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R. McClatchey

Publications and source records attributed to R. McClatchey.

18 recordsLinked to original sources
arXiv2015

Facilitating Evolution during Design and Implementation

The volumes and complexity of data that companies need to handle are increasing at an accelerating rate. In order to compete effectively and ensure their commercial sustainability, it is becoming crucial for them to achieve robust traceability in both their data and the evolving designs of their systems. This is addressed by the CRISTAL software which was originally developed at CERN by UWE, Bristol, for one of the particle detectors at the Large Hadron Collider, and has been subsequently transferred into the commercial world. Companies have been able to demonstrate increased agility, generate additional revenue, and improve the efficiency and cost-effectiveness with which they develop and implement systems in various areas, including business process management (BPM), healthcare and accounting applications. CRISTALs ability to manage data and its provenance at the terabyte scale, with full traceability over extended timescales, together with its description-driven approach, has provided the flexible adaptability required to future proof dynamically evolving software for these businesses.

cs.SE↗
arXiv2014

Providing Traceability for Neuroimaging Analyses

With the increasingly digital nature of biomedical data and as the complexity of analyses in medical research increases, the need for accurate information capture, traceability and accessibility has become crucial to medical researchers in the pursuance of their research goals. Grid- or Cloud-based technologies, often based on so-called Service Oriented Architectures (SOA), are increasingly being seen as viable solutions for managing distributed data and algorithms in the bio-medical domain. For neuroscientific analyses, especially those centred on complex image analysis, traceability of processes and datasets is essential but up to now this has not been captured in a manner that facilitates collaborative study. Over the past decade, we have been working with mammographers, paediatricians and neuroscientists in three generations of projects to provide the data management and provenance services now required for 21st century medical research. This paper outlines the finding of a requirements study and a resulting system architecture for the production of services to support neuroscientific studies of biomarkers for Alzheimers Disease. The paper proposes a software infrastructure and services that provide the foundation for such support. It introduces the use of the CRISTAL software to provide provenance management as one of a number of services delivered on a SOA, deployed to manage neuroimaging projects that have been studying biomarkers for Alzheimers disease.

cs.SE↗
arXiv2007

A Multi Interface Grid Discovery System

Discovery Systems (DS) can be considered as entry points for global loosely coupled distributed systems. An efficient Discovery System in essence increases the performance, reliability and decision making capability of distributed systems. With the rapid increase in scale of distributed applications, existing solutions for discovery systems are fast becoming either obsolete or incapable of handling such complexity. They are particularly ineffective when handling service lifetimes and providing up-to-date information, poor at enabling dynamic service access and they can also impose unwanted restrictions on interfaces to widely available information repositories. In this paper we present essential the design characteristics, an implementation and a performance analysis for a discovery system capable of overcoming these deficiencies in large, globally distributed environments.

cs.DC↗
arXiv2007

Mobile Computing in Physics Analysis - An Indicator for eScience

This paper presents the design and implementation of a Grid-enabled physics analysis environment for handheld and other resource-limited computing devices as one example of the use of mobile devices in eScience. Handheld devices offer great potential because they provide ubiquitous access to data and round-the-clock connectivity over wireless links. Our solution aims to provide users of handheld devices the capability to launch heavy computational tasks on computational and data Grids, monitor the jobs status during execution, and retrieve results after job completion. Users carry their jobs on their handheld devices in the form of executables (and associated libraries). Users can transparently view the status of their jobs and get back their outputs without having to know where they are being executed. In this way, our system is able to act as a high-throughput computing environment where devices ranging from powerful desktop machines to small handhelds can employ the power of the Grid. The results shown in this paper are readily applicable to the wider eScience community.

cs.DC↗
arXiv2007

Semantic Information Retrieval from Distributed Heterogeneous Data Sources

Information retrieval from distributed heterogeneous data sources remains a challenging issue. As the number of data sources increases more intelligent retrieval techniques, focusing on information content and semantics, are required. Currently ontologies are being widely used for managing semantic knowledge, especially in the field of bioinformatics. In this paper we describe an ontology assisted system that allows users to query distributed heterogeneous data sources by hiding details like location, information structure, access pattern and semantic structure of the data. Our goal is to provide an integrated view on biomedical information sources for the Health-e-Child project with the aim to overcome the lack of sufficient semantic-based reformulation techniques for querying distributed data sources. In particular, this paper examines the problem of query reformulation across biomedical data sources, based on merged ontologies and the underlying heterogeneous descriptions of the respective data sources.

