The non-invasive method to track fibers of the human brain by analyzing diffusion weighted magnetic resonance images improves research of human brain structures and becomes therefore increasingly important. With fiber tracking, a connectivity map which depicts the degree of connectivity of the single voxels can be generated and used to improve knowledge about the human brain. Several tools exist to produce connectivity maps. One of them is part of the FMRIB Software Library (FSL) and free for non-commercial purposes. Due to long and therefore impracticable computing time on small computer cluster solutions, a GUI and the necessary software were implemented for the German MediGRID infrastructure. This was achieved by using wrapper scripts and a workflow for the Generic Workflow Execution Service (GWES). The solution is about 15 times faster than a small local cluster installation, depending on the number of employed MediGRID resources. This enables processing of connectivity maps for practical use in biomedical research. By using the D-Grid infrastructure, this solution is also suitable for small institutes without compute center capacities. For usability reasons, the GUI ConBrain was developed.

The Charité Grid Portal combines portal components from different groups and projects to provide domain researchers a gateway to Grid-based biomedical applications. Trusted users can securely access and employ Grid resources and services. In this paper, five portal components are presented: (1) The credential management administrates the user-credentials and authenticates them to the Grid. (2) The brain imaging data analysis (FSL) submits workflows to the Grid as part of Medical Image processing. (3) The integrated web services of Generic Workflow Execution Service (GWES) manage workflows executed by users in the Grid. (4) The data management component provides secure and efficient data management in a Grid environment, and enables high-speed data transports between user and Grid. (5) The lung sound analysis application provides twofold-pseudonymization before data-transferred to the Grid. The implementation as standardized portlets allows easy integration of specific components into different Grid portals such as the VO specific MediGRID and PneumoGrid portals.

This article describes a collaboration methodology for virtual organizations where the processes can be automatically executed using a hybrid web service, grid or cloud resources. Typically, the process of deriving executable workflows from process models is cumbersome and can be automated only in part or specific to a particular distributed system. The approach introduced in this paper, exemplified by the construction industry field, integrates existing technology within a process-centric framework. The solution on the basis of a hybrid system architecture in conjunction with semantic methods for consistency saving and the framework for modeling VO processes and their automated transformation and execution are discussed in detail.

Einleitung: Die Nutzung von Telemedizin und Grid-Technologie in klinischer Forschung und Versorgung nimmt weltweit zu. Das Projekt PneumoGrid, vom BMBF im Rahmen der D-GRID-Initiative gefördert, entwickelt eine gridbasierte Infrastruktur zur Unterstützung von Diagnostik und Therapie der COPD. Dabei soll die Lungenventilation u.a. mittels Lungengeräuschanalyse visualisiert werden. Die Signalanalyse der Datenmengen wird mittels Gridtechnologie umgesetzt. Methodik: Griddienste werden entwickelt, welche die rechtlichen Rahmenbedingungen und Standards für multizentrische Studien und klinische Anwendungen erfüllen. Wir nutzen zur Validierung der Services die PneumoGrid-Technologie zur Analyse von lokalen Tracheal- und Lungengeräuschen, welche mit der PulmoTrack®-Hardware mittels eines für die Langzeitregistrierung geeigneten Systems (dem WHolter) bei 10 gesunden Probanden im Alter zwischen 18–50 Jahren während einer 6–8-stündigen nächtlichen Schlafphase aufgezeichnet wurden. Ergebnisse: Detaillierte Regelungen zur Erhöhung der Datensicherheit im Grid sind zu beachten. Neben einem Audit- Trail ist eine durchgängige zweistufige Pseudonymisierung entsprechend der generischen Datenschutzkonzepte der Telematikplattform für medizinische Forschungsnetze e.V. geplant, mit gridweit nur temporär gültigen Pseudonymen. Prinzipiell sollen aus Datenschutzgründen sensible Daten nur temporär im Grid gespeichert werden. Diskussion: Die Analyse lokaler Lungengeräusche erweitert das Spektrum der diagnostischen Methoden durch die Möglichkeit, die Lungenventilation über lange Zeiträume, z.B. während der Schlafphase, zu messen. Neben der Unterstützung der klinischen Versorgung und Nutzen für die akademische Forschung ergeben sich potentielle Nutzungsmöglichkeiten für Industriepartner (Medizintechnik und Pharmaunternehmen). Die Implementierung einer Sicherheitsinfrastruktur zum Datenschutz und Dokumentation der Verarbeitungswege ist Voraussetzung für den Erfolg von PneumoGrid.

Scientific workflow systems often operate in highly unreliable, heterogeneous and dynamic environments, and have accordingly incorporated different fault tolerance techniques. We propose an exception-handling mechanism, based on techniques adopted in programming languages, for modifying at run-time the structure of a workflow. In contrast to other proposals that achieve the required flexibility by means of the infrastructure, our proposal expresses the exception-handling mechanism within the workflow language—primarily as two exception-handling patterns that are exclusively based on the Reference Nets-within-Nets formalism (a specific type of Petri nets). When an exception is detected, a workflow in our approach can be re-written (replaced), based on the particular failure condition that has been detected. This enables workflow users to have better control and understanding of the behaviour of their workflow without having to be aware of the underlying infrastructure. Copyright © 2009 John Wiley & Sons, Ltd.

