Eighth Workshop and Tutorial on Practical Use of Coloured Petri Nets and the CPN Tools, Aarhus, Denmark, October 22-24, 2007

This booklet contains the proceedings of the Eighth Workshop on Practical Use of Coloured Petri Nets and the CPN Tools, October 22-24, 2007. The workshop is organised by the CPN group at the Department of Computer Science, University of Aarhus, Denmark. The papers are also available in electronic form via the web pages: http://www.daimi.au.dk/CPnets/workshop0

Modeling biochemical transformation processes and information processing with Narrator

BACKGROUND: Software tools that model and simulate the dynamics of biological processes and systems are becoming increasingly important. Some of these tools offer sophisticated graphical user interfaces (GUIs), which greatly enhance their acceptance by users. Such GUIs are based on symbolic or graphical notations used to describe, interact and communicate the developed models. Typically, these graphical notations are geared towards conventional biochemical pathway diagrams. They permit the user to represent the transport and transformation of chemical species and to define inhibitory and stimulatory dependencies. A critical weakness of existing tools is their lack of supporting an integrative representation of transport, transformation as well as biological information processing. RESULTS: Narrator is a software tool facilitating the development and simulation of biological systems as Co-dependence models. The Co-dependence Methodology complements the representation of species transport and transformation together with an explicit mechanism to express biological information processing. Thus, Co-dependence models explicitly capture, for instance, signal processing structures and the influence of exogenous factors or events affecting certain parts of a biological system or process. This combined set of features provides the system biologist with a powerful tool to describe and explore the dynamics of life phenomena. Narrator's GUI is based on an expressive graphical notation which forms an integral part of the Co-dependence Methodology. Behind the user-friendly GUI, Narrator hides a flexible feature which makes it relatively easy to map models defined via the graphical notation to mathematical formalisms and languages such as ordinary differential equations, the Systems Biology Markup Language or Gillespie's direct method. This powerful feature facilitates reuse, interoperability and conceptual model development. CONCLUSION: Narrator is a flexible and intuitive systems biology tool. It is specifically intended for users aiming to construct and simulate dynamic models of biology without recourse to extensive mathematical detail. Its design facilitates mappings to different formal languages and frameworks. The combined set of features makes Narrator unique among tools of its kind. Narrator is implemented as Java software program and available as open-source from

Scientific Workflow Scheduling for Cloud Computing Environments

The scheduling of workflow applications consists of assigning their tasks to computer resources to fulfill a final goal such as minimizing total workflow execution time. For this reason, workflow scheduling plays a crucial role in efficiently running experiments. Workflows often have many discrete tasks and the number of different task distributions possible and consequent time required to evaluate each configuration quickly becomes prohibitively large. A proper solution to the scheduling problem requires the analysis of tasks and resources, production of an accurate environment model and, most importantly, the adaptation of optimization techniques. This study is a major step toward solving the scheduling problem by not only addressing these issues but also optimizing the runtime and reducing monetary cost, two of the most important variables. This study proposes three scheduling algorithms capable of answering key issues to solve the scheduling problem. Firstly, it unveils BaRRS, a scheduling solution that exploits parallelism and optimizes runtime and monetary cost. Secondly, it proposes GA-ETI, a scheduler capable of returning the number of resources that a given workflow requires for execution. Finally, it describes PSO-DS, a scheduler based on particle swarm optimization to efficiently schedule large workflows. To test the algorithms, five well-known benchmarks are selected that represent different scientific applications. The experiments found the novel algorithms solutions substantially improve efficiency, reducing makespan by 11% to 78%. The proposed frameworks open a path for building a complete system that encompasses the capabilities of a workflow manager, scheduler, and a cloud resource broker in order to offer scientists a single tool to run computationally intensive applications

A framework for automated conflict detection and resolution in medical guidelines

This research is supported by the MRC-funded UK Research and Innovation grant MR/S003819/1 and by EPSRC grant EP/M014290/1.Common chronic conditions are routinely treated following standardised procedures known as clinical guidelines. For patients suffering from two or more chronic conditions, known as multimorbidity, several guidelines have to be applied simultaneously, which may lead to severe adverse effects when the combined recommendations and prescribed medications are inconsistent or incomplete. This paper presents an automated formal framework to detect, highlight and resolve conflicts in the treatments used for patients with multimorbidities focusing on medications. The presented extended framework has a front-end which takes guidelines captured in a standard modelling language and returns the visualisation of the detected conflicts as well as suggested alternative treatments. Internally, the guidelines are transformed into formal models capturing the possible unfoldings of the guidelines. The back-end takes the formal models associated with multiple guidelines and checks their correctness with a theorem prover, and inherent inconsistencies with a constraint solver. Key to our approach is the use of an optimising constraint solver which enables us to search for the best solution that resolves/minimises conflicts according to medication efficacy and the degree of severity in case of harmful combinations, also taking into account their temporal overlapping. The approach is illustrated throughout with a real medical example.Publisher PDFPeer reviewe

