Parcus: Energy-Aware and Robust Parallelization of AUTOSAR Legacy Applications

Embedded multicore processors are an attractive alternative to sophisticated single-core processors for the use in automobile electronic control units (ECUs), due to their expected higher performance and energy efficiency. Parallelization approaches for AUTOSAR legacy software exploit these benefits. Nevertheless, these approaches focus on extracting performance neglecting the system's worst-case sensor/actuator latency and energy consumption. This paper presents Parcus, an energy-and latency-aware parallelization technique that combines both runnable-and tasklevel parallelism. Parcus explicitly models the traversal of data from sensor to actuator through task instances, enabling to consider the latency imposed by parallelization techniques. The parallel schedule quality (PSQ) metric quantifies the success of the parallelization, for which it takes the latency and the processor frequency into account. We demonstrate the applicability of Parcus with an automotive case study. The results show that Parcus can fully utilize the processor's energy-saving potential.This research received funding from the EU FP7 no. 287519 (parMERASA), the ARTEMIS-JU no. 621429 (EMC2), and the German Federal Ministry of Education and Research.Peer ReviewedPostprint (author's final draft

How do users design scientific workflows? The Case of Snakemake

Scientific workflows automate the analysis of large-scale scientific data, fostering the reuse of data processing operators as well as the reproducibility and traceability of analysis results. In exploratory research, however, workflows are continuously adapted, utilizing a wide range of tools and software libraries, to test scientific hypotheses. Script-based workflow engines cater to the required flexibility through direct integration of programming primitives but lack abstractions for interactive exploration of the workflow design by a user during workflow execution. To derive requirements for such interactive workflows, we conduct an empirical study on the use of Snakemake, a popular Python-based workflow engine. Based on workflows collected from 1602 GitHub repositories, we present insights on common structures of Snakemake workflows, as well as the language features typically adopted in their specification

An Analysis of Lazy and Eager Limited Preemption Approaches under DAG-Based Global Fixed Priority Scheduling

DAG-based scheduling models have been shown to effectively express the parallel execution of current many-core heterogeneous architectures. However, their applicability to real-time settings is limited by the difficulties to find tight estimations of the worst-case timing parameters of tasks that may arbitrarily be preempted/migrated at any instruction. An efficient approach to increase the system predictability is to limit task preemptions to a set of pre-defined points. This limited preemption model supports two different preemption approaches, eager and lazy, which have been analyzed only for sequential task-sets. This paper proposes a new response time analysis that computes an upper bound on the lower priority blocking that each task may incur with eager and lazy preemptions. We evaluate our analysis with both, synthetic DAG-based task-sets and a real case-study from the automotive domain. Results from the analysis demonstrate that, despite the eager approach generates a higher number of priority inversions, the blocking impact is generally smaller than in the lazy approach, leading to a better schedulability performance.This work was funded by the EU projects P-SOCRATES (FP7-ICT-2013-10) and HERCULES (H2020/ICT/2015/688860), and the Spanish Ministry of Science and Innovation under contract TIN2015-65316-P.Peer ReviewedPostprint (author's final draft

Phylogenetic distribution of plant snoRNA families

Background: Small nucleolar RNAs (snoRNAs) are one of the most ancient families amongst non-protein-coding RNAs. They are ubiquitous in Archaea and Eukarya but absent in bacteria. Their main function is to target chemical modifications of ribosomal RNAs. They fall into two classes, box C/D snoRNAs and box H/ACA snoRNAs, which are clearly distinguished by conserved sequence motifs and the type of chemical modification that they govern. Similarly to microRNAs, snoRNAs appear in distinct families of homologs that affect homologous targets. In animals, snoRNAs and their evolution have been studied in much detail. In plants, however, their evolution has attracted comparably little attention. Results: In order to chart the phylogenetic distribution of individual snoRNA families in plants, we applied a sophisticated approach for identifying homologs of known plant snoRNAs across the plant kingdom. In response to the relatively fast evolution of snoRNAs, information on conserved sequence boxes, target sequences, and secondary structure is combined to identify additional snoRNAs. We identified 296 families of snoRNAs in 24 species and traced their evolution throughout the plant kingdom. Many of the plant snoRNA families comprise paralogs. We also found that targets are well-conserved for most snoRNA families. Conclusions: The sequence conservation of snoRNAs is sufficient to establish homologies between phyla. The degree of this conservation tapers off, however, between land plants and algae. Plant snoRNAs are frequently organized in highly conserved spatial clusters. As a resource for further investigations we provide carefully curated and annotated alignments for each snoRNA family under investigation

