A Purely Functional Computer Algebra System Embedded in Haskell

We demonstrate how methods in Functional Programming can be used to implement a computer algebra system. As a proof-of-concept, we present the computational-algebra package. It is a computer algebra system implemented as an embedded domain-specific language in Haskell, a purely functional programming language. Utilising methods in functional programming and prominent features of Haskell, this library achieves safety, composability, and correctness at the same time. To demonstrate the advantages of our approach, we have implemented advanced Gr\"{o}bner basis algorithms, such as Faug\`{e}re's $F_4$ and $F_5$, in a composable way.Comment: 16 pages, Accepted to CASC 201

MBSPDiscover: An Automatic Benchmark for MultiBSP Performance Analysis

International audienceMulti-Bulk Synchronous Parallel (MultiBSP) is a recently proposed parallel programming model for multicore machines that extends the classic BSP model. MultiBSP is very useful to design algorithms and estimate their running time, which are hard to do in High Performance Computing applications. For a correct estimation of the running time, the main parameters of the MultiBSP model for different multicore architectures need to be determined. This article presents a benchmark proposal for measuring the parameters that characterize the communication and synchronization cost for the model. Our approach discovers automatically the hierarchical structure of the multicore architecture by using a specific tool (hwloc) that allows obtaining runtime information about the machine. We describe the design, implementation and the results of benchmarking two multicore machines. Furthermore, we report the validation of the proposed method by using a real MultiBSP implementation of the vector inner product algorithm and comparing the predicted execution time against the real execution time

Система управления инцидентами и проблемами производства с использованием методологии ITSM и системы проектирования Bizagi

В статье рассмотрены общие принципы подсистемы управления качеством, разобраны понятия инцидента и проблемы. Подробно рассмотрен технологический бизнес-процесс обработки инцидента, приведены наиболее сложные процессы совершенствования. Представлено поэтапное разделение обработки инцидентов и их реализация в системе управления качеством.The article is about discussing of general principles of quality management subsystem. Particular it presents incidents and problems. It’s considered in detail technology business process elaborating of incidents, this point focusing on difficult processes which improves describing subsystem. In the text illustrate how incidents are elaborating and how they are realize in the quality management subsystem

CDK targets Sae2 to control DNA-end resection and homologous recombination

DNA double-strand breaks (DSBs) are repaired by two principal mechanisms: non-homologous end-joining (NHEJ) and homologous recombination (HR)1. HR is the most accurate DSB repair mechanism but is generally restricted to the S and G2 phases of the cell cycle, when DNA has been replicated and a sister chromatid is available as a repair template2-5. By contrast, NHEJ operates throughout the cell cycle but assumes most importance in G1 (refs 4​, ​6). The choice between repair pathways is governed by cyclin-dependent protein kinases (CDKs)2,3,5,7, with a major site of control being at the level of DSB resection, an event that is necessary for HR but not NHEJ, and which takes place most effectively in S and G2 (refs 2​, ​5). Here we establish that cell-cycle control of DSB resection in Saccharomyces cerevisiae results from the phosphorylation by CDK of an evolutionarily conserved motif in the Sae2 protein. We show that mutating Ser 267 of Sae2 to a non-phosphorylatable residue causes phenotypes comparable to those of a sae2Δ null mutant, including hypersensitivity to camptothecin, defective sporulation, reduced hairpin-induced recombination, severely impaired DNA-end processing and faulty assembly and disassembly of HR factors. Furthermore, a Sae2 mutation that mimics constitutive Ser 267 phosphorylation complements these phenotypes and overcomes the necessity of CDK activity for DSB resection. The Sae2 mutations also cause cell-cycle-stage specific hypersensitivity to DNA damage and affect the balance between HR and NHEJ. These findings therefore provide a mechanistic basis for cell-cycle control of DSB repair and highlight the importance of regulating DSB resection

