BarraCUDA - a fast short read sequence aligner using graphics processing units.

BACKGROUND: With the maturation of next-generation DNA sequencing (NGS) technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU), extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC) clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. FINDINGS: Using the NVIDIA Compute Unified Device Architecture (CUDA) software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. CONCLUSIONS: BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology.BarraCUDA is currently available from http://seqbarracuda.sf.net.

Heterogeneous reconfigurable system for adaptive particle filters in real-time applications

This paper presents a heterogeneous reconfigurable system for real-time applications applying particle filters. The system consists of an FPGA and a multi-threaded CPU. We propose a method to adapt the number of particles dynamically and utilise the run-time reconfigurability of the FPGA for reduced power and energy consumption. An application is developed which involves simultaneous mobile robot localisation and people tracking. It shows that the proposed adaptive particle filter can reduce up to 99% of computation time. Using run-time reconfiguration, we achieve 34% reduction in idle power and save 26-34% of system energy. Our proposed system is up to 7.39 times faster and 3.65 times more energy efficient than the Intel Xeon X5650 CPU with 12 threads, and 1.3 times faster and 2.13 times more energy efficient than an NVIDIA Tesla C2070 GPU. © 2013 Springer-Verlag.

Control of bimanual rhythmic movements: Trading efficiency for robustness depending on the context

This paper investigates how the efficiency and robustness of a skilled rhythmic task compete against each other in the control of a bimanual movement. Human subjects juggled a puck in 2D through impacts with two metallic arms, requiring rhythmic bimanual actuation. The arms kinematics were only constrained by the position, velocity and time of impacts while the rest of the trajectory did not influence the movement of the puck. In order to expose the task robustness, we manipulated the task context in two distinct manners: the task tempo was assigned at four different values (hence manipulating the time available to plan and execute each impact movement individually); and vision was withdrawn during half of the trials (hence reducing the sensory inflows). We show that when the tempo was fast, the actuation was rhythmic (no pause in the trajectory) while at slow tempo, the actuation was discrete (with pause intervals between individual movements). Moreover, the withdrawal of visual information encouraged the rhythmic behavior at the four tested tempi. The discrete versus rhythmic behavior give different answers to the efficiency/robustness trade-off: discrete movements result in energy efficient movements, while rhythmic movements impact the puck with negative acceleration, a property preserving robustness. Moreover, we report that in all conditions the impact velocity of the arms was negatively correlated with the energy of the puck. This correlation tended to stabilize the task and was influenced by vision, revealing again different control strategies. In conclusion, this task involves different modes of control that balance efficiency and robustness, depending on the context. © 2008 Springer-Verlag.

Theoretical study of line narrowing in a sub-terahertz monolithic dual laser source with an integrated reflector

A monolithic design is proposed for low-noise sub-THz signal generation by integrating a reflector onto a dual laser source. The reflectivity and the position of such a reflector can be adjusted to obtain constructive feedback from the reflector to both lasers, thus causing a Vernier feedback effect. As a result, 10-fold line narrowing, the narrowing being limited by the resolution of the simulation, is predicted using a transmission line model. Finally, a simple control scheme using an electrical feedback loop to adjust laser biases is proposed to maintain the line narrowing performance. This line narrowing technique, comprising a passive integrated reflector, could allow the development of a low-cost, compact and energy-efficient solution for high-purity sub-THz signal generation. © The Institution of Engineering and Technology 2014.

Hopping robot based on free vibration of an elastic curved beam

This study presents a novel approach to the design of low-cost and energy-efficient hopping robots, which makes use of free vibration of an elastic curved beam. We found that a hopping robot could benefit from an elastic curved beam in many ways such as low manufacturing cost, light body weight and small energy dissipation in mechanical interactions. A challenging problem of this design strategy, however, lies in harnessing the mechanical dynamics of free vibration in the elastic curved beam: because the free vibration is the outcome of coupled mechanical dynamics between actuation and mechanical structures, it is not trivial to systematically design mechanical structures and control architectures for stable locomotion. From this perspective, this paper investigates a case study of simple hopping robot to identify the design principles of mechanics and control. We developed a hopping robot consisting of an elastic curved beam and a small rotating mass, which was then modeled and analyzed in simulation. The experimental results show that the robot is capable of exhibiting stable hopping gait patterns by using a small actuation with no sensory feedback owing to the intrinsic stability of coupled mechanical dynamics. Furthermore, an additional analysis shows that, by exploiting free vibration of the elastic curved beam, cost of transport of the proposed hopping locomotion can be in the same rage of animals' locomotion including human running. © 2011 IEEE.

