Shingle 2.0: generalising self-consistent and automated domain discretisation for multi-scale geophysical models

The approaches taken to describe and develop spatial discretisations of the domains required for geophysical simulation models are commonly ad hoc, model or application specific and under-documented. This is particularly acute for simulation models that are flexible in their use of multi-scale, anisotropic, fully unstructured meshes where a relatively large number of heterogeneous parameters are required to constrain their full description. As a consequence, it can be difficult to reproduce simulations, ensure a provenance in model data handling and initialisation, and a challenge to conduct model intercomparisons rigorously. This paper takes a novel approach to spatial discretisation, considering it much like a numerical simulation model problem of its own. It introduces a generalised, extensible, self-documenting approach to carefully describe, and necessarily fully, the constraints over the heterogeneous parameter space that determine how a domain is spatially discretised. This additionally provides a method to accurately record these constraints, using high-level natural language based abstractions, that enables full accounts of provenance, sharing and distribution. Together with this description, a generalised consistent approach to unstructured mesh generation for geophysical models is developed, that is automated, robust and repeatable, quick-to-draft, rigorously verified and consistent to the source data throughout. This interprets the description above to execute a self-consistent spatial discretisation process, which is automatically validated to expected discrete characteristics and metrics.Comment: 18 pages, 10 figures, 1 table. Submitted for publication and under revie

An ontology for software component matching

The Web is likely to be a central platform for software development in the future. We investigate how Semantic Web technologies, in particular ontologies, can be utilised to support software component development in a Web environment. We use description logics, which underlie Semantic Web ontology languages such as DAML+OIL, to develop an ontology for matching requested and provided components. A link between modal logic and description logics will prove invaluable for the provision of reasoning support for component and service behaviour

JSB Composability and Web Services Interoperability Via Extensible Modeling & Simulation Framework (XMSF), Model Driven Architecture (MDA), Component Repositories, and Web-based Visualization

Study Report prepared for the U. S. Air Force, Joint Synthetic Battlespace Analysis of Technical Approaches (ATA) Studies & Prototyping Overview: This paper summarizes research work conducted by organizations concerned with interoperable distributed information technology (IT) applications, in particular the Naval Postgraduate School (NPS) and Old Dominion University (ODU). Although the application focus is distributed modeling & simulation (M&S) the results and findings are in general easily applicable to other distributed concepts as well, in particular the support of operations by M&S applications, such as distributed mission operations. The core idea of this work is to show the necessity of applying open standards for component description, implementation, and integration accompanied by aligned management processes and procedures to enable continuous interoperability for legacy and new M&S components of the live, virtual, and constructive domain within the USAF Joint Synthetic Battlespace (JSB). JSB will be a common integration framework capable of supporting the future emerging simulation needs ranging from training and battlefield rehearsal to research, system development and acquisition in alignment with other operational requirements, such as integration of command and control, support of operations, integration of training ranges comprising real systems, etc. To this end, the study describes multiple complementary Integrated Architecture Framework approaches and shows, how the various parts must be orchestrated in order to support the vision of JSB effectively and efficiently. Topics of direct relevance include Web Services via Extensible Modeling & Simulation Framework (XMSF), the Object Management Group (OMG)’s Model Driven Architecture (MDA), XML-based resource repositories, and Web-based X3D visualization. To this end, the report shows how JSB can − Utilize Web Services throughout all components via XMSF methodologies, − Compose diverse system visualizations using Web-based X3D graphics, − Benefit from distributed modeling methods using MDA, and − Best employ resource repositories for broad and consistent composability. Furthermore, the report recommends the establishment of necessary management organizations responsible for the necessary alignment of management processes and procedures within the JSB as well as with neighbored domains. Continuous interoperability cannot be accomplished by technical standards alone. The application of technical standards targets the implementation level of the system of systems, which results in an interoperable solution valid only for the actual 2 implementation. To insure continuity, the influence of updates, upgrades and introduction of components on the system of systems must be captured in the project management procedures of the participating systems. Finally, the report proposes an exemplifying set of proof-of-capability demonstration prototypes and a five-year technical/institutional transformation plan. All key references are online available at http://www.movesinstitute.org/xmsf/xmsf.html (if not explicitly stated otherwise)

TinkerCell: Modular CAD Tool for Synthetic Biology

Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. An application named TinkerCell has been created in order to serve as a CAD tool for synthetic biology. TinkerCell is a visual modeling tool that supports a hierarchy of biological parts. Each part in this hierarchy consists of a set of attributes that define the part, such as sequence or rate constants. Models that are constructed using these parts can be analyzed using various C and Python programs that are hosted by TinkerCell via an extensive C and Python API. TinkerCell supports the notion of a module, which are networks with interfaces. Such modules can be connected to each other, forming larger modular networks. Because TinkerCell associates parameters and equations in a model with their respective part, parts can be loaded from databases along with their parameters and rate equations. The modular network design can be used to exchange modules as well as test the concept of modularity in biological systems. The flexible modeling framework along with the C and Python API allows TinkerCell to serve as a host to numerous third-party algorithms. TinkerCell is a free and open-source project under the Berkeley Software Distribution license. Downloads, documentation, and tutorials are available at www.tinkercell.com.Comment: 23 pages, 20 figure

