DIVERSE: a Software Toolkit to Integrate Distributed Simulations with Heterogeneous Virtual Environments

We present DIVERSE (Device Independent Virtual Environments- Reconfigurable, Scalable, Extensible), which is a modular collection of complimentary software packages that we have developed to facilitate the creation of distributed operator-in-the-loop simulations. In DIVERSE we introduce a novel implementation of remote shared memory (distributed shared memory) that uses Internet Protocol (IP) networks. We also introduce a new method that automatically extends hardware drivers (not in the operating system kernel driver sense) into inter-process and Internet hardware services. Using DIVERSE, a program can display in a CAVE™, ImmersaDesk™, head mounted display (HMD), desktop or laptop without modification. We have developed a method of configuring user programs at run-time by loading dynamic shared objects (DSOs), in contrast to the more common practice of creating interpreted configuration languages. We find that by loading DSOs the development time, complexity and size of DIVERSE and DIVERSE user applications is significantly reduced. Configurations to support different I/O devices, device emulators, visual displays, and any component of a user application including interaction techniques, can be changed at run-time by loading different sets of DIVERSE DSOs. In addition, interpreted run-time configuration parsers have been implemented using DIVERSE DSOs; new ones can be created as needed. DIVERSE is free software, licensed under the terms of the GNU General Public License (GPL) and the GNU Lesser General Public License (LGPL) licenses. We describe the DIVERSE architecture and demonstrate how DIVERSE was used in the development of a specific application, an operator-in-the-loop Navy ship-board crane simulator, which runs unmodified on a desktop computer and/or in a CAVE with motion base motion queuing

Parallel machine architecture and compiler design facilities

The objective is to provide an integrated simulation environment for studying and evaluating various issues in designing parallel systems, including machine architectures, parallelizing compiler techniques, and parallel algorithms. The status of Delta project (which objective is to provide a facility to allow rapid prototyping of parallelized compilers that can target toward different machine architectures) is summarized. Included are the surveys of the program manipulation tools developed, the environmental software supporting Delta, and the compiler research projects in which Delta has played a role

Physically Interacting With Four Dimensions

Thesis (Ph.D.) - Indiana University, Computer Sciences, 2009People have long been fascinated with understanding the fourth dimension. While making pictures of 4D objects by projecting them to 3D can help reveal basic geometric features, 3D graphics images by themselves are of limited value. For example, just as 2D shadows of 3D curves may have lines crossing one another in the shadow, 3D graphics projections of smooth 4D topological surfaces can be interrupted where one surface intersects another. The research presented here creates physically realistic models for simple interactions with objects and materials in a virtual 4D world. We provide methods for the construction, multimodal exploration, and interactive manipulation of a wide variety of 4D objects. One basic achievement of this research is to exploit the free motion of a computer-based haptic probe to support a continuous motion that follows the \emph{local continuity\/} of a 4D surface, allowing collision-free exploration in the 3D projection. In 3D, this interactive probe follows the full local continuity of the surface as though we were in fact \emph{physically touching\/} the actual static 4D object. Our next contribution is to support dynamic 4D objects that can move, deform, and collide with other objects as well as with themselves. By combining graphics, haptics, and collision-sensing physical modeling, we can thus enhance our 4D visualization experience. Since we cannot actually place interaction devices in 4D, we develop fluid methods for interacting with a 4D object in its 3D shadow image using adapted reduced-dimension 3D tools for manipulating objects embedded in 4D. By physically modeling the correct properties of 4D surfaces, their bending forces, and their collisions in the 3D interactive or haptic controller interface, we can support full-featured physical exploration of 4D mathematical objects in a manner that is otherwise far beyond the real-world experience accessible to human beings

Search based software engineering: Trends, techniques and applications

© ACM, 2012. This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version is available from the link below.In the past five years there has been a dramatic increase in work on Search-Based Software Engineering (SBSE), an approach to Software Engineering (SE) in which Search-Based Optimization (SBO) algorithms are used to address problems in SE. SBSE has been applied to problems throughout the SE lifecycle, from requirements and project planning to maintenance and reengineering. The approach is attractive because it offers a suite of adaptive automated and semiautomated solutions in situations typified by large complex problem spaces with multiple competing and conflicting objectives. This article provides a review and classification of literature on SBSE. The work identifies research trends and relationships between the techniques applied and the applications to which they have been applied and highlights gaps in the literature and avenues for further research.EPSRC and E

Safe and Optimal Techniques Enabling Recovery, Integrity, and Assurance

There is a trend in the aviation industry to go from federated to integrated computing systems. Combining a number of traditional stand-alone federated systems into an integrated common platform (called Integrated Modular Avionics, IMA) has the benefit of increased power efficiency, reduced support hardware, and reduced cabling. However, changing from federated to integrated has a significant impact on the system architecture and hence the process of how avionic systems are to be analyzed. Traditional approaches to safety analysis become inefficient when functional boundaries can no longer be assumed for failure independence and fault isolation. In this report, we describe a tool that we developed to accelerate the safety engineer's ability to perform safety analysis of IMA systems through modeling, as well as optimize the system engineer's ability to develop a system through architecture synthesis. This work was the result of a three-year research effort called SOTERIA (Safe and Optimal Techniques Enabling Recovery, Integrity, and Assurance). We developed a compositional modeling language that supports rapid development, modification, and evaluation of architectures. The modeling language is structured such that the end-user defines a library of components with information on component reliability, connectivity, and fault propagation logic. The system model is built by instantiating the components from the library, connecting the components, and identifying the top-level faults of interest. Our tool is compositional in that the end-user only needs to define safety aspects at the component level. The tool takes the model and automatically synthesizes both the qualitative and quantitative safety analyses. We go further by allowing users to describe system information such as components to use in an architecture and their connection compatibility and automatically synthesize an architecture that meets the top-level probability target adhering to end-user specified constraints. This capability allows users to rapidly explore a design space.

A Framework of Multi-Dimensional and Multi-Scale Modeling with Applications

In this dissertation, a framework for multi-dimensional and multi-scale modeling is proposed. The essential idea is based on oriented space curves, which can be represented as a 3D slender object or 1D step parameters. SMILES and Masks provide functionalities that extend slender objects into branched and other objects. We treat the conversion between 1D, 2D, 3D, and 4D representations as data unification. A mathematical analysis of different methods applied to helices (a special type of space curves) is also provided. Computational implementation utilizes Model-ViewController design principles to integrate data unification with graphical visualizations to create a dashboard. Applications of multi-dimensional and multi-scale modeling are provided to study “Magic Snake”, “Nanocar” and “Genome Dashboard”

Network analysis of circular permutations in multidomain proteins reveals functional linkages for uncharacterized proteins.

Various studies have implicated different multidomain proteins in cancer. However, there has been little or no detailed study on the role of circular multidomain proteins in the general problem of cancer or on specific cancer types. This work represents an initial attempt at investigating the potential for predicting linkages between known cancer-associated proteins with uncharacterized or hypothetical multidomain proteins, based primarily on circular permutation (CP) relationships. First, we propose an efficient algorithm for rapid identification of both exact and approximate CPs in multidomain proteins. Using the circular relations identified, we construct networks between multidomain proteins, based on which we perform functional annotation of multidomain proteins. We then extend the method to construct subnetworks for selected cancer subtypes, and performed prediction of potential link-ages between uncharacterized multidomain proteins and the selected cancer types. We include practical results showing the performance of the proposed methods