Trajectory control based on discrete full-range dynamics

There has been an increasing interest in the use of mechanical dynamics, (e.g., assive, Elastic, And viscous dynamics) for energy efficient and agile control of robotic systems. Despite the impressive demonstrations of behavioural performance, The mechanical dynamics of this class of robotic systems is still very limited as compared to those of biological systems. For example, Passive dynamic walkers are not capable of generating joint torques to compensate for disturbances from complex environments. In order to tackle such a discrepancy between biological and artificial systems, We present the concept and design of an adaptive clutch mechanism that discretely covers the full-range of dynamics. As a result, The system is capable of a large variety of joint operations, including dynamic switching among passive, actuated and rigid modes. The main innovation of this paper is the framework and algorithm developed for controlling the trajectory of such joint. We present different control strategies that exploit passive dynamics. Simulation results demonstrate a significant improvement in motion control with respect to the speed of motion and energy efficiency. The actuator is implemented in a simple pendulum platform to quantitatively evaluate this novel approach.

Motor control optimization of compliant one-legged locomotion in rough terrain

While underactuated robotic systems are capable of energy efficient and rapid dynamic behavior, we still do not fully understand how body dynamics can be actively used for adaptive behavior in complex unstructured environment. In particular, we can expect that the robotic systems could achieve high maneuverability by flexibly storing and releasing energy through the motor control of the physical interaction between the body and the environment. This paper presents a minimalistic optimization strategy of motor control policy for underactuated legged robotic systems. Based on a reinforcement learning algorithm, we propose an optimization scheme, with which the robot can exploit passive elasticity for hopping forward while maintaining the stability of locomotion process in the environment with a series of large changes of ground surface. We show a case study of a simple one-legged robot which consists of a servomotor and a passive elastic joint. The dynamics and learning performance of the robot model are tested in simulation, and then transferred the results to the real-world robot. ©2007 IEEE.

节能有效的无线传感器网络状态信息收集算法

网络状态信息收集协议既要保证信息收集的准确性、实时性,又要保证协议算法的轻量级特性。为解决上述矛盾问题,提出了一种轻量级的、能量有效的、基于无损聚合的层次分簇数据收集机制(QTBDC)。QTBDC首先对网络节点编码并在节点间建立起一个逻辑层次簇结构,然后利用各个子簇状态数据的相似性和编码的连续性,实现了网内无损聚合。该监测机制使得网络状态信息的收集在不丢失数据细节信息的情况下,数据通信量大大减少。经过仿真分析表明,该方法与现有经典数据收集方法相比,实现了节能,延长了网络的生命期。

无线传感器网络中一种启发式最小连通支配集算法

针对最小连通配集问题设计了一种具有较高能量效率的启发式算法。算法首先把网络中所有的节点作为最小连通支配集的一个初始解,然后利用启发式修剪策略剔除冗余节点从而减小最小连通支配集的大小,直到没有冗余节点存在。文中将算法分成集中式和分布式两种情况进行了详细讨论。仿真结果表明,由于实现简便,该算法与其他已有算法相比较,在算法复杂性和算法稳定运行时间上有一定的优势。

Super insulated aerogel windows: Impact on daylighting and thermal performance.

Window design plays an important role in achieving energy efficient buildings and in providing thermal comfort of building occupants. This paper investigates a newly developed aerogel window and the potential improvement on the comfort factors of an office in relation to daylighting. Improved comfort levels can impact on health and wellbeing of building occupants leading to knock on effects on absenteeism and productivity. A simulation tool was presently created that will easily enable comparison of different façade design and their impact on heat and light transmission and therefore enable optimisation. One of the most important aspects of the present work was comparing the performance of the newly developed aerogel window against the more traditional Argon-filled, coated double-glazing. Whereas the aerogel window provided an extremely low heat-loss index of 0.3 W/m2K, the latter usually offered a centre-glazing U-value of 1.4 W/m2K. On a like-with-like basis the daylight transmission of the aerogel window was significantly lower than double-glazing. However, in view of low thermal loss larger areas of the former can be deployed. This article presents the influence of three key parameters that may lead to an optimum design: daylight, thermal loss and solar gain.

