Methodology for object-oriented real-time systems analysis and design: Software engineering

Successful application of software engineering methodologies requires an integrated analysis and design life-cycle in which the various phases flow smoothly 'seamlessly' from analysis through design to implementation. Furthermore, different analysis methodologies often lead to different structuring of the system so that the transition from analysis to design may be awkward depending on the design methodology to be used. This is especially important when object-oriented programming is to be used for implementation when the original specification and perhaps high-level design is non-object oriented. Two approaches to real-time systems analysis which can lead to an object-oriented design are contrasted: (1) modeling the system using structured analysis with real-time extensions which emphasizes data and control flows followed by the abstraction of objects where the operations or methods of the objects correspond to processes in the data flow diagrams and then design in terms of these objects; and (2) modeling the system from the beginning as a set of naturally occurring concurrent entities (objects) each having its own time-behavior defined by a set of states and state-transition rules and seamlessly transforming the analysis models into high-level design models. A new concept of a 'real-time systems-analysis object' is introduced and becomes the basic building block of a series of seamlessly-connected models which progress from the object-oriented real-time systems analysis and design system analysis logical models through the physical architectural models and the high-level design stages. The methodology is appropriate to the overall specification including hardware and software modules. In software modules, the systems analysis objects are transformed into software objects

Parallel Graph Transformation for Model Simulation applied to Timed Transition Petri Nets

Proceedings of the Workshop on Graph Transformation and Visual Modelling Techniques (GT-VMT 2004)This work discusses the use of parallel graph transformation systems for (multi-formalism) modeling and simulation and their implementation in the meta-modeling tool AToM3. As an example, a simulator for Timed Transition Petri Nets (TTPN) is modeled using parallel graph transformation.This work has been partially sponsored by the SEGRAVIS network and the Spanish Ministry of Science and Technology (TIC2002-01948)

Enterprise model verification and validation : an approach

This article presents a verification and validation approach which is used here in order to complete the classical tool box the industrial user may utilize in enterprise modeling and integration domain. This approach, which has been defined independently from any application domain is based on several formal concepts and tools presented in this paper. These concepts are property concepts, property reference matrix, properties graphs, enterprise modeling domain ontology, conceptual graphs and formal reasoning mechanisms

Developing and applying heterogeneous phylogenetic models with XRate

Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded gene features. However, beyond a modest level of model complexity, manual coding of models becomes prohibitively labor-intensive. We demonstrate, via a set of case studies, the new built-in model-prototyping capabilities of XRate (macros and Scheme extensions). These features allow rapid implementation of phylogenetic models which would have previously been far more labor-intensive. XRate's new capabilities for lineage-specific models, ancestral sequence reconstruction, and improved annotation output are also discussed. XRate's flexible model-specification capabilities and computational efficiency make it well-suited to developing and prototyping phylogenetic grammar models. XRate is available as part of the DART software package: http://biowiki.org/DART .Comment: 34 pages, 3 figures, glossary of XRate model terminolog