Data and Activity Representation for Grid Computing

Computational grids are becoming increasingly popular as an infrastructure for computa- tional science research. The demand for high-level tools and problem solving environments has prompted active research in Grid Computing Environments (GCEs). Many GCEs have been one-o development eorts. More recently, there have been many eorts to dene component ar- chitectures for constructing important pieces of a GCE. This paper examines another approach, based on a `data-centric' framework for building powerful, context-aware GCEs spanning mul- tiple layers of abstraction. We describe a scheme for representing data and activities in a GCE and outline various tools under development which use this representation

Composing Systemic Aspects into Component-Oriented DOC Middleware

The advent and maturation of component-based middleware frameworks have sim-plified the development of large-scale distributed applications by separating system devel-opment and configuration concerns into different aspects that can be specified and com-posed at various stages of the application development lifecycle. Conventional component middleware technologies, such as J2EE [73] and .NET [34], were designed to meet the quality of service (QoS) requirements of enterprise applications, which focus largely on scalability and reliability. Therefore, conventional component middleware specifications and implementations are not well suited for distributed real-time and embedded (DRE) ap-plications with more stringent QoS requirements, such as low latency/jitter, timeliness, and online fault recovery. In the DRE system development community, a new generation of enhanced commercial off-the-shelf (COTS) middleware, such as Real-time CORBA 1.0 (RT-CORBA)[39], is increasingly gaining acceptance as (1) the cost and time required to develop and verify DRE applications precludes developers from implementing complex DRE applications from scratch and (2) implementations of standard COTS middleware specifications mature and encompass key QoS properties needed by DRE systems. However, although COTS middleware standardizes mechanisms to configure and control underlying OS support for an application’s QoS requirements, it does not yet provide sufficient abstractions to separate QoS policy configurations such as real-time performance requirements, from application functionality. Developers are therefore forced to configure QoS policies in an ad hoc way, and the code to configure these policies is often scattered throughout and tangled with other parts of a DRE system. As a result, it is hard for developers to configure, validate, modify, and evolve complex DRE systems consistently. It is therefore necessary to create a new generation of QoS-enabled component middleware that provides more comprehensive support for addressing QoS-related concerns modularly, so that they can be introduced and configured as separate systemic aspects. By analyzing and identifying the limitations of applying conventional middleware technologies for DRE applications, this dissertation presents a new design and its associated techniques for enhancing conventional component-oriented middleware to provide programmability of DRE relevant real-time QoS concerns. This design is realized in an implementation of the standard CORBA Component Model (CCM) [38], called the Component-Integrated ACE ORB (CIAO). This dissertation also presents both architectural analysis and empirical results that demonstrate the effectiveness of this approach. This dissertation provides three contributions to the state of the art in composing systemic behaviors into component middleware frameworks. First, it illustrates how component middleware can simplify development and evolution of DRE applications while ensuring stringent QoS requirements by composing systemic QoS aspects. Second, it contributes to the design and implementation of QoS-enabled CCM by analyzing and documenting how systemic behaviors can be composed into component middleware. Finally, it presents empirical and analytical results to demonstrate the effectiveness and the advantage of composing systemic behaviors in component middleware. The work in this dissertation has a broader impact beyond the CCM in which it was developed, as it can be applied to other component-base middleware technologies which wish to support DRE applications

The DaveMLTranslator: An Interface for DAVE-ML Aerodynamic Models

It can take weeks or months to incorporate a new aerodynamic model into a vehicle simulation and validate the performance of the model. The Dynamic Aerospace Vehicle Exchange Markup Language (DAVE-ML) has been proposed as a means to reduce the time required to accomplish this task by defining a standard format for typical components of a flight dynamic model. The purpose of this paper is to describe an object-oriented C++ implementation of a class that interfaces a vehicle subsystem model specified in DAVE-ML and a vehicle simulation. Using the DaveMLTranslator class, aerodynamic or other subsystem models can be automatically imported and verified at run-time, significantly reducing the elapsed time between receipt of a DAVE-ML model and its integration into a simulation environment. The translator performs variable initializations, data table lookups, and mathematical calculations for the aerodynamic build-up, and executes any embedded static check-cases for verification. The implementation is efficient, enabling real-time execution. Simple interface code for the model inputs and outputs is the only requirement to integrate the DaveMLTranslator as a vehicle aerodynamic model. The translator makes use of existing table-lookup utilities from the Langley Standard Real-Time Simulation in C++ (LaSRS++). The design and operation of the translator class is described and comparisons with existing, conventional, C++ aerodynamic models of the same vehicle are given