Basic Results for Two Types of High-Level Replacement Systems1 1Research partially supported by the European Community under TMR Network GETGRATS and the ESPRIT Working Group APPLIGRAPH.

AbstractThe general idea of high-level replacement systems is to generalize the concept of graph transformation systems and graph grammars from graphs to all kinds of structures which are of interest in Computer Science and Mathematics. Within the algebraic approach of graph transformation this is possible by replacing graphs, graph morphisms, and pushouts (gluing) of graphs by objects, morphisms, and pushouts in a suitable category. Of special interest are categories for all kinds of labelled and typed graphs, hypergraphs, algebraic specifications and Petri nets. In this paper, we review the basic results for high-level replacement systems in the algebraic double-pushout approach in the symmetric case, where both rule morphisms belong to a distinguished class M . Moreover we present for the first time the asymmetric type of high-level replacement systems, where only the left rule morphism K → L belongs to M

NOViSE: a virtual natural orifice transluminal endoscopic surgery simulator

Purpose: Natural Orifice Transluminal Endoscopic Surgery (NOTES) is a novel technique in minimally invasive surgery whereby a flexible endoscope is inserted via a natural orifice to gain access to the abdominal cavity, leaving no external scars. This innovative use of flexible endoscopy creates many new challenges and is associated with a steep learning curve for clinicians. Methods: We developed NOViSE - the first force-feedback enabled virtual reality simulator for NOTES training supporting a flexible endoscope. The haptic device is custom built and the behaviour of the virtual flexible endoscope is based on an established theoretical framework – the Cosserat Theory of Elastic Rods. Results: We present the application of NOViSE to the simulation of a hybrid trans-gastric cholecystectomy procedure. Preliminary results of face, content and construct validation have previously shown that NOViSE delivers the required level of realism for training of endoscopic manipulation skills specific to NOTES Conclusions: VR simulation of NOTES procedures can contribute to surgical training and improve the educational experience without putting patients at risk, raising ethical issues or requiring expensive animal or cadaver facilities. In the context of an experimental technique, NOViSE could potentially facilitate NOTES development and contribute to its wider use by keeping practitioners up to date with this novel surgical technique. NOViSE is a first prototype and the initial results indicate that it provides promising foundations for further development

M-adhesive transformation systems with nested application conditions. Part 1: parallelism, concurrency and amalgamation

Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG geförderten) Allianz- bzw. Nationallizenz frei zugänglich.This publication is with permission of the rights owner freely accessible due to an Alliance licence and a national licence (funded by the DFG, German Research Foundation) respectively.Nested application conditions generalise the well-known negative application conditions and are important for several application domains. In this paper, we present Local Church–Rosser, Parallelism, Concurrency and Amalgamation Theorems for rules with nested application conditions in the framework of M-adhesive categories, where M-adhesive categories are slightly more general than weak adhesive high-level replacement categories. Most of the proofs are based on the corresponding statements for rules without application conditions and two shift lemmas stating that nested application conditions can be shifted over morphisms and rules

Seamless Coarse Grained Parallelism Integration in Intensive Bioinformatics Workflows

To be easily constructed, shared and maintained, complex in silico bioinformatics analysis are structured as workflows. Furthermore, the growth of computational power and storage demand from this domain, requires workflows to be efficiently executed. However, workflow performances usually rely on the ability of the designer to extract potential parallelism. But atomic bioinformatics tasks do not often exhibit direct parallelism which may appears later in the workflow design process. In this paper, we propose a Model-Driven Architecture approach for capturing the complete design process of bioinformatics workflows. More precisely, two workflow models are specified: the first one, called design model, graphically captures a low throughput prototype. The second one, called execution model, specifies multiple levels of coarse grained parallelism. The execution model is automatically generated from the design model using annotation derived from the EDAM ontology. These annotations describe the data types connecting differents elementary tasks. The execution model can then be interpreted by a workflow engine and executed on hardware having intensive computation facility

An asynchronous and task-based implementation of Peridynamics utilizing HPX -- the C++ standard library for parallelism and concurrency

On modern supercomputers, asynchronous many task systems are emerging to address the new architecture of computational nodes. Through this shift of increasing cores per node, a new programming model with the focus on handle the fine-grain parallelism of this increasing amount of cores per computational node is needed. Asynchronous Many Task (AMT) run time systems represent an emerging paradigm for addressing fine-grain parallelism since they handle the increasing amount of threads per node and concurrency. HPX, a open source C++ standard library for parallelism and concurrency, is one AMT which is confirm with the C++ standard. Which means that HPX's Application Programming Interface (API) is confirm with its definition by the C++ standard committee. For example for the concept of futurization the hpx:future can be replaced by std::future without breaking the API. Peridynamics is a non-local generalization of continuum mechanics tailored to address discontinuous displacement fields arising in fracture mechanics. As many non-local approaches, peridynamics requires considerable computing resources to solve practical problems. This paper investigates the implementation of a peridynamics EMU nodal discretization in an asynchronous task-based fashion. The scalability of asynchronous task-based implementation is to be in agreement with theoretical estimations. In addition, to the scalabilty the code is convergent for implicit time integration and recovers theoretical solutions. Explicit time integration, convergence results are presented to showcase the agreement of results with theoretical claims in previous works