Enabling computationally intensive bioinformatics applications on the Grid platform

Bioinformatics is a recent and emerging discipline which aims at studying biological problems through computational approaches. Most branches of bioinformatics such as Genomics, Proteomics and Molecular Dynamics are particularly computationally intensive, requiring huge amount of computational resources for running algorithms of everincreasing complexity over data of everincreasing size. In the search for computational power, the EGEE Grid platform, world's largest community of interconnected clusters load balanced as a whole, seems particularly promising and is considered the new hope for satisfying the everincreasing computational requirements of bioinformatics, as well as physics and other computational sciences. The EGEE platform, however, is rather new and not yet free of problems. In addition, specific requirements of bioinformatics need to be addressed in order to use this new platform effectively for bioinformatics tasks. In my three years' Ph.D. work I addressed numerous aspects of this Grid platform, with particular attention to those needed by the bioinformatics domain. I hence created three major frameworks, Vnas, GridDBManager and SETest, plus an additional smaller standalone solution, to enhance the support for bioinformatics applications in the Grid environment and to reduce the effort needed to create new applications, additionally addressing numerous existing Grid issues and performing a series of optimizations. The Vnas framework is an advanced system for the submission and monitoring of Grid jobs that provides an abstraction with reliability over the Grid platform. In addition, Vnas greatly simplifies the development of new Grid applications by providing a callback system to simplify the creation of arbitrarily complex multistage computational pipelines and provides an abstracted virtual sandbox which bypasses Grid limitations. Vnas also reduces the usage of Grid bandwidth and storage resources by transparently detecting equality of virtual sandbox files based on content, across different submissions, even when performed by different users. BGBlast, evolution of the earlier project GridBlast, now provides a Grid Database Manager (GridDBManager) component for managing and automatically updating biological flatfile databases in the Grid environment. GridDBManager sports very novel features such as an adaptive replication algorithm that constantly optimizes the number of replicas of the managed databases in the Grid environment, balancing between response times (performances) and storage costs according to a programmed cost formula. GridDBManager also provides a very optimized automated management for older versions of the databases based on reverse delta files, which reduces the storage costs required to keep such older versions available in the Grid environment by two orders of magnitude. The SETest framework provides a way to the user to test and regressiontest Python applications completely scattered with side effects (this is a common case with Grid computational pipelines), which could not easily be tested using the more standard methods of unit testing or test cases. The technique is based on a new concept of datasets containing invocations and results of filtered calls. The framework hence significantly accelerates the development of new applications and computational pipelines for the Grid environment, and the efforts required for maintenance. An analysis of the impact of these solutions will be provided in this thesis. This Ph.D. work originated various publications in journals and conference proceedings as reported in the Appendix. Also, I orally presented my work at numerous international conferences related to Grid and bioinformatics.

The NreABC system of Staphylococcus carnosus combines nitrate and oxygen sensing by an NreA,NreB sensor complex

Staphylococcus carnosus is a facultative anaerobic bacterium which features the cytoplasmic NreABC system. It is necessary for regulation of nitrate respiration and the nitrate reductase gene narG in response to oxygen and nitrate availability. NreB is a sensor kinase of a two-component system and represents the oxygen sensor of the system. It binds an oxygen labile [4Fe-4S]2+ cluster under anaerobic conditions. NreB autophosphorylates and phosphoryl transfer activates the response regulator NreC which induces narG expression. The third component of the Nre system is the nitrate receptor NreA. In this study the role of the nitrate receptor protein NreA in nitrate regulation and its functional and physiological effect on oxygen regulation and interaction with the NreBC two-component system were detected. In vivo, a reporter gene assay for measuring expression of the NreABC regulated nitrate reductase gene narG was used for quantitative evaluation of NreA function. Maximal narG expression in wild type S. carnosus required anaerobic conditions and the presence of nitrate. Deletion of nreA allowed expression of narG under aerobic conditions, and under anaerobic conditions nitrate was no longer required for maximal induction. This indicates that NreA is a nitrate regulated inhibitor of narG expression. Purified NreA and variant NreA(Y95A) inhibited the autophosphorylation of anaerobic NreB in part and completely, respectively. Neither NreA nor NreA(Y95A) stimulated dephosphorylation of NreB-phosphate, however. Inhibition of phosphorylation was relieved completely when NreA with bound nitrate (NreA•[NO3-]) was used. The same effects of NreA were monitored with aerobically isolated Fe-S-less NreB, which indicates that NreA does not have an influence on the iron-sulfur cluster of NreB. In summary, the data of this study show that NreA interacts with the oxygen sensor NreB and controls its phosphorylation level in a nitrate dependent manner. This modulation of NreB-function by NreA and nitrate results in nitrate/oxygen co-sensing by an NreA/NreB sensory unit. It transmits the regulatory signal from oxygen and nitrate in a joint signal to target promoters. Therefore, nitrate and oxygen regulation of nitrate dissimilation follows a new mode of regulation not present in other facultative anaerobic bacteria.