CSR: Constrained Selfish Routing in Ad-hoc Networks

Routing protocols for ad-hoc networks assume that the nodes forming the network are either under a single authority, or else that they would be altruistically forwarding data for other nodes with no expectation of a return. These assumptions are unrealistic since in ad-hoc networks, nodes are likely to be autonomous and rational (selfish), and thus unwilling to help unless they have an incentive to do so. Providing such incentives is an important aspect that should be considered when designing ad-hoc routing protocols. In this paper, we propose a dynamic, decentralized routing protocol for ad-hoc networks that provides incentives in the form of payments to intermediate nodes used to forward data for others. In our Constrained Selfish Routing (CSR) protocol, game-theoretic approaches are used to calculate payments (incentives) that ensure both the truthfulness of participating nodes and the fairness of the CSR protocol. We show through simulations that CSR is an energy efficient protocol and that it provides lower communication overhead in the best and average cases compared to existing approaches.

Wireless sensor node design for heterogeneous networks

Two complementary wireless sensor nodes for building two-tiered heterogeneous networks are presented. A larger node with a 25 mm by 25 mm size acts as the backbone of the network, and can handle complex data processing. A smaller, cheaper node with a 10 mm by 10 mm size can perform simpler sensor-interfacing tasks. The 25mm node is based on previous work that has been done in the Tyndall National Institute that created a modular wireless sensor node. In this work, a new 25mm module is developed operating in the 433/868 MHz frequency bands, with a range of 3.8 km. The 10mm node is highly miniaturised, while retaining a high level of modularity. It has been designed to support very energy efficient operation for applications with low duty cycles, with a sleep current of 3.3 μA. Both nodes use commercially available components and have low manufacturing costs to allow the construction of large networks. In addition, interface boards for communicating with nodes have been developed for both the 25mm and 10mm nodes. These interface boards provide a USB connection, and support recharging of a Li-ion battery from the USB power supply. This paper discusses the design goals, the design methods, and the resulting implementation.

Experimental impulse radio IEEE 802.15.4a UWB based wireless sensor localization technology: Characterization, reliability and ranging

Ultra Wide Band (UWB) transmission has recently been the object of considerable attention in the field of next generation location aware wireless sensor networks. This is due to its fine time resolution, energy efficient and robustness to interference in harsh environments. This paper presents a thorough applied examination of prototype IEEE 802.15.4a impulse UWB transceiver technology to quantify the effect of line of sight (LOS) and non line of sight (NLOS) ranging in real indoor and outdoor environments. Results included draw on an extensive array of experiments that fully characterize the 802.15.4a UWB transceiver technology, its reliability and ranging capabilities for the first time. A new two way (TW) ranging protocol is proposed. The goal of this work is to validate the technology as a dependable wireless communications mechanism for the subset of sensor network localization applications where reliability and precision positions are key concerns.

Planning the deployment of fault-tolerant wireless sensor networks

Since Wireless Sensor Networks (WSNs) are subject to failures, fault-tolerance becomes an important requirement for many WSN applications. Fault-tolerance can be enabled in different areas of WSN design and operation, including the Medium Access Control (MAC) layer and the initial topology design. To be robust to failures, a MAC protocol must be able to adapt to traffic fluctuations and topology dynamics. We design ER-MAC that can switch from energy-efficient operation in normal monitoring to reliable and fast delivery for emergency monitoring, and vice versa. It also can prioritise high priority packets and guarantee fair packet deliveries from all sensor nodes. Topology design supports fault-tolerance by ensuring that there are alternative acceptable routes to data sinks when failures occur. We provide solutions for four topology planning problems: Additional Relay Placement (ARP), Additional Backup Placement (ABP), Multiple Sink Placement (MSP), and Multiple Sink and Relay Placement (MSRP). Our solutions use a local search technique based on Greedy Randomized Adaptive Search Procedures (GRASP). GRASP-ARP deploys relays for (k,l)-sink-connectivity, where each sensor node must have k vertex-disjoint paths of length ≤ l. To count how many disjoint paths a node has, we propose Counting-Paths. GRASP-ABP deploys fewer relays than GRASP-ARP by focusing only on the most important nodes – those whose failure has the worst effect. To identify such nodes, we define Length-constrained Connectivity and Rerouting Centrality (l-CRC). Greedy-MSP and GRASP-MSP place minimal cost sinks to ensure that each sensor node in the network is double-covered, i.e. has two length-bounded paths to two sinks. Greedy-MSRP and GRASP-MSRP deploy sinks and relays with minimal cost to make the network double-covered and non-critical, i.e. all sensor nodes must have length-bounded alternative paths to sinks when an arbitrary sensor node fails. We then evaluate the fault-tolerance of each topology in data gathering simulations using ER-MAC.

