Ersin Cem Kaletas

VLAM-G: A Grid-based virtual laboratory

The Grid-based Virtual Laboratory AMsterdam (VLAM-G), provides a science portal for distributed analysis in applied scientific research. It offers scientists remote experiment control, data management facilities and access to distributed resources by providing cross-institutional integration of information and resources in a familiar environment. The main goal is to provide a unique integration of existing standards and software packages. This paper describes the design and prototype implementation of the VLAM-G platform. In this testbed we applied several recent technologies such as the Globus toolkit, enhanced federated database systems, and visualization and simulation techniques. Several domain specific case studies are described in some detail. Information management will be discussed separately in a forthcoming paper.

Service Federation in Virtual Organizations

The practical implantation of the concept of dynamic virtual enterprise is still far from expectations due to a number of factors such as the lack of appropriate interoperable infrastructures and tools, lack of common ontology, and the socio-organizational difficulties. However, the creation of industry clusters supported by advanced information and communication tools can meanwhile provide a basis for the rapid creation of dynamic virtual enterprises in response to the market opportunities. A federated service management approach is introduced in this context and its application to the tourism industry is discussed. Finally, the support for the aggregation of simpler services into value-added services, implemented by distributed business processes within different organizations, is presented.

A reference architecture for scientific virtual laboratories

Abstract Recent advances in the IT can be applied to properly support certain complex requirements in the scientific and engineering domains. In experimental sciences, for instance, researchers should be assisted with conducting their complex scientific experimentation and supporting their collaboration with other scientists. The main requirements identified in such domains include the management of large data sets, distributed collaboration support, and high-performance issues, among others. The virtual laboratory project initiated at the University of Amsterdam aims at the development of a hardware and software reference architecture, and an open, flexible, and configurable laboratory framework to enable scientists and engineers with working on their experimentation problems, while making optimum use of modern information technology approaches. This paper describes the current stage of design of a reference architecture for this scientific virtual laboratory, and focuses further on the cooperative information management component of this architecture, and exemplifying its application to experimentation domain of biology.

Toward a Multi-layer Architecture for Scientific Virtual Laboratories

In order to assist researchers with conducting their complex scientific experimentation and to support their collaboration with other scientists, modern advances in the IT area can be properly applied to the domain of experimental sciences. The main requirements identified in this domain include management of large data sets, distributed collaboration support, and high-performance issues, among others. The Virtual Laboratory project initiated at the University of Amsterdam aims at the development of a hardware and software reference architecture, and an open, flexible and configurable laboratory framework to enable scientists and engineers to work on their experimentation problems, while making optimum use of modern information technology approaches. This paper first describes the current design of a multi-layer architecture for this Scientific Virtual Laboratory, and then focuses further on the cooperative information management layer of this architecture, and exemplifying its application to experimentation domain of biology.

The Potential of Grid, Virtual Laboratories and Virtual Organizations for Bio-sciences

VLAM-G, the Grid-based Virtual Laboratory AMsterdam, provides a science portal for distributed analysis in applied scientific research. It offers scientists the possibility to carry out their experiments in a familiar environment that provides seamless access to geographically distributed resources and devices. In this paper, the general design of the VLAM-G platform is introduced. Furthermore, the application of the VLAM-G and its extension with Virtual Organization concepts for specific scientific domains is presented, with focus on bio-sciences.

Virtual Laboratories and Virtual Organizations Supporting Biosciences

Emergence of advanced complex applications in applied sciences poses many challenges to both the scientists and the developers of tools and mechanisms for their supporting infrastructure. Although technological advances in high-throughput / high-performance technologies provide the base, tackling the challenges in this area require long-term multi-disciplinary efforts between scientists and computer science experts. One such multi-disciplinary effort is started in bio-informatics, considering the growing complexity of emerging experiments and data processing requirements in biosciences domain. Among others, challenges in bio-sciences include designing experiments that utilize advanced technologies for storage, manipulation, and integration/interlinking of vast amounts of data produced by experiments, analysis of results on high-performance computers, and accessing the highly heterogeneous information that resides at geographically scattered centers. In this paper, we propose an “enhancement environment” for a virtual laboratory approach, supporting scientists to overcome the above problems and assisting them during their experimentation. Furthermore, we describe how this enhancement environment can be extended applying the virtual organizations concept and infrastructures, to support the collaborative experiments among diverse, heterogeneous and autonomous centers in the biosciences domain1.

Modelling Multi-disciplinary Scientific Experiments and Information

Emergence of advanced complex experiments in applied sciences resulted in a change in the way of experimentation. Information management plays an important role in supporting such scientific experiments. In this paper, we address the modelling requirements of scientific experiments and information. We describe a novel experiment model as the base for a support environment, and data models developed for the representation of different components of the experiment model.

Emerging technologies and standards

In response to VO challenges, research and development efforts shall address different features and components of VO, that cover a wide spectrum of areas. Considering the complexity of building technical support infrastructures and applications for VOs, clearly at the time of such developments, the choice of best approach, standards, technology, commercial tools/systems, or R&D developed prototypes plays a major role in their efficiency and sustainability. To assist developers in this challenging process, this chapter suggests a careful and systematic study of the problem/solution areas. This study discusses the properties required for technical support of VOs, the main related R&D focus areas, commercial development efforts, and the current trends in these areas.

Using ontologies for collaborative information management: some challenges and ideas

Emerging collaborative networks (CNs) bring together the need for an effective collaborative information management (CIM) infrastructure. Achieving a common understanding of the concepts and entities in CNs, especially with the presence of different types of heterogeneity involved in such environments, represents a big challenge for the developers of the CIM infrastructure. This paper proposes some ontology-based solutions to this challenge in three different research domains. Among the described solutions, the first one addresses the challenges of data representation and implementation regarding the translation of semantic model into appropriate data structures, the second one suggests an ontology-based semi-automatic approach for the resolution of schematic and semantic heterogeneity, and the third one aims to assist scientists from different e-science domains when customizing their experimentation environments with user-defined experiments and data types.

A Methodology for Integrating New Scientific Domains and Applications in a Virtual Laboratory Environment

Emergence of advanced complex experiments in experimental sciences resulted in a change in the way of experimentation. Several solutions have been proposed to support scientists with their complex experimentations, ranging from simple data portals to virtual laboratories. These solutions offer a variety of facilities to scientists, such as management of experiments and experiment-related information, and management of resources. However, issues related to adding new types of experiments to proposed support environments still remain untouched, causing inefficient utilization of efforts and inadequate transfer of expertise. The main topic of this paper is to present a methodology for integrating new scientific domains and applications in a multi-disciplinary virtual laboratory environment. In order to complement the methodology with the right context, the paper also presents an experiment model that uniformly represents scientific experiments, data models for modelling experiment-related information, and mechanisms for the management of this information.