Miklos Kozlovszky

WS-PGRADE/gUSE Generic DCI Gateway Framework for a Large Variety of User Communities

The WS-PGRADE/gUSE generic DCI gateway framework has been developed to support a large variety of user communities. It provides a generic purpose, workflow-oriented graphical user interface to create and run workflows on various DCIs including clusters, Grids, desktop Grids and clouds. The framework can be used by NGIs to support small user communities who cannot afford to develop their own customized science gateway. The WS-PGRADE/gUSE framework also provides two API interfaces (Application Specific Module API and Remote API) to create application-specific science gateways according to the needs of different user communities. The paper describes in detail the workflow concept of WS-PGRADE, the DCI Bridge service that enables access to most of the popular European DCIs and the Application Specific Module and Remote API concepts to generate application-specific science gateways.

A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics

Structural bioinformatics applies computational methods to analyze and model three-dimensional molecular structures. There is a huge number of applications available to work with structural data on large scale. Using these tools on distributed computing infrastructures (DCIs), however, is often complicated due to a lack of suitable interfaces. The MoSGrid (Molecular Simulation Grid) science gateway provides an intuitive user interface to several widely-used applications for structural bioinformatics, molecular modeling, and quantum chemistry. It ensures the confidentiality, integrity, and availability of data via a granular security concept, which covers all layers of the infrastructure. The security concept applies SAML (Security Assertion Markup Language) and allows trust delegation from the user interface layer across the high-level middleware layer and the Grid middleware layer down to the HPC facilities. SAML assertions had to be integrated into the MoSGrid infrastructure in several places: the workflow-enabled Grid portal WS-PGRADE (Web Services Parallel Grid Runtime and Developer Environment), the gUSE (Grid User Support Environment) DCI services, and the cloud file system XtreemFS. The presented security infrastructure allows a single sign-on process to all involved DCI components and, therefore, lowers the hurdle for users to utilize large HPC infrastructures for structural bioinformatics.

ENABLING GENERIC DISTRIBUTED COMPUTING INFRASTRUCTURE COMPATIBILITY FOR WORKFLOW MANAGEMENT SYSTEMS

Solving workflow management system’s Distributed Computing Infrastructure (DCI) incompatibility and their workflow interoperability issues are very challenging and complex tasks. Workflow management systems (and therefore their workflows, workflow developers and also their end-users) are bounded tightly to some limited number of supported DCIs, and efforts required to allow additional DCI support. In this paper we are specifying a concept how to enable generic DCI compatibility for grid workflow management systems (such as ASKALON, MOTEUR, gUSE/WS-PGRADE, etc.) on job and indirectly on workflow level. To enable DCI compatibility among the different workflow management systems we have developed the DCI Bridge software solution. In this paper we will describe its internal architecture, provide usage scenarios to show how the developed service resolve the DCI interoperability issues between various middleware types. The generic DCI Bridge service enables the execution of jobs onto the existing major DCI platforms (such as Service Grids (Globus Toolkit 2 and 4, gLite, ARC, UNICORE), Desktop Grids, Web services, or even cloud based DCIs).

Parallel biomedical image processing with GPGPUs in cancer research

The main aim of this work is to show, how GPGPUs can facilitate certain type of image processing methods. The software used in this paper is used to detect special tissue part, the nuclei on (HE - hematoxilin eosin) stained colon tissue sample images. Since pathologists are working with large number of high resolution images - thus require significant storage space -, one feasible way to achieve reasonable processing time is the usage of GPGPUs. The CUDA software development kit was used to develop processing algorithms to NVIDIA type GPUs. Our work focuses on how to achieve better performance with coalesced global memory access when working with three-channel RGB tissue images, and how to use the on-die shared memory efficiently.

