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

Guidelines to Study Differences in Expressiveness between Ontology Specification Languages: A Case Of Study

We focus on our experiences on translating ontologies between two ontology languages, FLogic and Ontolingua, in the framework of Methontology and ODE. Rather than building "ad hoc" translators between languages or using KIF, our option consists of translating through ODE intermediate representations. So, we have built direct translators from ODE intermediate representations to Ontolingua and FLogic, and we have also built reverse translators from these two languages to ODE intermediate representations. Expressiveness of the target languages is the main feature to analyse when automatically generating ontologies from ODE intermediate representations. Therefore, we analyse the expressiveness of Ontolingua and FLogic for creating classes, instances, relations, functions and axioms, which are the essential components in ontologies. The motivation for this analysis can be found in the (KA)² initiative and can be easily extended to any other domains and languages

A Framework for Design and Composition of Semantic Web Services

Semantic Web Services (SWS) are Web Services (WS) whose description is semantically enhanced with markup languages (e.g., OWL-S). This semantic description will enable external agents and programs to discover, compose and invoke SWSs. However, as a previous step to the specification of SWSs in a language, it must be designed at a conceptual level to guarantee its correctness and avoid inconsistencies among its internal components. In this paper, we present a framework for design and (semi) automatic composition of SWSs at a language-independent and knowledge level. This framework is based on a stack of ontologies that (1) describe the different parts of a SWS; and (2) contain a set of axioms that are really design rules to be verified by the ontology instances. Based on these ontologies, design and composition of SWSs can be viewed as the correct instantiation of the ontologies themselves. Once these instances have been created they will be exported to SWS languages such as OWL-S

Object-oriented querying of existing relational databases

In this paper, we present algorithms which allow an object-oriented querying of existing relational databases. Our goal is to provide an improved query interface for relational systems with better query facilities than SQL. This seems to be very important since, in real world applications, relational systems are most commonly used and their dominance will remain in the near future. To overcome the drawbacks of relational systems, especially the poor query facilities of SQL, we propose a schema transformation and a query translation algorithm. The schema transformation algorithm uses additional semantic information to enhance the relational schema and transform it into a corresponding object-oriented schema. If the additional semantic information can be deducted from an underlying entity-relationship design schema, the schema transformation may be done fully automatically. To query the created object-oriented schema, we use the Structured Object Query Language (SOQL) which provides declarative query facilities on objects. SOQL queries using the created object-oriented schema are much shorter, easier to write and understand and more intuitive than corresponding S Q L queries leading to an enhanced usability and an improved querying of the database. The query translation algorithm automatically translates SOQL queries into equivalent SQL queries for the original relational schema

Modelling and simulation framework for reactive transport of organic contaminants in bed-sediments using a pure java object - oriented paradigm

Numerical modelling and simulation of organic contaminant reactive transport in the environment is being increasingly relied upon for a wide range of tasks associated with risk-based decision-making, such as prediction of contaminant profiles, optimisation of remediation methods, and monitoring of changes resulting from an implemented remediation scheme. The lack of integration of multiple mechanistic models to a single modelling framework, however, has prevented the field of reactive transport modelling in bed-sediments from developing a cohesive understanding of contaminant fate and behaviour in the aquatic sediment environment. This paper will investigate the problems involved in the model integration process, discuss modelling and software development approaches, and present preliminary results from use of CORETRANS, a predictive modelling framework that simulates 1-dimensional organic contaminant reaction and transport in bed-sediments

Active database behaviour: the REFLEX approach

Modern day and new generation applications have more demanding requirements than traditional database management systems (DBMS) are able to support. Two of these requirements, timely responses to the change of database state and application domain knowledge stored within the database, are embodied within active database technology. Currently, there are a number of research prototype active database systems throughout the world. In order for an organisation to use any such prototype system, it may have to forsake existing products and resources and embark on substantial reinvestment in the new database products and associated resources and retraining costs. This approach would clearly be unfavourable as it is expensive both in terms of time and money. A more suitable approach would be to allow active behaviour to be added onto their existing systems. This scenario is addressed within this research. It investigates how best active behaviour can be augmented to existing DBMSs, so as to preserve the investments in an organisation's resources, by examining the following issues, (i.) what form the knowledge model should take, (ii.) should rules and events be modelled as first class objects, (iii.) how will the triggering events be specified, (iv.) how the user will interact with the system. Various design decisions were taken, which were investigated by implementation of a series of working prototypes, on the ONTOS DBMS platform. The resultant REFLEX model was successfully ported and adapted onto a second POET platform. The porting process uncovered some interesting issues regarding preconceived ideas about the portability of open systems