The growing synergy between Web Services and Gridbased technologies [7] will potentially enable profound, dynamic interactions between scientific applications dispersed in geographic, institutional, and conceptual space. Such deep interoperability requires the simplicity, robustness, and extensibility for which SOAP [4,3] was conceived, thus making it a natural lingua franca. Concomitant with these advantages, however, is a degree of inefficiency that may limit the applicability of SOAP to some situations. In this paper, we investigate the limitations of SOAP for high-performance scientific computing. We analyze the processing of SOAP messages, and identify the issues of each stage. We present a high-performance SOAP implementation and a schema-specific parser based on the results of our investigation. After our SOAP optimizations are implemented, the most significant bottleneck is ASCII/double conversion. Instead of handling this using extensions to SOAP, we recommend a multiprotocol approach that uses SOAP to negotiate faster binary protocols between messaging participants.

BackgroundRigorous study of mitochondrial functions and cell biology in the budding yeast, Saccharomyces cerevisiae has advanced our understanding of mitochondrial genetics. This yeast is now a powerful model for population genetics, owing to large genetic diversity and highly structured populations among wild isolates. Comparative mitochondrial genomic analyses between yeast species have revealed broad evolutionary changes in genome organization and architecture. A fine-scale view of recent evolutionary changes within S. cerevisiae has not been possible due to low numbers of complete mitochondrial sequences.ResultsTo address challenges of sequencing AT-rich and repetitive mitochondrial DNAs (mtDNAs), we sequenced two divergent S. cerevisiae mtDNAs using a single-molecule sequencing platform (PacBio RS). Using de novo assemblies, we generated highly accurate complete mtDNA sequences. These mtDNA sequences were compared with 98 additional mtDNA sequences gathered from various published collections. Phylogenies based on mitochondrial coding sequences and intron profiles revealed that intraspecific diversity in mitochondrial genomes generally recapitulated the population structure of nuclear genomes. Analysis of intergenic sequence indicated a recent expansion of mobile elements in certain populations. Additionally, our analyses revealed that certain populations lacked introns previously believed conserved throughout the species, as well as the presence of introns never before reported in S. cerevisiae.ConclusionsOur results revealed that the extensive variation in S. cerevisiae mtDNAs is often population specific, thus offering a window into the recent evolutionary processes shaping these genomes. In addition, we offer an effective strategy for sequencing these challenging AT-rich mitochondrial genomes for small scale projects.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1664-4) contains supplementary material, which is available to authorized users.

The Common Component Architecture (CCA) provides a means for software developers to manage the complexity of large-scale scientific simulations and to move toward a plug-and-play environment for high-performance computing. In the scientific computing context, component models also promote collaboration using independently developed software, thereby allowing particular individuals or groups to focus on the aspects of greatest interest to them. The CCA supports parallel and distributed computing as well as local high-performance connections between components in a language-independent manner. The design places minimal requirements on components and thus facilitates the integration of existing code into the CCA environment. The CCA model imposes minimal overhead to minimize the impact on application performance. The focus on high performance distinguishes the CCA from most other component models. The CCA is being applied within an increasing range of disciplines, including combustion research, global climate simulation, and computational chemistry.

The dietary specialist fruit fly Drosophila sechellia has evolved to specialize on the toxic fruit of its host plant Morinda citrifolia. Toxicity of Morinda fruit is primarily due to high levels of octanoic acid (OA). Using RNA interference (RNAi), prior work found that knockdown of Osiris family genes Osiris 6 (Osi6), Osi7, and Osi8 led to increased susceptibility to OA in adult D. melanogaster flies, likely representing genes underlying a Quantitative Trait Locus (QTL) for OA resistance in D. sechellia. While genes in this major effect locus are beginning to be revealed, prior work has shown at least five regions of the genome contribute to OA resistance. Here, we identify new candidate OA resistance genes by performing differential gene expression analysis using RNA-sequencing (RNA-seq) on control and OA-exposed D. sechellia flies. We found 104 significantly differentially expressed genes with annotated orthologs in D. melanogaster, including six Osiris gene family members, consistent with previous functional studies and gene expression analyses. Gene ontology (GO) term enrichment showed significant enrichment for cuticle development in upregulated genes and significant enrichment of immune and defense responses in downregulated genes, suggesting important aspects of the physiology of D. sechellia that may play a role in OA resistance. In addition, we identified five candidate OA resistance genes that potentially underlie QTL peaks outside of the major effect region, representing promising new candidate genes for future functional studies.

No abstract