Alex Aravind

Pairwise sequence alignment algorithms: a survey

Pairwise sequence alignment is a fundamental compute-intensive problem in bioinformatics that has helped researchers analyse biological sequences. The analysis has helped biologists detect pathogens, develop drugs, and identify common genes. The biological sequence database has been growing rapidly due to new sequences being discovered. This has brought many new challenges including sequence database searching and aligning long sequences. To solve these problems, many sequence alignment algorithms have been developed. These algorithms employ various techniques to efficiently find optimal or nearly-optimal alignments. In this paper, we present the popular past and recent work on both local and global pairwise sequence alignment algorithms. In addition to identifying the techniques used, the advantages and limitations of the algorithms are also presented.

Towards modeling realistic mobility for performance evaluations in MANET

Simulation modeling plays crucial role in conducting research on complex dynamic systems like mobile ad hoc networks and often the only way. Simulation has been successfully applied in MANET for more than two decades. In several recent studies, it is observed that the credibility of the simulation results in the field has decreased while the use of simulation has steadily increased. Part of this credibility crisis has been attributed to the simulation of mobility of the nodes in the system. Mobility has such a fundamental influence on the behavior and performance of mobile ad hoc networks. Accurate modeling and knowledge of mobility of the nodes in the system is not only helpful but also essential for the understanding and interpretation of the performance of the system under study. Several ideas, mostly in isolation, have been proposed in the literature to infuse realism in the mobility of nodes. In this paper, we attempt a holistic analysis of creating realistic mobility models and then demonstrate creation and analysis of realistic mobility models using a software tool we have developed. Using our software tool, desired mobility of the nodes in the system can be specified, generated, analyzed, and then the trace can be exported to be used in the performance studies of proposed algorithms or systems.

A queue based mutual exclusion algorithm

A new elegant and simple algorithm for mutual exclusion of N processes is proposed. It only requires shared variables in a memory model where shared variables need not be accessed atomically. We prove mutual exclusion by reformulating the algorithm as a transition system (automaton), and applying simulation of automata. The proof has been verified with the higher-order interactive theorem prover PVS. Under an additional atomicity assumption, the algorithm is starvation free, and we conjecture that no competing process is passed by any other process more than once. This conjecture was verified by model checking for systems with at most five processes.

Yet Another Simple Solution for the Concurrent Programming Control Problem

As multicore processors are becoming increasingly common everywhere, the future computing systems and devices are becoming inevitably concurrent. Also, on the applications side, automation is steadily infiltrating into everyday life, and hence, most software systems are becoming increasingly complex and concurrent. As a result, recent developments and projections indicate that we are entering into the era of concurrent programming. Synchronizing asynchronous concurrent processes in accessing a shared resource is an important issue. Among the synchronization issues, mutual exclusion is fundamental. Solutions to most higher level synchronization problems rely on the assurance of mutual exclusion. Several algorithms with varying characteristics are proposed in the literature to solve the mutual exclusion problem. This paper presents two new algorithms to solve the mutual exclusion problem. The algorithms are simple and have many nice properties.

An arbitration algorithm for multiport memory systems

Multiport memories are increasingly used in smart-phones, multimode handsets, multiprocessor systems, network processors, graphics chips, and other high performance electronic devices [1,2,4,8]. This paper presents a fully distributed software solution to the arbitration problem in multiport memory systems. Our solution is simple, efficient, and assures LRU fairness.

RealMobiSim: realistic mobility simulator and analyzer

Simulation is extremely crucial and often the only way for conducting research in complex system like mobile computing. In a recent study, it is observed that the credibility of the simulation results in the field has decreased while the use of simulation has steadily increased. Part of this credibility crisis is related to the simulation of mobility of the nodes in the system. It is not surprising to see that mobility has such a fundamental influence on the behavior of mobile systems. Therefore, a clear knowledge about mobility used in the system is not only helpful but also essential for the understanding and interpretation of the system behavior under study. Proper knowledge about the mobility of the nodes in the system can be better obtained by having a tool or a component that is independent and interactive to specify, visualize, analyze, and then generate mobility traces for the simulation. We have developed such a mobility generator software called RealMobiSim. In this note we propose to demonstrate RealMobiSim to the 2008 MSWiM attendees.

Path-Adaptive On-Site Tracking in Wireless Sensor Networks

Wireless sensor networks present a promising opportunity for realizing many practical applications. Tracking is one of the important applications of these networks. Many approaches have been proposed in the literature to deal with the tracking problem. Recently, a particular type of tracking problem called on-site tracking has been introduced [15], [16]. On-site tracking has been characterized as the tracking in which the sink is eventually required to be present in the vicinity of the target, possibly to perform further actions. In this paper, first we propose two efficient on-site tracking algorithms. Then, we derive theoretical upper bounds for the tracking time and the number of messages generated by the sensor nodes during the tracking for our algorithms. Finally, we present a simulation study that we conducted to evaluate the performance of our algorithms. The results show that our algorithms are efficient as compared to the other existing methods that can solve the on-site tracking problem. In particular, the path adaptive nature of the sink in our algorithms allows the network to conserve the energy and the sink to reduce the tracking time.

A Fair and Efficient Gang Scheduling Algorithm for Multicore Processors

The trend in multicore processors indicates that all future processors will be multicore, and hence the future cloud systems are expected to have nodes and clusters based on multicore processors. On the application front, to utilize these multicore processors, most future applications are expected to be parallel programs. Gang scheduling is a popular strategy of scheduling parallel programs on multiprocessor systems. ‘Adaptive First-Come-First-Served’ and ‘Largest-Gang-First-Served’ are most popular gang scheduling algorithms, but they are susceptible to starvation and hence high variance in response time. To address starvation, process migration mechanisms have been proposed in the literature. Migrating a process to a new processor is generally expensive, and also it does not eliminate starvation. This paper presents a starvation free gang scheduling algorithm for multicore processors without using process migration. The algorithm is simple, fair, and efficient.

An efficient algorithm for local sequence alignment

DNA pairwise sequence alignment has been a subject of great interest in the past and still evokes large interest. Recent algorithms have either been slow and sensitive or fast and less sensitive. Here, we present a new algorithm which is fast and at the same time relatively sensitive. To increase the speed, we first build a suffix tree for both sequences and the alignment is triggered by the maximum matching substring. The algorithm employs mismatch seeds to increase both sensitivity and speed in the later stages. We tested our algorithm on randomly generated sequences of length up to 500 thousand and used Rosetta dataset to test the sensitivity of the algorithm.

Energy efficient on-site tracking of mobile target in wireless sensor networks

Tracking moving targets is one of the important problems of wireless sensor networks. Many approaches have been proposed to deal with this problem (Yang, H. and Sikdar, B., 2003; Gupta, R. and Das, S.R., 2003; Yu-Chee Tseng et al., 2003; Hegazy, T. and Vachtsevanos, G., 2004). Once the information about a moving target is received, subsequent actions are taken in most cases. Sometimes, a physical presence in the vicinity of the moving target is required to take these actions. We characterize this nature of tracking as the on-site tracking problem. Applying existing approaches to solve the on-site tracking problem normally requires excessive message communication and navigation strategies. We propose an ant-based approach which effectively exploits the mobility dependency property inherent in the system to solve the on-site tracking problem. Our approach is simple and energy efficient.