UNICORE and GRIP: experiences of grid middleware development

We describe our experiences with the UNICORE Grid environment. Several lessons of general applicability can be drawn in regard to user uptake and security. The principal lesson is that more effort should be taken to be made to meet the needs of the target user community of the middleware development. Novel workflow strategies, in particular, should not be imposed on an existing community

Semantically Resolving Type Mismatches in Scientific Workflows

Scientists are increasingly utilizing Grids to manage large data sets and execute scientific experiments on distributed resources. Scientific workflows are used as means for modeling and enacting scientific experiments. Windows Workflow Foundation (WF) is a major component of Microsoft’s .NET technology which offers lightweight support for long-running workflows. It provides a comfortable graphical and programmatic environment for the development of extended BPEL-style workflows. WF’s visual features ease the syntactic composition of Web services into scientific workflows but do nothing to assure that information passed between services has consistent semantic types or representations or that deviant flows, errors and compensations are handled meaningfully. In this paper we introduce SAWSDL-compliant annotations for WF and use them with a semantic reasoner to guarantee semantic type correctness in scientific workflows. Examples from bioinformatics are presented

Version Control in Online Software Repositories

Software version control repositories provide a uniform and stable interface to manage documents and their version histories. Unfortunately, Open Source systems, for example, CVS, Subversion, and GNU Arch are not well suited to highly collaborative environments and fail to track semantic changes in repositories. We introduce document provenance as our Description Logic framework to track the semantic changes in software repositories and draw interesting results about their historic behaviour using a rule-based inference engine. To support the use of this framework, we have developed our own online collaborative tool, leveraging the fluency of the modern WikiWikiWeb

Version Control in Online Software Repositories

Software version control repositories provide a uniform and stable interface to manage documents and their version histories. Unfortunately, Open Source systems, for example, CVS, Subversion, and GNU Arch are not well suited to highly collaborative environments and fail to track semantic changes in repositories. We introduce document provenance as our Description Logic framework to track the semantic changes in software repositories and draw interesting results about their historic behaviour using a rule-based inference engine. To support the use of this framework, we have developed our own online collaborative tool, leveraging the fluency of the modern WikiWikiWeb

Mitotic Regulation of Protein Kinase CK2

Protein kinase CK2 is a serine/threonine kinase with a multitude of substrates and roles in many cellular processes, including mitosis. CK2 is constitutively active, yet we hypothesize that CK2 is indeed regulated in mitosis through subtle means, enabling CK2 to perform its functions unique to cell division. Our aims were to examine the roles of mitotic phosphorylation, subcellular localization, and interplay with mitotic kinases in the regulation of CK2 activity. We first examined the role of four highly conserved mitotic phosphorylation sites located in the unique C-terminus of CK2α. Phosphospecific antibodies generated against the sites show that CK2α phosphorylation is temporally regulated and occurs during prophase and metaphase during normal mitotic progression. Proper phosphorylation of CK2α is required for proper mitotic progression, as stable cell lines expressing phosphorylation site mutants of CK2α display severe mitotic defects. We next examined the impact of these phosphorylation events on the subcellular localization of CK2. We show that CK2α, but not CK2α’, localizes to the mitotic spindle. Localization of CK2α to the mitotic spindle is phosphodependent, and requires the peptidyl-prolyl isomerase Pin1. These results are a rare example of functional divergence between the two catalytic isoforms of CK2, and suggest that the role of CK2α phosphorylation during mitosis is to promote localization of CK2 to the mitotic spindle. Finally, we examined the possibility that CK2 activity during mitosis is regulated through hierarchal phosphorylation events, wherein CK2 would phosphorylate proteins only after priming phosphorylation events catalyzed by other mitotic kinases, particularly Cdk1. As this phenomenon has never been systematically investigated, we have investigated the consensus requirements for CK2 primed phosphorylation, and in particular Cdk/CK2 hierarchical phosphorylation. A genome-wide search for potential mitotic substrates matching the consensus sequence suggests that Cdk1/CK2 hierarchical phosphorylation may indeed contribute to mitotic signaling, particularly on the mitotic spindle. Taken together, our results confirm the importance of CK2 in mitotic cell division, and highlight several examples of subtle regulation of CK2, through phosphorylation, subcellular localization, and interplay with other protein kinases. This helps explain how CK2, a constitutively active kinase, can participate in tightly regulated cellular processes like mitosis

SMT-Based Refutation of Spurious Bug Reports in the Clang Static Analyzer

We describe and evaluate a bug refutation extension for the Clang Static Analyzer (CSA) that addresses the limitations of the existing built-in constraint solver. In particular, we complement CSA's existing heuristics that remove spurious bug reports. We encode the path constraints produced by CSA as Satisfiability Modulo Theories (SMT) problems, use SMT solvers to precisely check them for satisfiability, and remove bug reports whose associated path constraints are unsatisfiable. Our refutation extension refutes spurious bug reports in 8 out of 12 widely used open-source applications; on average, it refutes ca. 7% of all bug reports, and never refutes any true bug report. It incurs only negligible performance overheads, and on average adds 1.2% to the runtime of the full Clang/LLVM toolchain. A demonstration is available at {\tt https://www.youtube.com/watch?v=ylW5iRYNsGA}.Comment: 4 page

A self consistent chemically stratified atmosphere model for the roAp star 10 Aquilae

Context: Chemically peculiar A type (Ap) stars are a subgroup of the CP2 stars which exhibit anomalous overabundances of numerous elements, e.g. Fe, Cr, Sr and rare earth elements. The pulsating subgroup of the Ap stars, the roAp stars, present ideal laboratories to observe and model pulsational signatures as well as the interplay of the pulsations with strong magnetic fields and vertical abundance gradients. Aims: Based on high resolution spectroscopic observations and observed stellar energy distributions we construct a self consistent model atmosphere, that accounts for modulations of the temperature-pressure structure caused by vertical abundance gradients, for the roAp star 10 Aquilae (HD 176232). We demonstrate that such an analysis can be used to determine precisely the fundamental atmospheric parameters required for pulsation modelling. Methods: Average abundances were derived for 56 species. For Mg, Si, Ca, Cr, Fe, Co, Sr, Pr, and Nd vertical stratification profiles were empirically derived using the ddafit minimization routine together with the magnetic spectrum synthesis code synthmag. Model atmospheres were computed with the LLModels code which accounts for the individual abundances and stratification of chemical elements. Results: For the final model atmosphere Teff=7550 K and log g=3.8 were adopted. While Mg, Si, Co and Cr exhibit steep abundance gradients Ca, Fe and Sr showed much wider abundance gradients between log tau_5000=-1.5 and 0.5. Elements Mg and Co were found to be the least stratified, while Ca and Sr showed strong depth variations in abundance of up to ~ 6 dex.Comment: 9 pages, 15 figure