A Collaborative Mobile Crowdsensing System for Smart Cities

Nowadays words like Smart City, Internet of Things, Environmental Awareness surround us with the growing interest of Computer Science and Engineering communities. Services supporting these paradigms are definitely based on large amounts of sensed data, which, once obtained and gathered, need to be analyzed in order to build maps, infer patterns, extract useful information. Everything is done in order to achieve a better quality of life. Traditional sensing techniques, like Wired or Wireless Sensor Network, need an intensive usage of distributed sensors to acquire real-world conditions. We propose SenSquare, a Crowdsensing approach based on smartphones and a central coordination server for time-and-space homogeneous data collecting. SenSquare relies on technologies such as CoAP lightweight protocol, Geofencing and the Military Grid Reference System.

The HarmonyGrid : music, space and performance in grid music systems

This research explores music in space, as experienced through performing and music-making with interactive systems. It explores how musical parameters may be presented spatially and displayed visually with a view to their exploration by a musician during performance. Spatial arrangements of musical components, especially pitches and harmonies, have been widely studied in the literature, but the current capabilities of interactive systems allow the improvisational exploration of these musical spaces as part of a performance practice. This research focuses on quantised spatial organisation of musical parameters that can be categorised as grid music systems (GMSs), and interactive music systems based on them. The research explores and surveys existing and historical uses of GMSs, and develops and demonstrates the use of a novel grid music system designed for whole body interaction. Grid music systems provide plotting of spatialised input to construct patterned music on a two-dimensional grid layout. GMSs are navigated to construct a sequence of parametric steps, for example a series of pitches, rhythmic values, a chord sequence, or terraced dynamic steps. While they are conceptually simple when only controlling one musical dimension, grid systems may be layered to enable complex and satisfying musical results. These systems have proved a viable, effective, accessible and engaging means of music-making for the general user as well as the musician. GMSs have been widely used in electronic and digital music technologies, where they have generally been applied to small portable devices and software systems such as step sequencers and drum machines. This research shows that by scaling up a grid music system, music-making and musical improvisation are enhanced, gaining several advantages: (1) Full body location becomes the spatial input to the grid. The system becomes a partially immersive one in four related ways: spatially, graphically, sonically and musically. (2) Detection of body location by tracking enables hands-free operation, thereby allowing the playing of a musical instrument in addition to “playing” the grid system. (3) Visual information regarding musical parameters may be enhanced so that the performer may fully engage with existing spatial knowledge of musical materials. The result is that existing spatial knowledge is overlaid on, and combined with, music-space. Music-space is a new concept produced by the research, and is similar to notions of other musical spaces including soundscape, acoustic space, Smalley's “circumspace” and “immersive space” (2007, 48-52), and Lotis's “ambiophony” (2003), but is rather more textural and “alive”—and therefore very conducive to interaction. Music-space is that space occupied by music, set within normal space, which may be perceived by a person located within, or moving around in that space. Music-space has a perceivable “texture” made of tensions and relaxations, and contains spatial patterns of these formed by musical elements such as notes, harmonies, and sounds, changing over time. The music may be performed by live musicians, created electronically, or be prerecorded. Large-scale GMSs have the capability not only to interactively display musical information as music representative space, but to allow music-space to co-exist with it. Moving around the grid, the performer may interact in real time with musical materials in music-space, as they form over squares or move in paths. Additionally he/she may sense the textural matrix of the music-space while being immersed in surround sound covering the grid. The HarmonyGrid is a new computer-based interactive performance system developed during this research that provides a generative music-making system intended to accompany, or play along with, an improvising musician. This large-scale GMS employs full-body motion tracking over a projected grid. Playing with the system creates an enhanced performance employing live interactive music, along with graphical and spatial activity. Although one other experimental system provides certain aspects of immersive music-making, currently only the HarmonyGrid provides an environment to explore and experience music-space in a GMS.