Computational Methods in Science and Engineering : Proceedings of the Workshop SimLabs@KIT, November 29 - 30, 2010, Karlsruhe, Germany

In this proceedings volume we provide a compilation of article contributions equally covering applications from different research fields and ranging from capacity up to capability computing. Besides classical computing aspects such as parallelization, the focus of these proceedings is on multi-scale approaches and methods for tackling algorithm and data complexity. Also practical aspects regarding the usage of the HPC infrastructure and available tools and software at the SCC are presented

Model-Based Design for High-Performance Signal Processing Applications

Developing high-performance signal processing applications requires not only effective signal processing algorithms but also efficient software design methods that can take full advantage of the available processing resources. An increasingly important type of hardware platform for high-performance signal processing is a multicore central processing unit (CPU) combined with a graphics processing unit (GPU) accelerator. Efficiently coordinating computations on both the host (CPU) and device (GPU), and managing host-device data transfers are critical to utilizing CPU-GPU platforms effectively. However, such coordination is challenging for system designers, given the complexity of modern signal processing applications and the stringent constraints under which they must operate. Dataflow models of computation provide a useful framework for addressing this challenge. In such a modeling approach, signal processing applications are represented as directed graphs that can be viewed intuitively as high-level signal flow diagrams. The formal, high-level abstraction provided by dataflow principles provides a useful foundation to investigate model-based analysis and optimization for new challenges in design and implementation of signal processing systems. This thesis presents a new model-based design methodology and an evolution of three novel design tools. These contributions provide an automated design flow for high performance signal processing. The design flow takes high-level dataflow representations as input and systematically derives optimized implementations on CPU-GPU platforms. The proposed design flow and associated design methodology are inspired by a previously-developed application programming interface (API) called the Hybrid Task Graph Scheduler (HTGS). HTGS was developed for implementing scalable workflows for high-performance computing applications on compute nodes that have large numbers of processing cores, and that may be equipped with multiple GPUs. However, HTGS has a limitation due to its relatively loose use of dataflow techniques (or other forms of model-based design), which results in a significant designer effort being required to apply the provided APIs effectively. The main contributions of the thesis are summarized as follows: (1) Development of a companion tool to HTGS that is called the HTGS Model-based Engine (HMBE). HMBE introduces novel capabilities to automatically analyze application dataflow graphs and generate efficient schedules for these graphs through hybrid compile-time and runtime analysis. The systematic, model-based approaches provided by HMBE enable the automation of complex tasks that must be performed manually when using HTGS alone. We have demonstrated the effectiveness of HMBE and the associated model-based design methodology through extensive experiments involving two case studies: an image stitching application for large scale microscopy images, and a background subtraction application for multispectral video streams. (2) Integration of HMBE with HTGS to develop a new design tool for the design and implementation of high-performance signal processing systems. This tool, called HMBE-Integrated-HTGS (HI-HTGS), provides novel capabilities for model-based system design, memory management, and scheduling targeted to multicore platforms. HMBE takes as input a single- or multi-dimensional dataflow model of the given signal processing application. The tool then expands the dataflow model into an expanded representation that exposes more parallelism and provides significantly more detail on the interactions between different application tasks (dataflow actors). This expanded representation is derived by HI-HTGS at compile-time and provided as input to the HI-HTGS runtime system. The runtime system in turn applies the expanded representation to guide dynamic scheduling decisions throughout system execution. (3) Extension of HMBE to the class of CPU-GPU platforms motivated above. We call this new model-based design tool the CPU-GPU Model-Based Engine (CGMBE). CGMBE uses an unfolded dataflow graph representation of the application along with thread-pool-based executors, which are optimized for efficient operation on the targeted CPU-GPU platform. This approach automates complex aspects of the design and implementation process for signal processing system designers while maximizing the utilization of computational power, reducing the memory footprint for both the CPU and GPU, and facilitating experimentation for tuning performance-oriented designs