S. Bozic

A service-oriented framework for integration of domain-specific data models in scientific workflows

Abstract Managing data exchange in scientific workflow simulations is a challenge for which existing solutions have only limited success. Basing on a data-model approach we developed a service-oriented, platform- and language-independent framework which provides seamless access for heterogeneous applications to data storage resources distributed over grids and clouds. After implementing a working prototype of the framework we demonstrated its benefits for a complex workflow application from the domain of multiscale materials modeling. Because of its generic architecture and wide standards conformity the framework can be deployed as grid or cloud middleware for various other domains of computational science to enable rapid development of complex workflow applications.

Sustainable support for WLCG through the EGI distributed infrastructure

Grid computing is now in a transition phase from development in research projects to routine usage in a sustainable infrastructure. This is mirrored in Europe by the transition from the series of EGEE projects to the European Grid Initiative (EGI). EGI aims at establishing a self-sustained grid infrastructure across Europe. The main building blocks of EGI are the national grid initiatives in the participating countries and a central coordinating institution (EGI.eu). The middleware used is provided by consortia outside of EGI. Also the user communities are organized separately from EGI. The transition to a self-sustained grid infrastructure is aided by the EGI-InSPIRE project, aiming at reducing the project-funding needed to run EGI over the course of its four year duration. Providing user support in this framework poses new technical and organisational challenges as it has to cross the boundaries of various projects and infrastructures. The EGI user support infrastructure is built around the Gobal Grid User Support system (GGUS) that was also the basis of user support in EGEE. Utmost care was taken that during the transition from EGEE to EGI support services which are already used in production were not perturbed. A year into the EGI-InSPIRE project, in this paper we would like to present the current status of the user support infrastructure provided by EGI for WLCG, new features that were needed to match the new infrastructure, issues and challenges that occurred during the transition and give an outlook on future plans and developments.

Integration of eSBMTools into the MoSGrid Portal Using the gUSE Technology

Native structure based models are a broadly used technique in bio molecular simulation allowing understanding of complex processes in the living cell involving bio macromolecules. Based on energy landscape theory and the principle of minimal frustration, these models find wide application in simulating complex biological processes as diverse as protein or RNA folding and assembly, conformational transitions associated with allostery, to structure prediction. To allow rapid adoption by scientists, especially experimentalists, having no background in programming or high performance computing, we here provide an effective user interface to existing applications running on distributed computing resources. Based on the gateway technologies WS-PGRADE and gUSE, we developed a web-based community application service for native structure based modeling by integrating a powerful user interface to an existing UNICORE grid application based on the eSBMTools package. The eSBM port let has been integrated into the MoSGrid portal and is immediately accessible for the bioinformatics, biophysics and structural biology communities.

Native structure-based modeling and simulation of biomolecular systems per mouse click

BackgroundMolecular dynamics (MD) simulations provide valuable insight into biomolecular systems at the atomic level. Notwithstanding the ever-increasing power of high performance computers current MD simulations face several challenges: the fastest atomic movements require time steps of a few femtoseconds which are small compared to biomolecular relevant timescales of milliseconds or even seconds for large conformational motions. At the same time, scalability to a large number of cores is limited mostly due to long-range interactions. An appealing alternative to atomic-level simulations is coarse-graining the resolution of the system or reducing the complexity of the Hamiltonian to improve sampling while decreasing computational costs. Native structure-based models, also called Gō-type models, are based on energy landscape theory and the principle of minimal frustration. They have been tremendously successful in explaining fundamental questions of, e.g., protein folding, RNA folding or protein function. At the same time, they are computationally sufficiently inexpensive to run complex simulations on smaller computing systems or even commodity hardware. Still, their setup and evaluation is quite complex even though sophisticated software packages support their realization.ResultsHere, we establish an efficient infrastructure for native structure-based models to support the community and enable high-throughput simulations on remote computing resources via GridBeans and UNICORE middleware. This infrastructure organizes the setup of such simulations resulting in increased comparability of simulation results. At the same time, complete workflows for advanced simulation protocols can be established and managed on remote resources by a graphical interface which increases reusability of protocols and additionally lowers the entry barrier into such simulations for, e.g., experimental scientists who want to compare their results against simulations. We demonstrate the power of this approach by illustrating it for protein folding simulations for a range of proteins.ConclusionsWe present software enhancing the entire workflow for native structure-based simulations including exception-handling and evaluations. Extending the capability and improving the accessibility of existing simulation packages the software goes beyond the state of the art in the domain of biomolecular simulations. Thus we expect that it will stimulate more individuals from the community to employ more confidently modeling in their research.

An EMF-based toolkit for creation of domain-specific data services

Development of composite workflow applications in science and engineering is troublesome and costly due to high heterogeneity of data representations and data access interfaces of the underlying individual components. As an effective solution we present a generic toolkit enabling domain experts to develop data models and automatically generate a self-contained data access service. We defined a custom metamodel based on Ecore which can be readily used to create domain-specific data models. Using the generated data access service, instances of the modeled data residing on heterogeneous and distributed resources, such as databases and cloud data stores, are accessible from the individual application components via a language-independent Web service interface. We discuss the framework architecture, the toolkit implementation, the deployment process, as well as the performance of the data access service. Workflow designers as target users would benefit from the toolkit by using it for rapid and cost-efficient application integration.