Development of gas sensing technology for ground and airborne applications powered by solar energy : methodology and experimental results

Monitoring gases for environmental, industrial and agricultural fields is a demanding task that requires long periods of observation, large quantity of sensors, data management, high temporal and spatial resolution, long term stability, recalibration procedures, computational resources, and energy availability. Wireless Sensor Networks (WSNs) and Unmanned Aerial Vehicles (UAVs) are currently representing the best alternative to monitor large, remote, and difficult access areas, as these technologies have the possibility of carrying specialised gas sensing systems, and offer the possibility of geo-located and time stamp samples. However, these technologies are not fully functional for scientific and commercial applications as their development and availability is limited by a number of factors: the cost of sensors required to cover large areas, their stability over long periods, their power consumption, and the weight of the system to be used on small UAVs. Energy availability is a serious challenge when WSN are deployed in remote areas with difficult access to the grid, while small UAVs are limited by the energy in their reservoir tank or batteries. Another important challenge is the management of data produced by the sensor nodes, requiring large amount of resources to be stored, analysed and displayed after long periods of operation. In response to these challenges, this research proposes the following solutions aiming to improve the availability and development of these technologies for gas sensing monitoring: first, the integration of WSNs and UAVs for environmental gas sensing in order to monitor large volumes at ground and aerial levels with a minimum of sensor nodes for an effective 3D monitoring; second, the use of solar energy as a main power source to allow continuous monitoring; and lastly, the creation of a data management platform to store, analyse and share the information with operators and external users. The principal outcomes of this research are the creation of a gas sensing system suitable for monitoring any kind of gas, which has been installed and tested on CH4 and CO2 in a sensor network (WSN) and on a UAV. The use of the same gas sensing system in a WSN and a UAV reduces significantly the complexity and cost of the application as it allows: a) the standardisation of the signal acquisition and data processing, thereby reducing the required computational resources; b) the standardisation of calibration and operational procedures, reducing systematic errors and complexity; c) the reduction of the weight and energy consumption, leading to an improved power management and weight balance in the case of UAVs; d) the simplification of the sensor node architecture, which is easily replicated in all the nodes. I evaluated two different sensor modules by laboratory, bench, and field tests: a non-dispersive infrared module (NDIR) and a metal-oxide resistive nano-sensor module (MOX nano-sensor). The tests revealed advantages and disadvantages of the two modules when used for static nodes at the ground level and mobile nodes on-board a UAV. Commercial NDIR modules for CO2 have been successfully tested and evaluated in the WSN and on board of the UAV. Their advantage is the precision and stability, but their application is limited to a few gases. The advantages of the MOX nano-sensors are the small size, low weight, low power consumption and their sensitivity to a broad range of gases. However, selectivity is still a concern that needs to be addressed with further studies. An electronic board to interface sensors in a large range of resistivity was successfully designed, created and adapted to operate on ground nodes and on-board UAV. The WSN and UAV created were powered with solar energy in order to facilitate outdoor deployment, data collection and continuous monitoring over large and remote volumes. The gas sensing, solar power, transmission and data management systems of the WSN and UAV were fully evaluated by laboratory, bench and field testing. The methodology created to design, developed, integrate and test these systems was extensively described and experimentally validated. The sampling and transmission capabilities of the WSN and UAV were successfully tested in an emulated mission involving the detection and measurement of CO2 concentrations in a field coming from a contaminant source; the data collected during the mission was transmitted in real time to a central node for data analysis and 3D mapping of the target gas. The major outcome of this research is the accomplishment of the first flight mission, never reported before in the literature, of a solar powered UAV equipped with a CO2 sensing system in conjunction with a network of ground sensor nodes for an effective 3D monitoring of the target gas. A data management platform was created using an external internet server, which manages, stores, and shares the data collected in two web pages, showing statistics and static graph images for internal and external users as requested. The system was bench tested with real data produced by the sensor nodes and the architecture of the platform was widely described and illustrated in order to provide guidance and support on how to replicate the system. In conclusion, the overall results of the project provide guidance on how to create a gas sensing system integrating WSNs and UAVs, how to power the system with solar energy and manage the data produced by the sensor nodes. This system can be used in a wide range of outdoor applications, especially in agriculture, bushfires, mining studies, zoology, and botanical studies opening the way to an ubiquitous low cost environmental monitoring, which may help to decrease our carbon footprint and to improve the health of the planet.

