Matchmaking for covariant hierarchies

We describe a model of matchmaking suitable for the implementation of services, rather than their for their discovery and composition. In the model, processing requirements are modelled by client requests and computational resources are software processors that compete for request processing as the covariant implementations of an open service interface. Matchmaking then relies on type analysis to rank processors against requests in support of a wide range of dispatch strategies. We relate the model to the autonomicity of service provision and briefly report on its deployment within a production-level infrastructure for scientic computing

Detailed evaluation of data analysis tools for subtyping of bacterial isolates based on whole genome sequencing : Neisseria meningitidis as a proof of concept

Whole genome sequencing is increasingly recognized as the most informative approach for characterization of bacterial isolates. Success of the routine use of this technology in public health laboratories depends on the availability of well-characterized and verified data analysis methods. However, multiple subtyping workflows are now often being used for a single organism, and differences between them are not always well described. Moreover, methodologies for comparison of subtyping workflows, and assessment of their performance are only beginning to emerge. Current work focuses on the detailed comparison of WGS-based subtyping workflows and evaluation of their suitability for the organism and the research context in question. We evaluated the performance of pipelines used for subtyping of Neisseria meningitidis, including the currently widely applied cgMLST approach and different SNP-based methods. In addition, the impact of the use of different tools for detection and filtering of recombinant regions and of different reference genomes were tested. Our benchmarking analysis included both assessment of technical performance of the pipelines and functional comparison of the generated genetic distance matrices and phylogenetic trees. It was carried out using replicate sequencing datasets of high- and low-coverage, consisting mainly of isolates belonging to the clonal complex 269. We demonstrated that cgMLST and some of the SNP-based subtyping workflows showed very good performance characteristics and highly similar genetic distance matrices and phylogenetic trees with isolates belonging to the same clonal complex. However, only two of the tested workflows demonstrated reproducible results for a group of more closely related isolates. Additionally, results of the SNP-based subtyping workflows were to some level dependent on the reference genome used. Interestingly, the use of recombination-filtering software generally reduced the similarity between the gene-by-gene and SNP-based methodologies for subtyping of N. meningitidis. Our study, where N. meningitidis was taken as an example, clearly highlights the need for more benchmarking comparative studies to eventually contribute to a justified use of a specific WGS data analysis workflow within an international public health laboratory context

A Type System For Call-By-Name Exceptions

We present an extension of System F with call-by-name exceptions. The type system is enriched with two syntactic constructs: a union type for programs whose execution may raise an exception at top level, and a corruption type for programs that may raise an exception in any evaluation context (not necessarily at top level). We present the syntax and reduction rules of the system, as well as its typing and subtyping rules. We then study its properties, such as confluence. Finally, we construct a realizability model using orthogonality techniques, from which we deduce that well-typed programs are weakly normalizing and that the ones who have the type of natural numbers really compute a natural number, without raising exceptions.Comment: 25 page

Compositional Reasoning for Explicit Resource Management in Channel-Based Concurrency

We define a pi-calculus variant with a costed semantics where channels are treated as resources that must explicitly be allocated before they are used and can be deallocated when no longer required. We use a substructural type system tracking permission transfer to construct coinductive proof techniques for comparing behaviour and resource usage efficiency of concurrent processes. We establish full abstraction results between our coinductive definitions and a contextual behavioural preorder describing a notion of process efficiency w.r.t. its management of resources. We also justify these definitions and respective proof techniques through numerous examples and a case study comparing two concurrent implementations of an extensible buffer.Comment: 51 pages, 7 figure