COEL: A Web-based Chemistry Simulation Framework

The chemical reaction network (CRN) is a widely used formalism to describe macroscopic behavior of chemical systems. Available tools for CRN modelling and simulation require local access, installation, and often involve local file storage, which is susceptible to loss, lacks searchable structure, and does not support concurrency. Furthermore, simulations are often single-threaded, and user interfaces are non-trivial to use. Therefore there are significant hurdles to conducting efficient and collaborative chemical research. In this paper, we introduce a new enterprise chemistry simulation framework, COEL, which addresses these issues. COEL is the first web-based framework of its kind. A visually pleasing and intuitive user interface, simulations that run on a large computational grid, reliable database storage, and transactional services make COEL ideal for collaborative research and education. COEL's most prominent features include ODE-based simulations of chemical reaction networks and multicompartment reaction networks, with rich options for user interactions with those networks. COEL provides DNA-strand displacement transformations and visualization (and is to our knowledge the first CRN framework to do so), GA optimization of rate constants, expression validation, an application-wide plotting engine, and SBML/Octave/Matlab export. We also present an overview of the underlying software and technologies employed and describe the main architectural decisions driving our development. COEL is available at http://coel-sim.org for selected research teams only. We plan to provide a part of COEL's functionality to the general public in the near future.Comment: 23 pages, 12 figures, 1 tabl

A Collaborative Visualization Framework Using JINI™ Technology

It is difficult to achieve mutual understanding of complex information between individuals that are separated geographically. Two well-known techniques commonly used to deal with this difficultly are collaboration and information visualization. This thesis develops a generic flexible framework that supports both collaboration and information visualization. It introduces the Collaborative Visualization Environment (COVE) framework, which simplifies the development of real-time synchronous multi-user applications by decoupling the elements of collaboration from the application. This allows developers to focus on building applications and leave the difficulties of collaboration (i.e., concurrency controls, user awareness, session management, etc.) to the framework. The framework uses an object sharing approach to share information and views between participants in a collaborative session. This approach takes advantage of several Java technologies (i.e., JavaBeans™, Jini™, and JavaSpaces™). JavaBeans™ establish a well-known standard for applications to operate within the framework. Jini™ services provide framework stability and enable code sharing across the network. Objects are shared between remote clients through the JavaSpaces™ service

Component metadata management and publication for the grid

There is growing attention to component-oriented software design of Grid applications. Within this framework, applications are built by assembling together independently developed software components. Two main approaches are commonly used to manage, develop and publish software components: one is based on an Interface Description Language (IDL); the other is typical, for instance, of Java and is based on introspection and design conventions. In this paper, we compare them and we propose a third approach that merges the flexibility and fast learning curve of the latter, with the rigor of the former. Our proposal is meant to help the transition towards more modern tools, which is required to develop versatile Grid applications. © 2005 IEEE

An Architecture for the Integration of Internet and Telecommunication Services

In this paper, we propose an architecture for hybrid services, i.e., services that span many network technologies, especially the PSTN and the Internet. These services will play an important role in the future, because they leverage on the existing infrastructures, rather than requiring brand-new and sophisticated mechanisms to be deployed. We explore a few issues related to hybrid services and propose a platform, as well as a set of components, to facilitate their creation and deployment. The existing infrastructure is only required to generate specific events when requests for hybrid services are detected. We present the design of s service layer, based on Java, that handles the treatment of these special requests. Our service layer is provided with a set of generic components realized as Java Beans. Hence, we can provide hybrid services without changing the existing infrastructure. We illustrate this strength of our architecture by discussing the call forwarding service