Fault tolerant vessel stabiliser control system

A vessel stabilizer control system includes a sensor fault detection means which senses the availability of sensing signals from a gyrostabilizer precession motion sensor and a vessel roll motion sensor. The control system controls the action of a gyro-actuator which is mechanically coupled to a gyrostabilizer. The benefit of employing fault sensing of the sensors providing the process control variables is that the sensed number of available process control variables (or sensors) can be used to activate a tiered system of control modes. Each tiered control mode is designed to utilize the available process control variables to ensure safe and effective operation of the gyrostabilizer that is tolerant of sensor faults and loss of power supply. A control mode selector is provided for selecting the appropriate control mode based on the number of available process control variables.

Secure Concurrency Control in Firm Real-Time Database Systems

Many real-time database applications arise in electronic financial services, safety-critical installations and military systems where enforcing security is crucial to the success of the enterprise. For real-time database systems supporting applications with firm deadlines, we investigate here the performance implications, in terms of killed transactions, of guaranteeing multilevel secrecy. In particular, we focus on the concurrency control (CC) aspects of this issue. Our main contributions are the following: First, we identify which among the previously proposed real-time CC protocols are capable of providing covert-channel-free security. Second, using a detailed simulation model, we profile the real-time performance of a representative set of these secure CC protocols for a variety of security-classified workloads and system configurations. Our experiments show that a prioritized optimistic CC protocol, OPT-WAIT, provides the best overall performance. Third, we propose and evaluate a novel "dual-CC" approach that allows the real-time database system to simultaneously use different CC mechanisms for guaranteeing security and for improving real-time performance. By appropriately choosing these different mechanisms, concurrency control protocols that provide even better performance than OPT-WAIT are designed. Finally, we propose and evaluate GUARD, an adaptive admission-control policy designed to provide fairness with respect to the distribution of killed transactions across security levels. Our experiments show that GUARD efficiently provides close to ideal fairness for real-time applications that can tolerate covert channel bandwidths of upto one bit per second.

Intruder detection over sensor placement in a hexagonal lattice

The problem of intrusion detection and location identification in the presence of clutter is considered for a hexagonal sensor-node geometry. It is noted that in any practical application,for a given fixed intruder or clutter location, only a small number of neighboring sensor nodes will register a significant reading. Thus sensing may be regarded as a local phenomenon and performance is strongly dependent on the local geometry of the sensor nodes. We focus on the case when the sensor nodes form a hexagonal lattice. The optimality of the hexagonal lattice with respect to density of packing and covering and largeness of the kissing number suggest that this is the best possible arrangement from a sensor network viewpoint. The results presented here are clearly relevant when the particular sensing application permits a deterministic placement of sensors. The results also serve as a performance benchmark for the case of a random deployment of sensors. A novel feature of our analysis of the hexagonal sensor grid is a signal-space viewpoint which sheds light on achievable performance.Under this viewpoint, the problem of intruder detection is reduced to one of determining in a distributed manner, the optimal decision boundary that separates the signal spaces SI and SC associated to intruder and clutter respectively. Given the difficulty of implementing the optimal detector, we present a low-complexity distributive algorithm under which the surfaces SI and SC are separated by a wellchosen hyperplane. The algorithm is designed to be efficient in terms of communication cost by minimizing the expected number of bits transmitted by a sensor.

Operational experience on a grid connected 100 kWe biomass gasification power plant in Karnataka, India

The paper reports the operational experience from a 100 kWe gasification power plant connected to the grid in Karnataka. Biomass Energy for Rural India (BERI) is a program that implemented gasification based power generation with an installed capacity of 0.88 MWe distributed over three locations to meet the electrical energy needs in the district of Tumkur. The operation of one 100 kWe power plant was found unsatisfactory and not meeting the designed performance. The Indian Institute of Science, Bangalore, the technology developer, took the initiative to ensure the system operation, capacity building and prove the designed performance. The power plant connected to the grid consists of the IISc gasification system which includes reactor, cooling, cleaning system, fuel drier and water treatment system to meet the producer gas quality for an engine. The producer gas is used as a fuel in Cummins India Limited, GTA 855 G model, turbo charged engine and the power output is connected to the grid. The system has operated for over 1000 continuous hours, with only about 70 h of grid outages. The total biomass consumption for 1035 h of operation was 111 t at an average of 107 kg/h. Total energy generated was 80.6 MWh reducing over loot of CO(2) emissions. The overall specific fuel consumption was about 1.36 kg/kWh, amounting to an overall efficiency from biomass to electricity of about 18%. The present operations indicate that a maintenance schedule for the plant can be at the end of 1000 h. The results for another 1000 h of operation by the local team are also presented. (C) 2011 International Energy Initiative. Published by Elsevier Inc. All rights reserved.