Combined Health Monitoring and Emergency Management through Android Based Mobile Device for Elderly People

We have developed a combined Android based mobile data acquisition (DAQ) and emergency management solution, which can collect information remotely from patient and send the information towards to the medical data and dispatcher centre for further processing. The mobile device is capable to collect information from various sensors via Bluetooth and USB connection, and further more able to capture and forward manually initiated alarm signals in case of an emergency situation. Beside the alarm signal the system collects and sends information about the patient’s location, and it also enables two ways audio communication between the central dispatcher and the patient automatically. The developed software solution is suitable for different skilled users. Its user interface is highly configurable to support elderly persons (high contrast, huge characters, simple UI, etc.), and also provides advanced mode for the “power” users. The developed system becomes part of our testing program, which is carried out in our Hungarian Living Lab infrastructure. The combination of a mobile DAQ device and mobile emergency alarm device within a single software solution enables care givers to provide better and more effective services in elderly patient monitoring.

Preparing initial population of genetic algorithm for region growing parameter optimization

The processing of microscopic tissue images is nowadays done more and more using special immunodiagnostic-evaluation software products. Often to evaluate the samples, the first step is determining the number and location of cell nuclei. To do this, one of the most promising methods is the region growing, but this algorithm is very sensitive to the appropriate setting of different parameters. Due to the large number of parameters and due to the big set of possible values setting those parameters manually is a quite hard task, so we developed a genetic algorithm to optimize these values. The first step of the development is the statistical analysis of the parameters, and the determination of the important features, to extract valuable information for a to-be-implemented genetic algorithm that will perform the optimization.

Enabling OMNeT++-based simulations on grid systems

Simulations are typically computationally intensive problems, and lend themselves for execution on large-scale PC clusters or grids. Using grid infrastructure for discrete event simulation is currently not prevalent, but making grid technology easily accessible to simulation users can change that picture significantly. In this paper we give a detailed overview how the OMNeT++ simulation framework was ported onto a gLite-based grid infrastructure. The porting of the simulation framework to the grid infrastructure was supported by the GASUC Team of the EGEE III project. Later on in the paper we show an example grid service which is able to execute queuing network simulations, and assess its performance on the grid.

Minimal sufficient information about the scientific workflows to create reproducible experiment

The reproducibility of an in-silico experiment is a great challenge because of the parallel and distributed environment and the complexity of the scientific workflows. In order to solve such problems on one hand provenance data has to be captured about the dataflow, the ancestry of the results and the environment of the execution, on the other hand description data has to be collected from the scientist and stored about the essential details, the types and samples of input/output data, and the operation of the experiment. The ultimate goal of our work is to propose a minimal dataset for recording and reporting scientific workflow based experiment, which will facilitate the reproducibility of such experiments, the public repositories and enable to share and reuse the scientific results. One part of the dataset can be filled in manually by the scientist, certain part can be filled in automatically by the system and other part can be filled in from provenance data.

A novel cloud bursting technique

Companies (even SMEs) are roused by the success and potentials of the public clouds and they build their own private cloud infrastructures. Thus, they open the door to an easier and more flexible way for outsourcing their IT services than before. However, the currently available software solutions still do not provide seamless extensibility by cloud bursting. Therefore, the IaaS users have to prepare their images in every infrastructure. This paper presents the criteria for idealistic cloud bursting and introduces a method that overcomes the current cloud bursting issues (e.g. different administration domains and networking policies). The proposed technique uses nested virtualization, that reduces the complexity of the cloud bursting procedure. Furthermore, we have evaluated the applicability of our design by performance tests. The evaluation showed that the seamless extensibility has a cost of 5-10% overhead on the deployment time.

A Science Gateway Getting Ready for Serving the International Molecular Simulation Community

The project MoSGrid (Molecular Simulation Grid) has been developing a web-based science gateway supporting the community with various services for quantum chemistry, molecular modeling, and docking. Users gain access to distributed computing infrastructures (DCIs) via intuitive user interfaces for sophisticated tools, specialized workflows, and distributed repositories. Currently, the MoSGrid community consists of about 120 users from a number of fields related to chemistry and bioinformatics located in Germany. However, the underlying security infrastructure is generally applicable and can be deployed in arbitrary projects. MoSGrid intends to address the international community by participating in the EU-projects SCI-BUS (Scientific gateway Based User Support) and ER-flow (Building an European Research Community through Interoperable Workflows and Data), and collaborating with the EU-project EDGI (European Desktop Grid Initiative).