The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome

Although a variety of possible functions have been proposed for inverted repeat sequences (IRs), it is not known which of them might occur in vivo. We investigate this question by assessing the distributions and properties of IRs in the Saccharomyces cerevisiae (SC) genome. Using the IRFinder algorithm we detect 100,514 IRs having copy length greater than 6 bp and spacer length less than 77 bp. To assess statistical significance we also determine the IR distributions in two types of randomization of the S. cerevisiae genome. We find that the S. cerevisiae genome is significantly enriched in IRs relative to random. The S. cerevisiae IRs are significantly longer and contain fewer imperfections than those from the randomized genomes, suggesting that processes to lengthen and/or correct errors in IRs may be operative in vivo. The S. cerevisiae IRs are highly clustered in intergenic regions, while their occurrence in coding sequences is consistent with random. Clustering is stronger in the 3′ flanks of genes than in their 5′ flanks. However, the S. cerevisiae genome is not enriched in those IRs that would extrude cruciforms, suggesting that this is not a common event. Various explanations for these results are considered

Segmental Duplication Implicated in the Genesis of Inversion 2Rj of Anopheles gambiae

The malaria vector Anopheles gambiae maintains high levels of inversion polymorphism that facilitate its exploitation of diverse ecological settings across tropical Africa. Molecular characterization of inversion breakpoints is a first step toward understanding the processes that generate and maintain inversions. Here we focused on inversion 2Rj because of its association with the assortatively mating Bamako chromosomal form of An. gambiae, whose distinctive breeding sites are rock pools beside the Niger River in Mali and Guinea. Sequence and computational analysis of 2Rj revealed the same 14.6 kb insertion between both breakpoints, which occurred near but not within predicted genes. Each insertion consists of 5.3 kb terminal inverted repeat arms separated by a 4 kb spacer. The insertions lack coding capacity, and are comprised of degraded remnants of repetitive sequences including class I and II transposable elements. Because of their large size and patchwork composition, and as no other instances of these insertions were identified in the An. gambiae genome, they do not appear to be transposable elements. The 14.6 kb modules inserted at both 2Rj breakpoint junctions represent low copy repeats (LCRs, also called segmental duplications) that are strongly implicated in the recent (∼0.4Ne generations) origin of 2Rj. The LCRs contribute to further genome instability, as demonstrated by an imprecise excision event at the proximal breakpoint of 2Rj in field isolates

A Parallel, Backjumping Subgraph Isomorphism Algorithm Using Supplemental Graphs

This registry entry contains a reference to the code, data and experimental scripts needed to reproduce the subgraph isomorphism paper: Ciaran McCreesh and Patrick Prosser, "A Parallel, Backjumping Subgraph Isomorphism Algorithm using Supplemental Graphs". To appear at the 21st International Conference on Principles and Practice of Constraint Programming (CP 2015)

Systematic Identification of Balanced Transposition Polymorphisms in Saccharomyces cerevisiae

High-throughput techniques for detecting DNA polymorphisms generally do not identify changes in which the genomic position of a sequence, but not its copy number, varies among individuals. To explore such balanced structural polymorphisms, we used array-based Comparative Genomic Hybridization (aCGH) to conduct a genome-wide screen for single-copy genomic segments that occupy different genomic positions in the standard laboratory strain of Saccharomyces cerevisiae (S90) and a polymorphic wild isolate (Y101) through analysis of six tetrads from a cross of these two strains. Paired-end high-throughput sequencing of Y101 validated four of the predicted rearrangements. The transposed segments contained one to four annotated genes each, yet crosses between S90 and Y101 yielded mostly viable tetrads. The longest segment comprised 13.5 kb near the telomere of chromosome XV in the S288C reference strain and Southern blotting confirmed its predicted location on chromosome IX in Y101. Interestingly, inter-locus crossover events between copies of this segment occurred at a detectable rate. The presence of low-copy repetitive sequences at the junctions of this segment suggests that it may have arisen through ectopic recombination. Our methodology and findings provide a starting point for exploring the origins, phenotypic consequences, and evolutionary fate of this largely unexplored form of genomic polymorphism