In this paper, we describe the grid integration of medical image processing applications as grid workflows. The workflow management system is able to execute all tasks related to grid communication, such as authorization, scheduling and monitoring. It remains to the developer to make the code accessible for the workflow manager, and to define, what to do with it. Coarse-grained parallelization of processing steps for runtime reduction can easily be realized. We describe the procedure how to port the code to the grid and show exemplarily the integration of segmentation and registration algorithms for transrectal ultrasound guided prostate biopsies.

Grid-Middleware erlaubt den verteilten Zugriff auf Softwareund Hardwareressourcen, indem sie prinzipiell solche Ressourcen beschreibt und einem Anwender über Protokoll und API auf seinem Arbeitsplatz zur Verfügung stellt. Ressourcen liegen auf entfernten Knoten, ihr Zustand ist jederzeit ermittelbar und Daten werden über definierte Protokolle ausgetauscht. Höherwertige Anwendungen werden durch Aggregation einzelner Ressourcen in Workflows komponiert, die durch entsprechende Werkzeuge vom Anwender modellierbar sind. Im Bereich „Kooperative Informationssysteme“ auf Basis einer SOA benötigt man aber eine Architektur, die es dem Anwender erlaubt, durch Formulierung eines Informationsinteresses einen dynamischen evtl. zyklischen Workflow zu starten, der zum Anfragezeitpunkt noch gar nicht bekannt ist, sondern vom System durch Vergleich der verfügbaren Ressourcen mit den angefragten Informationsobjekten erzeugt wird. Statische Workflowsysteme z.B. auf Basis von WS-BPEL (Web Services Business Process Execution Language) eignen sich nicht für diese Anforderung. Stattdessen verwenden wir einen Ansatz aus dem Bereich semantische Webservices, um zielgetriebene verteilte Aufgabenverarbeitung in einem Anwendungsbereich kooperativer Informationssysteme für die Luftbildauswertung zu realisieren. Jedoch berücksichtigen die Standardframeworks aus diesem Bereich keine Grid-Dienste und die dort eingeführten Formate, eine Integration ist aufgrund derselben technischen Schnittstelle (WSRF – Web Service Resource Framework) aber möglich. Die Hauptaufgabe dafür liegt in der Integration der Beschreibungselemente der Grid-Ressourcen in den Erzeugungsprozess des Workflows als nicht-funktionale Parameter. Die hier vorgestellten Arbeiten sind Bestandteil zu einem möglichen Semantik Grid Ansatz als Basis für eine service-orientierte Architektur.

This paper addresses the process-oriented collaboration based on a grid-based platform for the support of virtual organizations (VO), illustrated on the example of the construction industry. Distributed, organizational and IT-structures of teams involved in vintage complex projects cannot be managed with conventional methods in an appropriate manner. Both using a grid platform and grid-based services, in conjunction with semantic methods for consistency saving and goal-oriented process management can increase the efficiency of collaboration processes in large-scale projects. A hybrid gridand web service-based architecture for the next generation of VO service and a gateway solution was developed integrating the process-oriented perspective and prototypically implemented. The problem, as well as the solution on the basis of the hybrid system architecture combing the benefits of the cutting-edge technologies, the methodical concept for modeling VO processes and their automated execution on a grid platform are discussed in detail.

Many scenarios in medical research are predestined for grid computing. Large amounts of data in complex medical image, biosignal and genome processing demand large computing power and data storage. Integration of distributed, heterogeneous data, e.g. correlation between phenotype and genotype data are playing an essential part in life sciences. Sharing of specialized software, data and processing results for collaborative work are further tasks which would strongly benefit from the use of grid infrastructures. However, two major barriers are identified in existing grid environments that prevent extensive use within the life sciences community: Extended security requirements and appropriate usability. To meet these requirements, the MediGRID project is enhancing the basic D-Grid infrastructure along with the implementation of prototype applications from different fields of biomedical research. In this paper, we focus on the developments for ease-of-use under consideration of different aspects of security. They encompass not only security within the grid infrastructure, but also the boundary conditions of network security on the site of the research institutions. For medical grids, we propose a strictly web-portal-based access to grid resources for end-users, with user-guiding, application specific, graphical interfaces. Different levels of authorization are implemented, from fully authorized users to guests without certificate authentication in order to allow hands-on experience for potential grid users.

The analysis of biosignals, such as the electroencephalogram EEG or the electrocardiogram (ECG), is essential for diagnosis in many medical areas, in particular sleep medicine and sleep research. A standard method in this field is the polysomnography, a multidimensional biosignal recording during the whole bedtime phase. Within the SIESTA project, a European multicenter study, comprehensive clinical and polysommnographic records from over 300 persons has been collected. To make the data available for researchers as reference for clinical research and development of new analysis tools, the SIESTA database is implemented into a grid infrastructure. To date, the complete data is stored into the grid and different algorithms for automated ECG analysis are implemented. The database can be queried and the matching data can be analysed on record level and collection level. The application is modelled as a workflow and integrated into the grid using a workflow manager. A graphical user interface is implemented as a grid portlet. It allows the initialization of new computation tasks as well as the monitoring and result-retrieval from already launched analyses.

