Distributed data mining on grids: services, tools, and applications

Data mining algorithms are widely used today for the analysis of large corporate and scientific datasets stored in databases and data archives. Industry, science, and commerce fields often need to analyze very large datasets maintained over geographically distributed sites by using the computational power of distributed and parallel systems. The grid can play a significant role in providing an effective computational support for distributed knowledge discovery applications. For the development of data mining applications on grids we designed a system called Knowledge Grid. This paper describes the Knowledge Grid framework and presents the toolset provided by the Knowledge Grid for implementing distributed knowledge discovery. The paper discusses how to design and implement data mining applications by using the Knowledge Grid tools starting from searching grid resources, composing software and data components, and executing the resulting data mining process on a grid. Some performance results are also discussed.     

Nature inspired supply chain solutions: definitions,analogies, and future research directions

ABSTRACT

Supply chains are becoming increasingly complex, and many companies and researchers are looking to nature for finding solutions. In this paper, we provide a narrative synthesis and systematic review to explore state-of-the-art, and identify key areas for exploration of nature inspired solutions in the supply chain area. We consider strategic, tactical, and operational decisions within supply chains and identify analogies between biological systems and supply chains to create a new research agenda. Our findings show that the majority of the research in nature inspired supply chains from the systemic perspective focuses on closed loop supply chains. In contrast, similar systemic solutions such as industrial symbiosis, circular economy, and industrial ecology have not been explored as frequently. Reducing production waste (industrial symbiosis) in addition to end-of-life product waste (closed loop supply chains), optimising raw material use and extending the life of used resources (circular economy), investigating the interactions between biosphere and technosphere (industrial ecology), and seeking solutions to industrial problems from nature (biomimicry) are all possible paths for reaching a zero-waste economy. These systemic solutions have a considerable impact on the supply chains at the strategic, tactical, and operational levels, which need to be explored to identify efficient and effective solutions.     

A grid environment for high-throughput proteomics

We connect in a grid-enabled pipeline an ontology-based environment for proteomics spectra management with a machine learning platform for unbiased predictive analysis. We exploit two existing software platforms (MS-Analyzer and BioDCV), the emerging proteomics standards, and the middleware and computing resources of the EGEE Biomed VO grid infrastructure. In the setup, BioDCV is accessed by the MS-Analyzer workflow as a Web service, thus providing a complete grid environment for proteomics data analysis. Predictive classification studies on MALDI-TOF data based on this environment are presented.     

Sarcopenia: Etiology,Nutritional Approaches,and miRNAs

Sarcopenia, an age-related decline in skeletal muscle mass and function, dramatically affects the quality of life. Although there is a consensus that sarcopenia is a multifactorial syndrome, the etiology and underlying mechanisms are not yet delineated. Moreover, research about nutritional interventions to prevent the development of sarcopenia is mainly focused on the amount and quality of protein intake. The impact of several nutrition strategies that consider timing of food intake, anti-inflammatory nutrients, metabolic control, and the role of mitochondrial function on the progression of sarcopenia is not fully understood. This narrative review summarizes the metabolic background of this phenomenon and proposes an integral nutritional approach (including dietary supplements such as creatine monohydrate) to target potential molecular pathways that may affect reduce or ameliorate the adverse effects of sarcopenia. Lastly, miRNAs, in particular those produced by skeletal muscle (MyomiR), might represent a valid tool to evaluate sarcopenia progression as a potential rapid and early biomarker for diagnosis and characterization.     

Automatic summarisation and annotation of microarray data

The study of biological processes within cells is based on the measurement of the activity of different molecules, in particular genes and proteins whose activities are strictly related. The activity of genes is measured through a systematic investigation carried out by microarrays. Such technology enables the investigation of all the genes of an organism in a single experiment, encoding meaningful biological information. Nevertheless, the preprocessing of raw microarray data needs automatic tools that standardise such phase in order to: (a) avoiding errors in analysis phases, and (b) making comparable the results of different laboratories. The preprocessing problem is as much relevant as considering results obtained from analysis platforms of different vendors. Nevertheless, there is currently a lack of tools that allow to manage and preprocess multivendor dataset. This paper presents a software platform (called GSAT, General-purpose Summarisation and Annotation Tool) able to manage and preprocess microarray data. The GSAT allows the summarisation, normalisation and annotation of multivendor microarray data, using web services technology. First experiments and results on Affymetrix data samples are also discussed. GSAT is available online at as a standalone application or as a plugin of the TMEV microarray data analysis platform.     

A parallel logic system on a multicomputer architecture

This paper describes the implementation of a logic programming language on a massively parallel architecture. This implementation is based on the AND/OR Process Model which allows the exploitation of both AND and OR parallelism in logic programs. A distributed memory model is used, and a decentralized control mechanism has been designed. The multicomputer, which the system has been implemented on, consists of a network of Inmos Transputers. The AND/OR processes are implemented as Occam processes mapped onto the Transputer nodes. After the presentation of the system architecture and a deep discussion of the distributed memory management, some preliminary performance results are discussed.     

Semantics and knowledge grids: building the next-generation grid

Just as the Internet is shifting its focus from information and communication to a knowledge delivery infrastructure, we see the Grid moving from computation and data management to a pervasive, worldwide knowledge management infrastructure. We have the technology to store and access data, but we seem to lack the ability to transform data tombs into useful data and extract knowledge from them. We review some of the current and future technologies that will impact the architecture, computational model, and applications of future grids. We attempt to forecast the evolution of computational grids into what we call the next-generation grid, with a particular focus on the use of semantics and knowledge discovery techniques and services. We propose a comprehensive software architecture for the next-generation grid, which integrates currently available services and components in Semantic Web, Semantic Grid, P2P, and ubiquitous systems. We'll also discuss a case study that shows how some new technologies can improve grid applications.     

Design,implementation and evaluation of a deadlock-free routing algorithm for concurrent computers

This paper describes the design, the implementation, and the performance results of a routing algorithm which provides deadlock-free communication in a tightly coupled message-passing concurrent computer. The algorithm is adaptive, isolated and uses the store-and-forward technique. It allows message communication between two processes regardless of where they are physically located on the network. The routing algorithm has many positive characteristics including provable deadlock freedom, guaranteed message arrival, and automatic local congestion reduction. It can be used as a basis for the design of high-level communication primitives. An Occam implementation on a network of inmos Transputers is discussed. The experimental results show that the routing algorithm is effective to support process to process communication on a concurrent computer.