows the visualization of crowds animated with co…
On the development of a communication-aware task mapping technique
Clusters have become a very cost-effective platform for high-performance computing. In these systems, although currently existing networks actually provide enough bandwidth for the existing applications and workstations, the trend is towards the interconnection network becoming the system bottleneck. Therefore, in the future, scheduling strategies will have to take into account the communication requirements of the applications and the communication bandwidth that the network can offer. One of the key issues in these strategies is the task mapping technique used when the network becomes the system bottleneck.In this paper, we propose a communication-aware mapping technique that tries to mat…
A Clustering Approach for Improving Network Performance in Heterogeneous Systems
A lot of research has focused on solving the problem of computation-aware task scheduling on heterogeneous systems. In this paper, we propose a clustering algorithm that, given a network topology, provides a network partition adapted to the communication requirements of the applications running on the machine. Also, we propose a criterion to measure the quality of each one of the possible mappings of processes to processors based on that network partition. Evaluation results show that these proposals can greatly improve network performance, providing a basis of a communication-aware scheduling technique.
Server implementations for improving the performance of CAR systems based on mobile phones
Collaborative Augmented Reality (CAR) systems allow multiple users to share a real world environment, including computer-generated images in real time. The hardware features of most current mobile phones include wireless network capabilities that offer a natural platform for CAR systems. However, the potential number of clients in CAR systems based on mobile phones is much larger than on CAR systems based on other kind of mobile devices, requiring a system design that takes into account scalability issues. This paper presents the experimental characterization of CAR systems based on mobile phones, providing quantitative results about well-known performance metrics in distributed systems. Th…
A New Genetic Approach for the Partitioning Problem in Distributed Virtual Environment Systems
The Partitioning problem is a key issue in the design of Distributed Virtual Environment (DVE) systems based on a server-network architecture. This problem consist of efficiently assigning the clients of the simulation (avatars) to the system servers. Despite the existing literature proposes different evolutive approaches for solving this NP-hard problem, an approach based on genetic algorithms is considered as the current best partitioning mechanism.
Comparison of WSN and IoT approaches for a real-time monitoring system of meal distribution trolleys: A case study
Abstract International regulations determine that food in hospitals and elderly homes must be served at given temperature ranges. However, the real-time surveillance of the meal distribution trolleys along all the institutions facilities, guaranteeing conformity to rules from the instant when all the meals are put in the distribution trolley until they are delivered to the patients, is still a challenge. In this paper, we present a comparison of two approaches based on Wireless Sensor Networks (WSN) and Internet of Things (IoT) technologies for implementing a Real-Time Monitoring System of Meal Distribution Trolleys in a hospital. The performance evaluation results show that the IoT impleme…
Distance Constrained Mapping to Support NoC Platforms Based on Source Routing
Efficient NoC is crucial for communication among processing elements in a highly parallel processing systems on chip. Mapping cores to slots in a NoC platform and designing efficient routing algorithms are two key problems in NoC design. Source routing offers major advantages over distributed routing especially for regular topology NoC platforms. But it suffers from a serious drawback of overhead since it requires whole communication path to be stored in every packet header. In this paper, we present a core mapping technique which helps to achieve a mapping with the constraint over the path length. We have found that the path length constraint of just 50% is sufficient in most cases. We als…
Design of an ICT Tool for Decision Making in Social and Health Policies
The governance requires technical support regarding the complexity in deciding health policies to assist people who require long-term care. Long-term care policies require the use of ICT simulation tools that can provide policy makers with the option of going into a decision theatre and virtually knowing the consequences of different policies prior to finally determining the real policy to be adopted. In this sense, there is an absence of simulation tools for decision making about long-term care policies. In this chapter, the authors propose the foundations and guidelines of SSIMSOWELL, a new scalable, multiagent simulation tool that increases the prediction capacity of governance in the lo…
Accelerating collision detection for large-scale crowd simulation on multi-core and many-core architectures
The computing capabilities of current multi-core and many-core architectures have been used in crowd simulations for both enhancing crowd rendering and simulating continuum crowds. However, improving the scalability of crowd simulation systems by exploiting the inherent parallelism of these architectures is still an open issue. In this paper, we propose different parallelization strategies for the collision check procedure that takes place in agent-based simulations. These strategies are designed for exploiting the parallelism in both multi-core and many-core architectures like graphic processing units (GPUs). As for the many-core implementations, we analyse the bottlenecks of a previous G…
On the Use of GPU for Accelerating Communication-Aware Mapping Techniques
Different communication-aware mapping techniques were proposed in recent years for improving the performance of distributed systems based on both, off-chip and on-chip networks. Some of these proposals were based on heuristic search for finding pseudo-optimal assignments of tasks and processing elements. However, the technology integration improvements have allowed a significant increase in the number of network nodes, requiring the acceleration of the heuristic search. In this paper, we propose a comparative study of the local search method used in a communication-aware mapping technique, when implemented on different parallel architectures. We compare the performance provided by a version…
A new system architecture for crowd simulation