cs.DB↗
arXiv2007

Experiences of Engineering Grid-Based Medical Software

Objectives: Grid-based technologies are emerging as potential solutions for managing and collaborating distributed resources in the biomedical domain. Few examples exist, however, of successful implementations of Grid-enabled medical systems and even fewer have been deployed for evaluation in practice. The objective of this paper is to evaluate the use in clinical practice of a Grid-based imaging prototype and to establish directions for engineering future medical Grid developments and their subsequent deployment. Method: The MammoGrid project has deployed a prototype system for clinicians using the Grid as its information infrastructure. To assist in the specification of the system requirements (and for the first time in healthgrid applications), use-case modelling has been carried out in close collaboration with clinicians and radiologists who had no prior experience of this modelling technique. A critical qualitative and, where possible, quantitative analysis of the MammoGrid prototype is presented leading to a set of recommendations from the delivery of the first deployed Grid-based medical imaging application. Results: We report critically on the application of software engineering techniques in the specification and implementation of the MammoGrid project and show that use-case modelling is a suitable vehicle for representing medical requirements and for communicating effectively with the clinical community. This paper also discusses the practical advantages and limitations of applying the Grid to real-life clinical applications and presents the consequent lessons learned.

cs.DC↗
arXiv2007

DIANA Scheduling Hierarchies for Optimizing Bulk Job Scheduling

The use of meta-schedulers for resource management in large-scale distributed systems often leads to a hierarchy of schedulers. In this paper, we discuss why existing meta-scheduling hierarchies are sometimes not sufficient for Grid systems due to their inability to re-organise jobs already scheduled locally. Such a job re-organisation is required to adapt to evolving loads which are common in heavily used Grid infrastructures. We propose a peer-to-peer scheduling model and evaluate it using case studies and mathematical modelling. We detail the DIANA (Data Intensive and Network Aware) scheduling algorithm and its queue management system for coping with the load distribution and for supporting bulk job scheduling. We demonstrate that such a system is beneficial for dynamic, distributed and self-organizing resource management and can assist in optimizing load or job distribution in complex Grid infrastructures.

cs.DC↗
arXiv2006

The Management and Integration of Biomedical Knowledge: Application in the Health-e-Child Project (Position Paper)

The Health-e-Child project aims to develop an integrated healthcare platform for European paediatrics. In order to achieve a comprehensive view of childrens health, a complex integration of biomedical data, information, and knowledge is necessary. Ontologies will be used to formally define this domain knowledge and will form the basis for the medical knowledge management system. This paper introduces an innovative methodology for the vertical integration of biomedical knowledge. This approach will be largely clinician-centered and will enable the definition of ontology fragments, connections between them (semantic bridges) and enriched ontology fragments (views). The strategy for the specification and capture of fragments, bridges and views is outlined with preliminary examples demonstrated in the collection of biomedical information from hospital databases, biomedical ontologies, and biomedical public databases.

cs.DB↗
arXiv2004

Grid Databases for Shared Image Analysis in the MammoGrid Project

The MammoGrid project aims to prove that Grid infrastructures can be used for collaborative clinical analysis of database-resident but geographically distributed medical images. This requires: a) the provision of a clinician-facing front-end workstation and b) the ability to service real-world clinician queries across a distributed and federated database. The MammoGrid project will prove the viability of the Grid by harnessing its power to enable radiologists from geographically dispersed hospitals to share standardized mammograms, to compare diagnoses (with and without computer aided detection of tumours) and to perform sophisticated epidemiological studies across national boundaries. This paper outlines the approach taken in MammoGrid to seamlessly connect radiologist workstations across a Grid using an "information infrastructure" and a DICOM-compliant object model residing in multiple distributed data stores in Italy and the UK

cs.DB↗
arXiv2001

XML for Domain Viewpoints

Within research institutions like CERN (European Organization for Nuclear Research) there are often disparate databases (different in format, type and structure) that users need to access in a domain-specific manner. Users may want to access a simple unit of information without having to understand detail of the underlying schema or they may want to access the same information from several different sources. It is neither desirable nor feasible to require users to have knowledge of these schemas. Instead it would be advantageous if a user could query these sources using his or her own domain models and abstractions of the data. This paper describes the basis of an XML (eXtended Markup Language) framework that provides this functionality and is currently being developed at CERN. The goal of the first prototype was to explore the possibilities of XML for data integration and model management. It shows how XML can be used to integrate data sources. The framework is not only applicable to CERN data sources but other environments too.

physics.ins-det↗
arXiv2001

A Component Based Approach to Scientific Workflow Management

CRISTAL is a distributed scientific workflow system used in the manufacturing and production phases of HEP experiment construction at CERN. The CRISTAL project has studied the use of a description driven approach, using meta- modelling techniques, to manage the evolving needs of a large physics community. Interest from such diverse communities as bio-informatics and manufacturing has motivated the CRISTAL team to re-engineer the system to customize functionality according to end user requirements but maximize software reuse in the process. The next generation CRISTAL vision is to build a generic component architecture from which a complete software product line can be generated according to the particular needs of the target enterprise. This paper discusses the issues of adopting a component product line based approach and our experiences of software reuse.

physics.ins-det↗
arXiv2001

Object Serialization and Deserialization Using XML

Interoperability of potentially heterogeneous databases has been an ongoing research issue for a number of years in the database community. With the trend towards globalization of data location and data access and the consequent requirement for the coexistence of new data stores with legacy systems, the cooperation and data interchange between data repositories has become increasingly important. The emergence of the eXtensible Markup Language (XML) as a database independent representation for data offers a suitable mechanism for transporting data between repositories. This paper describes a research activity within a group at CERN (called CMS) towards identifying and implementing database serialization and deserialization methods that can be used to replicate or migrate objects across the network between CERN and worldwide centres using XML to serialize the contents of multiple objects resident in object-oriented databases.