Database Systems - Present and Future

The database systems have nowadays an increasingly important role in the knowledge-based society, in which computers have penetrated all fields of activity and the Internet tends to develop worldwide. In the current informatics context, the development of the applications with databases is the work of the specialists. Using databases, reach a database from various applications, and also some of related concepts, have become accessible to all categories of IT users. This paper aims to summarize the curricular area regarding the fundamental database systems issues, which are necessary in order to train specialists in economic informatics higher education. The database systems integrate and interfere with several informatics technologies and therefore are more difficult to understand and use. Thus, students should know already a set of minimum, mandatory concepts and their practical implementation: computer systems, programming techniques, programming languages, data structures. The article also presents the actual trends in the evolution of the database systems, in the context of economic informatics.database systems - DBS, database management systems – DBMS, database – DB, programming languages, data models, database design, relational database, object-oriented systems, distributed systems, advanced database systems

Integration of Chicory components and Chicory optimization

Software is not built as monolithic structure. It is built in blocks by more than one person. This software then has to be put together and made to work. It is also important to ensure that the assembled software is performing optimally.;Chicory(TM) is such a Java(TM) software. It is made of numerous components, made by a lot of different people.;This thesis explores the complications associated with integrating these components. This is achieved by an exhaustive description of the architecture of the components and a detailed description of the design decisions. It explains in detail the interactions between various objects inside Chicory(TM). To explain the structure we first give an overview of the system and then explain the structural details and follow it by significant object interactions.;We also take care to explain the steps to be followed when extending the software to add functionality.;Software when built is not initially in its most optimized form. Structures and control flows exist which slow the application down when exposed to heavy loads. Data types used may not be fast enough to allow at least usable performances. Computation might be unnecessarily repeated. This thesis also explains the methods that we followed to optimize Chicory(TM). We explain methods applied to make Chicory(TM) use less memory and run faster and eliminate the problems explained above.;In putting forth these explanations we hope to impress on the user, the complexity associate with managing software of large proportions. We hope that the reader will gain significant insight into the functioning of Chicory(TM)

Search and Discovery Tools for Astronomical On-line Resources and Services

A growing number of astronomical resources and data or information services are made available through the Internet. However valuable information is frequently hidden in a deluge of non-pertinent or non up-to-date documents. At a first level, compilations of astronomical resources provide help for selecting relevant sites. Combining yellow-page services and meta-databases of active pointers may be an efficient solution to the data retrieval problem. Responses generated by submission of queries to a set of heterogeneous resources are difficult to merge or cross-match, because different data providers generally use different data formats: new endeavors are under way to tackle this problem. We review the technical challenges involved in trying to provide general search and discovery tools, and to integrate them through upper level interfaces.Comment: 7 pages, 2 Postscript figures; to be published in A&A

A middleware for service oriented computing in dynamic environments

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do Grau de Mestre em Engenharia InformáticaThe last years have witnessed a convergence on the SOA paradigm from industrial processes enterprises (like logistics or manufacturing), using standards for data and communication. SOA promotes reusability, interoperability and loose-coupling of applications. The convergence towards SOA shows that we are leading to an infrastructure composed by several heterogeneous devices, the "Internet of Things". In this infrastructure everything can be abstracted as a service, such as household appliances, mobile devices, or industrial machinery. It is expected that this trend will continue, and as these devices interoperate in service composition, new functionalities may be discovered. Existing approaches for service composition, namely in business processes, are too bound to BPEL. Several alternatives and extensions of BPEL have been developed, but they feel more like patches than solutions. In this context SeDeUse [29] model has been proposed as an exercise to define new language constructs promoting a separation from service awareness and use. The model also relies on a middleware layer to support the execution of the application in dynamic environments. The goal of this dissertation is to instantiate the SeDeUse model in a widely used programming language in order to provide a framework for its assessment and for its future development. The work consists on implementing a concrete syntax for the model, a compilation process, and a middleware layer. The syntax contains the new language constructs that are integrated in the hosting language. The compilation process is responsible for service definition and code generation. Finally, the middleware acts as a support for the application (generated code) requests. We have seamlessly integrated SeDeUse in the Java programming language and developed a functional prototype. To assess the prototype capability, three scenarios were developed in which we demonstrated that our implementation provides a new, and simpler, approach for abstracting resources as services