Crowd simulation requires both rendering visually plausible images and managing the behavior of autonomous agents. Therefore, these applications need an efficient design that allows them to simultaneously handle these two requirements. Although several proposals have focused on the software architectures for these systems, no proposals have focused on the computer systems supporting them. In this paper, we analyze the computer architectures used in the literature to support distributed virtual environments. Also, we propose a distributed computer architecture which is efficient enough to support simulations of thousand of autonomous agents. This proposal consists of a cluster of interconnec…
Integrating Social Skills in Task-Oriented 3D IVA
This paper presents a set of mechanisms oriented to incorporate social information into the decision taking of task-oriented 3DIVA. The aim of this approach is to integrate collaborative skills in different character's roles (seller/buyer, worker, pedestrian, etc.) in order to enhance its behavioral animation. The collective intelligence expected in this kind of multi-character domains (e.g. storytelling, urban simulation, interactive games, etc.) requires agents able to dialogue/interact with other characters, to autonomously group/ungroup (according to their goals), or to distribute tasks and coordinate their execution for solving possible conflicts. The social model implemented follows t…
A Communication-Aware Topological Mapping Technique for NoCs
Networks---on---Chip (NoCs) have been proposed as a promising solution to the complex on-chip communication problems derived from the increasing number of processor cores. The design of NoCs involves several key issues, being the topological mapping (the mapping of the Intellectual Properties (IPs) to network nodes) one of them. Several proposals have been focused on topological mapping last years, but they require the experimental validation of each mapping considered. In this paper, we propose a communication-aware topological mapping technique for NoCs. This technique is based on the experimental correlation of the network model with the actual network performance, thus avoiding the need…
Introducción de metodologías de aprendizaje basado en problemas mediante tecnologías multimedia
La propuesta de trabajar por competencias en lugar de hacerlo como se hacía tradicionalmente, por objetivos, ha hecho proliferar las propuestas y alternativas metodológicas para favorecer un cambio en la Educación Superior. Una de estas metodologías es el aprendizaje basado en problemas (ABP). El ABP es una metodología de aprendizaje en la cual el punto de partida es un problema construido por el profesor que permite al estudiante identificar necesidades para comprender mejor ese problema, identificar principios que sustentan el conocimiento y cumplir objetivos de aprendizaje relacionados con cada porción del contenido de la materia. En el caso de las tecnologías de la información y las com…
A comparative study of partitioning methods for crowd simulations
The simulation of large crowds of autonomous agents with realistic behavior is still a challenge for several computer research communities. In order to handle large crowds, some scalable architectures have been proposed. Nevertheless, the effective use of distributed systems requires the use of partitioning methods that can properly distribute the workload generated by agents among the existing distributed resources. In this paper, we analyze the use of irregular shape regions (convex hulls) for solving the partitioning problem. We have compared a partitioning method based on convex hulls with two techniques that use rectangular regions. The performance evaluation results show that the conv…
Hybrid P2P schemes for remote terrain interactive visualization systems
Over the last few years, there has been a lot of development of interactive terrain visualization applications using remote databases. One of the main problems that these applications must face is scalability. These applications usually use a client-server model that cannot support a large number of concurrent requests without using a considerable number of servers. In this paper, we present a full comparative study of new hybrid P2P schemes for terrain interactive visualization systems. The performance evaluation results show that the best strategy consists of avoiding the periodical reporting among peer nodes about the current information contained in each node, while using some servers a…
Analyzing Large-Scale Crowd Simulations for Building Evacuation
Animated virtual crowds have been used last years for analyzing human factors in scenarios where masses of people gather. A typical example is building evacuation in case of fire. Scalability still remains as an open issue for these multiagent systems applications. In this paper, we use a scalable architecture to simulate a large-scale version of a virtual crowd in a building evacuation. From the social point of view, the results provided by the large-scale version of the crowd add new and crucial information about the agents behavior, emphasizing the need for a small amount of trained leaders in order to save lives. From the system point of view, the results show that the trend of avatars …
Towards a Simulator of Integrated Long-Term Care Systems for Elderly People
In this paper, we propose a simulator for integrated long-term care systems using as a starting point a holistic model of care systems for people that need long term care, the Sustainable Socio-Health Model (SSHM). The implementation of the simulator on the Jason multi-agent platform allows the tool to include the human interactions, preferences, and social abilities that take place between elderly people and the staff of healthcare systems (doctors, social workers and nurses). In addition, the use of this multi-agent platform provides the required scalability for simulating population sizes of different orders of magnitude. The paper shows the model to be implemented in the simulator, the…
A new parallel pipeline for DNA methylation analysis of long reads datasets
Background DNA 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. Results In 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…
On the Use of Binary Trees for DNA Hydroxymethylation Analysis
DNA methylation (mC) and hydroxymethylation (hmC) can have a significant effect on normal human development, health and disease status. Hydroxymethylation studies require specific treatment of DNA, as well as software tools for their analysis. In this paper, we propose a parallel software tool for analyzing the DNA hydroxymethylation data obtained by TAB-seq. The software is based on the use of binary trees for searching the different occurrences of methylation and hydroxymethylation in DNA samples. The binary trees allow to efficiently store and access the information about the methylation of each methylated/hydroxymethylated cytosines in the samples. Evaluation results shows that the perf…