physics.ins-det↗
arXiv2001

The Reification of Patterns in the Design of Description-Driven Systems

To address the issues of reusability and evolvability in designing self- describing systems, this paper proposes a pattern-based, object-oriented, description-driven system architecture. The proposed architecture embodies four pillars - first, the adoption of a multi-layered meta-modeling architecture and reflective meta-level architecture, second, the identification of four data modeling relationships that must be made explicit such that they can be examined and modified dynamically, third, the identification of five design patterns which have emerged from practice and have proved essential in providing reusable building blocks for data management, and fourth, the encoding of the structural properties of the five design patterns by means of one pattern, the Graph pattern. The CRISTAL research project served as the basis onto which the pattern-based meta-object approach has been applied. The proposed architecture allows the realization of reusability and adaptability, and is fundamental in the specification of self-describing data management components.

physics.ins-det↗
arXiv1999

Design Patterns for Description-Driven Systems

In data modelling, product information has most often been handled separately from process information. The integration of product and process models in a unified data model could provide the means by which information could be shared across an enterprise throughout the system lifecycle from design through to production. Recently attempts have been made to integrate these two separate views of systems through identifying common data models. This paper relates description-driven systems to multi-layer architectures and reveals where existing design patterns facilitate the integration of product and process models and where patterns are missing or where existing patterns require enrichment for this integration. It reports on the construction of a so-called description-driven system which integrates Product Data Management (PDM) and Workflow Management (WfM) data models through a common meta-model.

physics.ins-det↗
arXiv1999

Getting Physics Data From the CMS ECAL Construction Database

CMS ECAL physicists must be able to extract physics characteristics from the ECAL construction database for the calibration of sets of detector components. Other applications, such as geometry for simulation and physics event reconstruction, will also need to extract data from the construction database. In each case, application software needs to query the construction database and to extract data that satisfies a particular view. These viewpoints are defined for a specific purpose (e.g. simulation, slow control, calibration) and data must be extracted into the viewpoint for a set of defined detector components (e.g. readout channels) called physics elements. The ECAL construction database follows an object-oriented design to maximise flexibility and reusability. An meta-modelling approach has been taken in its design, which promotes self-description and a degree of data independence. A query facility is being provided to allow navigation around so-called meta-objects in the construction database, facilitating the extraction of physics data into a particular viewpoint. This paper outlines how viewpoints can be populated with data extracted from the construction database, for a set of detector elements relevant for analysis.

physics.ins-det↗
arXiv1998

Detector Construction Management and Quality Control: Establishing and Using a CRISTAL System

The CRISTAL (Cooperating Repositories and an Information System for Tracking Assembly Lifecycles) project is delivering a software system to facilitate the management of the engineering data collected at each stage of production of CMS. CRISTAL captures all the physical characteristics of CMS components as each sub-detector is tested and assembled. These data are retained for later use in areas such as detector slow control, calibration and maintenance. CRISTAL must, therefore, support different views onto its data dependent on the role of the user. These data viewpoints are investigated in this paper. In the recent past two CMS Notes have been written about CRISTAL. The first note, CMS 1996/003, detailed the requirements for CRISTAL, its relationship to other CMS software, its objectives and reviewed the technology on which it would be based. CMS 1997/104 explained some important design concepts on which CRISTAL is and showed how CRISTAL integrated the domains of product data man- agement and workflow management. This note explains, through the use of diagrams, how CRISTAL can be established for detector production and used as the information source for analyses, such as calibration and slow controls, carried out by physicists. The reader should consult the earlier CMS Notes and conference papers for technical detail on CRISTAL - this note concentrates on issues surrounding the practical use of the CRISTAL software.

physics.ins-det↗
arXiv1998

From Design to Production Control Through the Integration of Engineering Data Management and Workflow Management Systems

At a time when many companies are under pressure to reduce "times-to-market" the management of product information from the early stages of design through assembly to manufacture and production has become increasingly important. Similarly in the construction of high energy physics devices the collection of (often evolving) engineering data is central to the subsequent physics analysis. Traditionally in industry design engineers have employed Engineering Data Management Systems (also called Product Data Management Systems) to coordinate and control access to documented versions of product designs. However, these systems provide control only at the collaborative design level and are seldom used beyond design. Workflow management systems, on the other hand, are employed in industry to coordinate and support the more complex and repeatable work processes of the production environment. Commercial workflow products cannot support the highly dynamic activities found both in the design stages of product development and in rapidly evolving workflow definitions. The integration of Product Data Management with Workflow Management can provide support for product development from initial CAD/CAM collaborative design through to the support and optimisation of production workflow activities. This paper investigates this integration and proposes a philosophy for the support of product data throughout the full development and production lifecycle and demonstrates its usefulness in the construction of CMS detectors.

physics.ins-det↗