Image analysis has been strongly present in several healthgrid initiatives from the start, and today we find many imaging projects with successful grid implementations and developments. An example is the analysis of functional MRI data on grids, which has been successfully realized by several projects and that could be of interest for others. However, crossing the borders of existing grids is not trivial because the infrastructures being created for these projects differ, each adopting a (slightly) different software stack. This paper describes our early attempts to cross the borders between the German and Dutch grid infrastructures for medical imaging, motivated by a true wish to share expertise about fMRI analysis on grids between these two communities. We describe how we used off-the-shelf, production-level, grid technology to implement supporting mechanisms for cooperation in fMRI at several levels (users, data, software, workflows and computing resources). This simple exercise provided us valuable insights into the problems of crossing the borders of real grids from a user's perspective. Besides technical aspects, we observed that security and usability are very important for the success of inter-operation of Healthgrid.

Medical grid networks typically deal with extremely sensitive information and therefore require a special diligence in terms of security and reliability. This holds especially true in Medical Imaging, which is why the medical community long established DICOM (Digital Imaging and Communication in Medicine), a world-wide imaging and communication standard for secure and reliable data interchange. Most healthgrid projects today use DICOM with a combination of GridFTP and the Reliable-File-Transfer (RFT) webservice. Due to the multiple protocols and services involved, this solution is not ideally suited in terms of reliability or fault-tolerance. The proposed solution in this paper replaces the GridFTP combination by an end- to-end Grid-enhanced DICOM implementation and models the GridDICOM transfers as complex, Petri-Nets-based workflows. Based on these workflows, a respective workflow engine can autonomously and reliably control transfers including complex fault recovery and optimized routing strategies. A first prototype of the service, the components, and the respective workflows have been developed and successfully tested in MediGRID, the German grid network for life-sciences.

Workflow scheduling on the Grid becomes more challenging when multiple scheduling criteria are considered. Existing studies provide different approaches to the multi-criteria Grid workflow scheduling problem, and address different variants of the problem. A profound understanding of the problem’s nature can be an important step towards more generic scheduling approaches. Based on the related work and on our own experience, we propose several novel taxonomies of the problem, considering five facets: workflow model, scheduling criteria, scheduling process, resource model, and task model. We make a survey of the existing related work, and classify it according to the proposed taxonomies, identifying the most common use cases and the areas that have not been sufficiently explored yet.

In MediGRID a diverse spectrum of application scenarios from areas of bioinformatics, medical image processing, numerical simulations and clinical trials will be integrated into a Grid environment. In this paper we present the MediGRID infrastructure especially as required by medical image processing. Motivated by this selected application scenario the major MediGRID components i) enhanced security requirements ii) data management, iii) portal technology iv) workflow management and v) information service are discussed.

Scientific applications executed with modern distributed t echnologies tend to be computed on various, dispersed resources, and workflows become a natural method of describi ng them. This method of the functional application decomposition allows for fully manual design only to a certain level of complexity. However, the scientific simulations usually expose non-trivial processing logic inclu ding multiple distinct processing elements connected with complicated control patterns. Thus an environment for semi-automated and assisted composition and orchestration of such application workflows is desired. This report describe s the concept and design of such a platform that analyzes user requirements regarding application results and leads the user in the process of possible solution construction, d ynamic refinement and execution. The tools forming the presen ted system use domain-specific knowledge and employ several levels of workflow abstractness in order to deliver t he functionality in a more natural way for the human user. This work presents a real-life case study from the city traffi c simulation domain, in order to introduce subsequent steps of workflow orchestration. It also supplies a discussi on on existing similar systems for workflow orchestration and it finishes with a conclusions section.

One approach to Grid application programming is to implement services with often-used functionality on high-performance Grid hosts. Complex applications are created by using several services and specifying the workflow between them. We discuss how the workflow of Grid applications can be described easily as a High-Level Petri Net (HLPN), in order to orchestrate and execute distributed applications on the Grid automatically. Petri Nets provide an intuitive graphical workflow description, which is easier to use than script-based descriptions and is much more expressive than directed acyclic graphs (DAG). In addition, the workflow description can be analysed for certain properties such as deadlocks and liveness, using standard algorithms for HLPNs. We propose a platform-independent, XML-based language, called Grid Workflow Description Language (GWorkflowDL), and show how it can be adapted to particular Grid platforms. As two example target platforms, we discuss Java/RMI and the current WSRF standard.

The complexity and the dynamics of the Grid environment and of the emering workflow-based applications on the Grid require novel performance monitoring and analysis services in order to capture monitoring data at multiple levels of abstraction, to analyze the data and to correlate metrics among entities. In this paper, we present the design of distributed monitoring and performance analysis services in the K-WfGrid project. We give an overview of the architecture of the performance and monitoring services and discuss useful performance and dependability metrics for workflows in K-WfGrid. We describe basic system components including the monitoring and instrumentation service, the performance analysis service along with data representation and service interface.