Pattern-based software architecture for service-oriented software systems

Service-oriented architecture is a recent conceptual framework for service-oriented software platforms. Architectures are of great importance for the evolution of software systems. We present a modelling and transformation technique for service-centric distributed software systems. Architectural configurations, expressed through hierarchical architectural patterns, form the core of a specification and transformation technique. Patterns on different levels of abstraction form transformation invariants that structure and constrain the transformation process. We explore the role that patterns can play in architecture transformations in terms of functional properties, but also non-functional quality aspects

HeteroGenius: A Framework for Hybrid Analysis of Heterogeneous Software Specifications

Nowadays, software artifacts are ubiquitous in our lives being an essential part of home appliances, cars, cell phones, and even in more critical activities like aeronautics and health sciences. In this context software failures may produce enormous losses, either economical or, in the worst case, in human lives. Software analysis is an area in software engineering concerned with the application of diverse techniques in order to prove the absence of errors in software pieces. In many cases different analysis techniques are applied by following specific methodological combinations that ensure better results. These interactions between tools are usually carried out at the user level and it is not supported by the tools. In this work we present HeteroGenius, a framework conceived to develop tools that allow users to perform hybrid analysis of heterogeneous software specifications. HeteroGenius was designed prioritising the possibility of adding new specification languages and analysis tools and enabling a synergic relation of the techniques under a graphical interface satisfying several well-known usability enhancement criteria. As a case-study we implemented the functionality of Dynamite on top of HeteroGenius.Comment: In Proceedings LAFM 2013, arXiv:1401.056

Virtual Machine Support for Many-Core Architectures: Decoupling Abstract from Concrete Concurrency Models

The upcoming many-core architectures require software developers to exploit concurrency to utilize available computational power. Today's high-level language virtual machines (VMs), which are a cornerstone of software development, do not provide sufficient abstraction for concurrency concepts. We analyze concrete and abstract concurrency models and identify the challenges they impose for VMs. To provide sufficient concurrency support in VMs, we propose to integrate concurrency operations into VM instruction sets. Since there will always be VMs optimized for special purposes, our goal is to develop a methodology to design instruction sets with concurrency support. Therefore, we also propose a list of trade-offs that have to be investigated to advise the design of such instruction sets. As a first experiment, we implemented one instruction set extension for shared memory and one for non-shared memory concurrency. From our experimental results, we derived a list of requirements for a full-grown experimental environment for further research

Sam2bam: High-Performance Framework for NGS Data Preprocessing Tools

This paper introduces a high-throughput software tool framework called {\it sam2bam} that enables users to significantly speedup pre-processing for next-generation sequencing data. The sam2bam is especially efficient on single-node multi-core large-memory systems. It can reduce the runtime of data pre-processing in marking duplicate reads on a single node system by 156-186x compared with de facto standard tools. The sam2bam consists of parallel software components that can fully utilize the multiple processors, available memory, high-bandwidth of storage, and hardware compression accelerators if available. The sam2bam provides file format conversion between well-known genome file formats, from SAM to BAM, as a basic feature. Additional features such as analyzing, filtering, and converting the input data are provided by {\it plug-in} tools, e.g., duplicate marking, which can be attached to sam2bam at runtime. We demonstrated that sam2bam could significantly reduce the runtime of NGS data pre-processing from about two hours to about one minute for a whole-exome data set on a 16-core single-node system using up to 130 GB of memory. The sam2bam could reduce the runtime for whole-genome sequencing data from about 20 hours to about nine minutes on the same system using up to 711 GB of memory

Computational statistics using the Bayesian Inference Engine

This paper introduces the Bayesian Inference Engine (BIE), a general parallel, optimised software package for parameter inference and model selection. This package is motivated by the analysis needs of modern astronomical surveys and the need to organise and reuse expensive derived data. The BIE is the first platform for computational statistics designed explicitly to enable Bayesian update and model comparison for astronomical problems. Bayesian update is based on the representation of high-dimensional posterior distributions using metric-ball-tree based kernel density estimation. Among its algorithmic offerings, the BIE emphasises hybrid tempered MCMC schemes that robustly sample multimodal posterior distributions in high-dimensional parameter spaces. Moreover, the BIE is implements a full persistence or serialisation system that stores the full byte-level image of the running inference and previously characterised posterior distributions for later use. Two new algorithms to compute the marginal likelihood from the posterior distribution, developed for and implemented in the BIE, enable model comparison for complex models and data sets. Finally, the BIE was designed to be a collaborative platform for applying Bayesian methodology to astronomy. It includes an extensible object-oriented and easily extended framework that implements every aspect of the Bayesian inference. By providing a variety of statistical algorithms for all phases of the inference problem, a scientist may explore a variety of approaches with a single model and data implementation. Additional technical details and download details are available from http://www.astro.umass.edu/bie. The BIE is distributed under the GNU GPL.Comment: Resubmitted version. Additional technical details and download details are available from http://www.astro.umass.edu/bie. The BIE is distributed under the GNU GP

GRIDCC: Real-time workflow system

The Grid is a concept which allows the sharing of resources between distributed communities, allowing each to progress towards potentially different goals. As adoption of the Grid increases so are the activities that people wish to conduct through it. The GRIDCC project is a European Union funded project addressing the issues of integrating instruments into the Grid. This increases the requirement of workflows and Quality of Service upon these workflows as many of these instruments have real-time requirements. In this paper we present the workflow management service within the GRIDCC project which is tasked with optimising the workflows and ensuring that they meet the pre-defined QoS requirements specified upon them