Benchmarking triple stores with biological data

We have compared the performance of five non-commercial triple stores, Virtuoso-open source, Jena SDB, Jena TDB, SWIFT-OWLIM and 4Store. We examined three performance aspects: the query execution time, scalability and run-to-run reproducibility. The queries we chose addressed different ontological or biological topics, and we obtained evidence that individual store performance was quite query specific. We identified three groups of queries displaying similar behavior across the different stores: 1) relatively short response time, 2) moderate response time and 3) relatively long response time. OWLIM proved to be a winner in the first group, 4Store in the second, and Virtuoso in the third. Our benchmarking showed Virtuoso to be a very balanced performer – its response time was better than average for all the 24 queries; it showed a very good scalability and a reasonable run-to-run reproducibility

Visions for the field by a pioneer

Only Presentation No Abstrac

Neutral low-dimensional assemblies of a Mn(III) schiff base complex and octacyanotungstate(V) : synthesis, characterization, and magnetic properties

International audienceTwo novel low-dimensional molecular magnetic materials were prepared by the self-assembly of 3d- and 5d-metal complexes. These are the first neutral heterobimetallic cyanobridged compounds involving one anisotropic Mn(III) Schiff base complex and one octacyanotungstate(V) per molecular unit. A slow diffusion of the constituents’ solutions leads to the formation of the 0D crystalline complex 1, due to coordination of a water molecule to the Mn center, which prevents polymer formation. A rapid mixing of reagents results in the precipitation of the microcrystalline powder of complex 2, which based on the totality of experimental data, possesses a 1D polymeric structure. The magnetic studies have shown that antiferromagnetic exchange interactions prevail in 1 (J/kB = −13.1(7) K, D = −3.0(1.3) K, zJ' = −0.16(20) K and gav = 2.00(1)); while the presence of the significant intramolecular Mn(III)–W(V) ferromagnetic coupling through cyanide bridge is characteristic for 2 (J/kB = 46.1(5) K, gMn = 2.11(3), fixed gW = 2.0). Due to the weak interchain interactions, zJ′/kB = −0.8(2) K, and compound 2 is a metamagnet with the Néel temperature of 9.5 K undergoing a spin-flip transition at 2 kOe. The slow magnetization dynamics of 2 were investigated at a DC field of 0 and 2 kOe, giving the values of τ0 32(15) and 36(15) ps, respectively, well within the range typical for single-chain magnets (SCMs). The respective ∆τ/kB values were 48.4(1.2) and 44.9(1.0) K

Metarel: an Ontology to support the inferencing of Semantic Web relations within Biomedical Ontologies

While OWL, the Web Ontology Language, is often regarded as the preferred language for Knowledge Representation in the world of the Semantic Web, the potential of direct representation in RDF, the Resource Description Framework, is underestimated. Here we show how ontologies adequately represented in RDF could be semantically enriched with SPARUL. To deal with the semantics of relations we created Metarel, a meta-ontology for relations. The utility of the approach is demonstrated by an application on Gene Ontology Annotation (GOA) RDF graphs in the RDF Knowledge Base BioGateway. We show that Metarel can facilitate inferencing in BioGateway, which allows for queries that are otherwise not possible. Metarel is available on http://www.metarel.org

An efficient MPI/OpenMP parallelization of the Hartree-Fock method for the second generation of Intel Xeon Phi processor

Modern OpenMP threading techniques are used to convert the MPI-only Hartree-Fock code in the GAMESS program to a hybrid MPI/OpenMP algorithm. Two separate implementations that differ by the sharing or replication of key data structures among threads are considered, density and Fock matrices. All implementations are benchmarked on a super-computer of 3,000 Intel Xeon Phi processors. With 64 cores per processor, scaling numbers are reported on up to 192,000 cores. The hybrid MPI/OpenMP implementation reduces the memory footprint by approximately 200 times compared to the legacy code. The MPI/OpenMP code was shown to run up to six times faster than the original for a range of molecular system sizes.Comment: SC17 conference paper, 12 pages, 7 figure