An Open Framework for Extensible Multi-Stage Bioinformatics Software

In research labs, there is often a need to customise software at every step in a given bioinformatics workflow, but traditionally it has been difficult to obtain both a high degree of customisability and good performance. Performance-sensitive tools are often highly monolithic, which can make research difficult. We present a novel set of software development principles and a bioinformatics framework, Friedrich, which is currently in early development. Friedrich applications support both early stage experimentation and late stage batch processing, since they simultaneously allow for good performance and a high degree of flexibility and customisability. These benefits are obtained in large part by basing Friedrich on the multiparadigm programming language Scala. We present a case study in the form of a basic genome assembler and its extension with new functionality. Our architecture has the potential to greatly increase the overall productivity of software developers and researchers in bioinformatics.Comment: 12 pages, 1 figure, to appear in proceedings of PRIB 201

Energy-Efficient Management of Data Center Resources for Cloud Computing: A Vision, Architectural Elements, and Open Challenges

Cloud computing is offering utility-oriented IT services to users worldwide. Based on a pay-as-you-go model, it enables hosting of pervasive applications from consumer, scientific, and business domains. However, data centers hosting Cloud applications consume huge amounts of energy, contributing to high operational costs and carbon footprints to the environment. Therefore, we need Green Cloud computing solutions that can not only save energy for the environment but also reduce operational costs. This paper presents vision, challenges, and architectural elements for energy-efficient management of Cloud computing environments. We focus on the development of dynamic resource provisioning and allocation algorithms that consider the synergy between various data center infrastructures (i.e., the hardware, power units, cooling and software), and holistically work to boost data center energy efficiency and performance. In particular, this paper proposes (a) architectural principles for energy-efficient management of Clouds; (b) energy-efficient resource allocation policies and scheduling algorithms considering quality-of-service expectations, and devices power usage characteristics; and (c) a novel software technology for energy-efficient management of Clouds. We have validated our approach by conducting a set of rigorous performance evaluation study using the CloudSim toolkit. The results demonstrate that Cloud computing model has immense potential as it offers significant performance gains as regards to response time and cost saving under dynamic workload scenarios.Comment: 12 pages, 5 figures,Proceedings of the 2010 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA 2010), Las Vegas, USA, July 12-15, 201

DevOps – fundamentos e perspetivas

DevOps is often defined by information technology professionals as a movement, cultural or professional, that brings a new approach to the delivery of software applications through the close collaboration between the development and operations teams. It is grounded by a diverse set of principles, such as culture, automation, lean, monitoring and sharing; and practices, such as, continuous integration and continuous deployment. This article aims to review various aspects of DevOps, highlighting the main benefits and barriers of its adoption.Este trabalho foi apoiado pela FCT - Fundação para a Ciência e Tecnologia no âmbito do projeto: UID/CEC/00319/201

Examining perceptions of agility in software development practice

This is the post-print version of the final published article that is available from the link below. Copyright @ 2010 ACM.Organizations undertaking software development are often reminded that successful practice depends on a number of non-technical issues that are managerial, cultural and organizational in nature. These issues cover aspects from appropriate corporate structure, through software process development and standardization to effective collaborative practice. Since the articulation of the 'software crisis' in the late-1960s, significant effort has been put into addressing problems related to the cost, time and quality of software development via the application of systematic processes and management practices for software engineering. Early efforts resulted in prescriptive structured methods, which have evolved and expanded over time to embrace consortia/ company-led initiatives such as the Unified Modeling Language and the Unified Process alongside formal process improvement frameworks such as the International Standards Organization's 9000 series, the Capability Maturity Model and SPICE. More recently, the philosophy behind traditional plan-based initiatives has been questioned by the agile movement, which seeks to emphasize the human and craft aspects of software development over and above the engineering aspects. Agile practice is strongly collaborative in its outlook, favoring individuals and interactions over processes and tools, working software over comprehensive documentation, customer collaboration over contract negotiation, and responding to change over following a plan (see Sidebar 1). Early experience reports on the use of agile practice suggest some success in dealing with the problems of the software crisis, and suggest that plan-based and agile practice are not mutually exclusive. Indeed, flexibility may arise from this unlikely marriage in an aim to strike a balance between the rigor of traditional plan-based approaches and the need for adaptation of those to suit particular development situations. With this in mind, this article surveys the current practice in software engineering alongside perceptions of senior development managers in relation to agile practice in order to understand the principles of agility that may be practiced implicitly and their effects on plan-based approach

How do particle physicists learn the programming concepts they need?

The ability to read, use and develop code efficiently and successfully is a key ingredient in modern particle physics. We report the experience of a training program, identified as "Advanced Programming Concepts", that introduces software concepts, methods and techniques to work effectively on a daily basis in a HEP experiment or other programming intensive fields. This paper illustrates the principles, motivations and methods that shape the "Advanced Computing Concepts" training program, the knowledge base that it conveys, an analysis of the feedback received so far, and the integration of these concepts in the software development process of the experiments as well as its applicability to a wider audience.Comment: 8 pages, 2 figures, CHEP2015 proceeding

Safety distance awareness system for Malaysian Driver

It is known that the risk of an accident increases exponentially with the speed of the vehicle and most collisions happen when the driver fails to brake at the required time and distance. The objective of this research is to create a Safety Distance Awareness System which aims at warning the driver of the potential frontal collision and to alter Malaysian driver attitudes. This system is to manipulate Malaysian driver attitude that likes to tailgating and to prevent rear-end collision in Malaysia. This is done by using a Sound Navigation and Ranging (SONAR) range finder to determine the distance of the vehicle or obstacle in front of the host vehicle. With the help of microcontroller, the distance of the host vehicle could be determined and a warning will be issued in the form of both visual and hearing so driver could take the correct preventive measure. There will be few stages of warning, the system will intensify the distress warning until the collision occurs. These SDAs do not take any automatic prevention or control to the vehicle to avoid collision. In overall the research hopes to achieve a more convenient driving experience and a safer driving environment by implementing the SDAS to keep drivers aware of the potential hazards ahead of their vehicle. Hopefully the Malaysian government will involve in this research, since the implementation of Safety Distance Awareness System can provide a new alternative in the safety system hence it can reduce accidents in Malaysia