René Jäkel

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.

Standards-based metadata management for molecular simulations

State‐of‐the‐art research in a variety of natural sciences depends heavily on methods of computational chemistry, for example, the calculation of the properties of materials, proteins, catalysts, and drugs. Applications providing such methods require a lot of expertise to handle their complexity and the usage of high‐performance computing. The MoSGrid (molecular simulation grid) infrastructure relieves this burden from scientists by providing a science gateway, which eases access to and usage of computational chemistry applications. One of its cornerstones is the molecular simulations markup language (MSML), an extension of the chemical markup language. MSML abstracts all chemical as well as computational aspects of simulations. An application and its results can be described with common semantics. Using such application, independent descriptions users can easily switch between different applications or compare them. This paper introduces MSML, its integration into a science gateway, and its usage for molecular dynamics, quantum chemistry, and protein docking. Copyright

Improved study of a possible Θ+ production in the pp→pK0Σ+ reaction with the COSY-TOF spectrometer

Abstract The p p → p K 0 Σ + reaction was investigated with the TOF spectrometer at COSY at 3.059 GeV / c incident beam momentum. The main objective was to clarify whether or not a narrow exotic S = + 1 resonance, the Θ + pentaquark, is populated at 1.53 GeV / c 2 in the p K 0 subsystem with a data sample of much higher statistical significance compared to the previously reported data in this channel. An analysis of these data does not confirm the existence of the Θ + pentaquark. This is expressed as an upper limit for the cross section σ ( p p → Σ + Θ + ) 0.15 μb at the 95% confidence level.

Systematic study of the pp

A systematic study of the production of

\rightarrow

\omega

pp

-mesons in proton-proton collisions was carried out in a kinematically complete experiment at three excess energies (

\omega

\varepsilon

reaction

= 92, 128, 173 MeV). Both protons were detected using the large-acceptance COSY-TOF spectrometer at an external beam line at the Cooler Synchrotron COSY at Forschungszentrum Jülich. The total cross-section, angular distributions of both

The pK0Σ+ final state in proton-proton collisions

\omega

Towards Generic Metadata Management in Distributed Science Gateway Infrastructures

-mesons and protons were measured and presented in various reference frames such as the overall CMS, helicity and Jackson frame. In addition, the orientation of the