Fiber Bragg Grating Sensor Instrumentation for Parking Space Occupancy Management

This work aims at providing an effective parking management system by reducing the drivers' searching time for vacant car-parking space, in turn improving the traffic flow in the car park areas. This is achieved by the use of Fiber Bragg Grating Sensor (FBG) sensor instrumentation in vehicle parking management system. Present work involves embedding an array of FBG sensors underground in the parking space, then determining the strain changes on the FBG sensor due to load applied by the vehicle parked in the parking space, occupancy of the parking space is determined. To validate the FBG sensor parking management system, three most common cases have been considered. This closed loop FBG parking management system can give real-time feed-back to space-guidance display board helping the driver in maneuvering the vehicle to the appropriate parking space. The proposed technique offers optimized usage of parking space for the various segments of cars and also facilitates in a conjoined automated billing system, as compared to conventional method of parking systems.

网格环境下的数据库系统

目前网格上的各类应用系统几乎郝是使用文件来保存数据，因此人们对如何将数据库系统集成入网格这个问题研完甚少。如果网格要在将来支持更大范围的应用系统，那么必须要解决将数据库系统集成入网格这个问题。本文在分析网格环境对数据库系统的需求的基础上，总结了将数据库系统集成入网格的两种方法，并分别对它们做出评价。

WEBCOM-G: A candidate middleware for Grid-Ireland

WebCom-G is a fledgling Grid Operating System, designed to provide independent service access through interoperability with existing middlewares. It offers an expressive programming model that automatically handles task synchronisation – load balancing, fault tolerance, and task allocation are handled at the WebCom-G system level – without burdening the application writer. These characteristics, together with the ability of its computing model to mix evaluation strategies to match the characteristics of the geographically dispersed facilities and the overall problem- solving environment, make WebCom-G a promising grid middleware candidate.

Intrusion Detection System for Network Security in Synchrophasor Systems

Synchrophasor systems will play a crucial role in next generation Smart Grid monitoring, protection and control. However these systems also introduce a multitude of potential vulnerabilities from malicious and inadvertent attacks, which may render erroneous operation or severe damage. This paper proposes a Synchrophasor Specific Intrusion Detection System (SSIDS) for malicious cyber attack and unintended misuse. The SSIDS comprises a heterogeneous whitelist and behavior-based approach to detect known attack types and unknown and so-called ‘zero-day’ vulnerabilities and attacks. The paper describes reconnaissance, Man-in-the-Middle (MITM) and Denial-of-Service (DoS) attack types executed against a practical synchrophasor system which are used to validate the real-time effectiveness of the proposed SSIDS cyber detection method.

Distribution system operation supported by contextual energy resource management based on intelligent SCADA

Future distribution systems will have to deal with an intensive penetration of distributed energy resources ensuring reliable and secure operation according to the smart grid paradigm. SCADA (Supervisory Control and Data Acquisition) is an essential infrastructure for this evolution. This paper proposes a new conceptual design of an intelligent SCADA with a decentralized, flexible, and intelligent approach, adaptive to the context (context awareness). This SCADA model is used to support the energy resource management undertaken by a distribution network operator (DNO). Resource management considers all the involved costs, power flows, and electricity prices, allowing the use of network reconfiguration and load curtailment. Locational Marginal Prices (LMP) are evaluated and used in specific situations to apply Demand Response (DR) programs on a global or a local basis. The paper includes a case study using a 114 bus distribution network and load demand based on real data.

An Encoded Infrared Sheet Of Light Navigational Beacon System For Precise Localization Of Indoor Mobile Robot Vehicles

A new localization approach to increase the navigational capabilities and object manipulation of autonomous mobile robots, based on an encoded infrared sheet of light beacon system, which provides position errors smaller than 0.02m is presented in this paper. To achieve this minimal position error, a resolution enhancement technique has been developed by utilising an inbuilt odometric/optical flow sensor information. This system respects strong low cost constraints by using an innovative assembly for the digitally encoded infrared transmitter. For better guidance of mobile robot vehicles, an online traffic signalling capability is also incorporated. Other added features are its less computational complexity and online localization capability all these without any estimation uncertainty. The constructional details, experimental results and computational methodologies of the system are also described