Optimizing Splicing Junction Detection in Next Generation Sequencing Data on a Virtual-GRID Infrastructure

The new protocol for sequencing the messenger RNA in a cell, named RNA-seq produce millions of short sequence fragments. Next Generation Sequencing technology allows more accurate analysis but increase needs in term of computational resources. This paper describes the optimization of a RNA-seq analysis pipeline devoted to splicing variants detection, aimed at reducing computation time and providing a multi-user/multisample environment. This work brings two main contributions. First, we optimized a well-known algorithm called TopHat by parallelizing some sequential mapping steps. Second, we designed and implemented a hybrid virtual GRID infrastructure allowing to efficiently execute multiple instances of TopHat running on different samples or on behalf of different users, thus optimizing the overall execution time and enabling a flexible multi-user environmen

Understanding the Computational Requirements of Virtualized Baseband Units using a Programmable Cloud Radio Access Network Testbed

Cloud Radio Access Network (C-RAN) is emerging as a transformative architecture for the next generation of mobile cellular networks. In C-RAN, the Baseband Unit (BBU) is decoupled from the Base Station (BS) and consolidated in a centralized processing center. While the potential benefits of C-RAN have been studied extensively from the theoretical perspective, there are only a few works that address the system implementation issues and characterize the computational requirements of the virtualized BBU. In this paper, a programmable C-RAN testbed is presented where the BBU is virtualized using the OpenAirInterface (OAI) software platform, and the eNodeB and User Equipment (UEs) are implemented using USRP boards. Extensive experiments have been performed in a FDD downlink LTE emulation system to characterize the performance and computing resource consumption of the BBU under various conditions. It is shown that the processing time and CPU utilization of the BBU increase with the channel resources and with the Modulation and Coding Scheme (MCS) index, and that the CPU utilization percentage can be well approximated as a linear increasing function of the maximum downlink data rate. These results provide real-world insights into the characteristics of the BBU in terms of computing resource and power consumption, which may serve as inputs for the design of efficient resource-provisioning and allocation strategies in C-RAN systems.Comment: In Proceedings of the IEEE International Conference on Autonomic Computing (ICAC), July 201

Algorithms for advance bandwidth reservation in media production networks

Media production generally requires many geographically distributed actors (e.g., production houses, broadcasters, advertisers) to exchange huge amounts of raw video and audio data. Traditional distribution techniques, such as dedicated point-to-point optical links, are highly inefficient in terms of installation time and cost. To improve efficiency, shared media production networks that connect all involved actors over a large geographical area, are currently being deployed. The traffic in such networks is often predictable, as the timing and bandwidth requirements of data transfers are generally known hours or even days in advance. As such, the use of advance bandwidth reservation (AR) can greatly increase resource utilization and cost efficiency. In this paper, we propose an Integer Linear Programming formulation of the bandwidth scheduling problem, which takes into account the specific characteristics of media production networks, is presented. Two novel optimization algorithms based on this model are thoroughly evaluated and compared by means of in-depth simulation results

From a Competition for Self-Driving Miniature Cars to a Standardized Experimental Platform: Concept, Models, Architecture, and Evaluation

Context: Competitions for self-driving cars facilitated the development and research in the domain of autonomous vehicles towards potential solutions for the future mobility. Objective: Miniature vehicles can bridge the gap between simulation-based evaluations of algorithms relying on simplified models, and those time-consuming vehicle tests on real-scale proving grounds. Method: This article combines findings from a systematic literature review, an in-depth analysis of results and technical concepts from contestants in a competition for self-driving miniature cars, and experiences of participating in the 2013 competition for self-driving cars. Results: A simulation-based development platform for real-scale vehicles has been adapted to support the development of a self-driving miniature car. Furthermore, a standardized platform was designed and realized to enable research and experiments in the context of future mobility solutions. Conclusion: A clear separation between algorithm conceptualization and validation in a model-based simulation environment enabled efficient and riskless experiments and validation. The design of a reusable, low-cost, and energy-efficient hardware architecture utilizing a standardized software/hardware interface enables experiments, which would otherwise require resources like a large real-scale test track.Comment: 17 pages, 19 figues, 2 table

Soft-Defined Heterogeneous Vehicular Network: Architecture and Challenges

Heterogeneous Vehicular NETworks (HetVNETs) can meet various quality-of-service (QoS) requirements for intelligent transport system (ITS) services by integrating different access networks coherently. However, the current network architecture for HetVNET cannot efficiently deal with the increasing demands of rapidly changing network landscape. Thanks to the centralization and flexibility of the cloud radio access network (Cloud-RAN), soft-defined networking (SDN) can conveniently be applied to support the dynamic nature of future HetVNET functions and various applications while reducing the operating costs. In this paper, we first propose the multi-layer Cloud RAN architecture for implementing the new network, where the multi-domain resources can be exploited as needed for vehicle users. Then, the high-level design of soft-defined HetVNET is presented in detail. Finally, we briefly discuss key challenges and solutions for this new network, corroborating its feasibility in the emerging fifth-generation (5G) era