Novel smart modules for imaging, communications, and displays

This dissertation proposes and demonstrates novel smart modules to solve challenging problems in the areas of imaging, communications, and displays. The smartness of the modules is due to their ability to be able to adapt to changes in operating environment and application using programmable devices, specifically, electronically variable focus lenses (ECVFLs) and digital micromirror devices (DMD). The proposed modules include imagers for laser characterization and general purpose imaging which smartly adapt to changes in irradiance, optical wireless communication systems which can adapt to the number of users and to changes in link length, and a smart laser projection display that smartly adjust the pixel size to achieve a high resolution projected image at each screen distance. The first part of the dissertation starts with the proposal of using an ECVFL to create a novel multimode laser beam characterizer for coherent light. This laser beam characterizer uses the ECVFL and a DMD so that no mechanical motion of optical components along the optical axis is required. This reduces the mechanical motion overhead that traditional laser beam characterizers have, making this laser beam characterizer more accurate and reliable. The smart laser beam characterizer is able to account for irradiance fluctuations in the source. Using image processing, the important parameters that describe multimode laser beam propagation have been successfully extracted for a multi-mode laser test source. Specifically, the laser beam analysis parameters measured are the M2 parameter, w0 the minimum beam waist, and zR the Rayleigh range. Next a general purpose incoherent light imager that has a high dynamic range (>100 dB) and automatically adjusts for variations in irradiance in the scene is proposed. Then a data efficient image sensor is demonstrated. The idea of this smart image sensor is to reduce the bandwidth needed for transmitting data from the sensor by only sending the information which is required for the specific application while discarding the unnecessary data. In this case, the imager demonstrated sends only information regarding the boundaries of objects in the image so that after transmission to a remote image viewing location, these boundaries can be used to map out objects in the original image. The second part of the dissertation proposes and demonstrates smart optical communications systems using ECVFLs. This starts with the proposal and demonstration of a zero propagation loss optical wireless link using visible light with experiments covering a 1 to 4 m range. By adjusting the focal length of the ECVFLs for this directed line-of-sight link (LOS) the laser beam propagation parameters are adjusted such that the maximum amount of transmitted optical power is captured by the receiver for each link length. This power budget saving enables a longer achievable link range, a better SNR/BER, or higher power efficiency since more received power means the transmitted power can be reduced. Afterwards, a smart dual mode optical wireless link is proposed and demonstrated using a laser and LED coupled to the ECVFL to provide for the first time features of high bandwidths and wide beam coverage. This optical wireless link combines the capabilities of smart directed LOS link from the previous section with a diffuse optical wireless link, thus achieving high data rates and robustness to blocking. The proposed smart system can switch from LOS mode to Diffuse mode when blocking occurs or operate in both modes simultaneously to accommodate multiple users and operate a high speed link if one of the users requires extra bandwidth. The last part of this section presents the design of fibre optic and free-space optical switches which use ECVFLs to deflect the beams to achieve switching operation. These switching modules can be used in the proposed optical wireless indoor network. The final section of the thesis presents a novel smart laser scanning display. The ECVFL is used to create the smallest beam spot size possible for the system designed at the distance of the screen. The smart laser scanning display increases the spatial resoluti on of the display for any given distance. A basic smart display operation has been tested for red light and a 4X improvement in pixel resolution for the image has been demonstrated.