Structured RNAs and synteny regions in the pig genome

BACKGROUND: Annotating mammalian genomes for noncoding RNAs (ncRNAs) is nontrivial since far from all ncRNAs are known and the computational models are resource demanding. Currently, the human genome holds the best mammalian ncRNA annotation, a result of numerous efforts by several groups. However, a more direct strategy is desired for the increasing number of sequenced mammalian genomes of which some, such as the pig, are relevant as disease models and production animals. RESULTS: We present a comprehensive annotation of structured RNAs in the pig genome. Combining sequence and structure similarity search as well as class specific methods, we obtained a conservative set with a total of 3,391 structured RNA loci of which 1,011 and 2,314, respectively, hold strong sequence and structure similarity to structured RNAs in existing databases. The RNA loci cover 139 cis-regulatory element loci, 58 lncRNA loci, 11 conflicts of annotation, and 3,183 ncRNA genes. The ncRNA genes comprise 359 miRNAs, 8 ribozymes, 185 rRNAs, 638 snoRNAs, 1,030 snRNAs, 810 tRNAs and 153 ncRNA genes not belonging to the here fore mentioned classes. When running the pipeline on a local shuffled version of the genome, we obtained no matches at the highest confidence level. Additional analysis of RNA-seq data from a pooled library from 10 different pig tissues added another 165 miRNA loci, yielding an overall annotation of 3,556 structured RNA loci. This annotation represents our best effort at making an automated annotation. To further enhance the reliability, 571 of the 3,556 structured RNAs were manually curated by methods depending on the RNA class while 1,581 were declared as pseudogenes. We further created a multiple alignment of pig against 20 representative vertebrates, from which RNAz predicted 83,859 de novo RNA loci with conserved RNA structures. 528 of the RNAz predictions overlapped with the homology based annotation or novel miRNAs. We further present a substantial synteny analysis which includes 1,004 lineage specific de novo RNA loci and 4 ncRNA loci in the known annotation specific for Laurasiatheria (pig, cow, dolphin, horse, cat, dog, hedgehog). CONCLUSIONS: We have obtained one of the most comprehensive annotations for structured ncRNAs of a mammalian genome, which is likely to play central roles in both health modelling and production. The core annotation is available in Ensembl 70 and the complete annotation is available at http://rth.dk/resources/rnannotator/susscr102/version1.02. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-459) contains supplementary material, which is available to authorized users

PopDel identifies medium-size deletions simultaneously in tens of thousands of genomes

Thousands of genomic structural variants (SVs) segregate in the human population and can impact phenotypic traits and diseases. Their identification in whole-genome sequence data of large cohorts is a major computational challenge. Most current approaches identify SVs in single genomes and afterwards merge the identified variants into a joint call set across many genomes. We describe the approach PopDel, which directly identifies deletions of about 500 to at least 10,000 bp in length in data of many genomes jointly, eliminating the need for subsequent variant merging. PopDel scales to tens of thousands of genomes as we demonstrate in evaluations on up to 49,962 genomes. We show that PopDel reliably reports common, rare and de novo deletions. On genomes with available high-confidence reference call sets PopDel shows excellent recall and precision. Genotype inheritance patterns in up to 6794 trios indicate that genotypes predicted by PopDel are more reliable than those of previous SV callers. Furthermore, PopDel’s running time is competitive with the fastest tested previous tools. The demonstrated scalability and accuracy of PopDel enables routine scans for deletions in large-scale sequencing studies

parMERASA Multi-Core Execution of Parallelised Hard Real-Time Applications Supporting Analysability

International audienceEngineers who design hard real-time embedded systems express a need for several times the performance available today while keeping safety as major criterion. A breakthrough in performance is expected by parallelizing hard real-time applications and running them on an embedded multi-core processor, which enables combining the requirements for high-performance with timing-predictable execution. parMERASA will provide a timing analyzable system of parallel hard real-time applications running on a scalable multicore processor. parMERASA goes one step beyond mixed criticality demands: It targets future complex control algorithms by parallelizing hard real-time programs to run on predictable multi-/many-core processors. We aim to achieve a breakthrough in techniques for parallelization of industrial hard real-time programs, provide hard real-time support in system software, WCET analysis and verification tools for multi-cores, and techniques for predictable multi-core designs with up to 64 cores

Compartmentation of Redox Metabolism in Malaria Parasites

Malaria, caused by the apicomplexan parasite Plasmodium, still represents a major threat to human health and welfare and leads to about one million human deaths annually. Plasmodium is a rapidly multiplying unicellular organism undergoing a complex developmental cycle in man and mosquito – a life style that requires rapid adaptation to various environments. In order to deal with high fluxes of reactive oxygen species and maintain redox regulatory processes and pathogenicity, Plasmodium depends upon an adequate redox balance. By systematically studying the subcellular localization of the major antioxidant and redox regulatory proteins, we obtained the first complete map of redox compartmentation in Plasmodium falciparum. We demonstrate the targeting of two plasmodial peroxiredoxins and a putative glyoxalase system to the apicoplast, a non-photosynthetic plastid. We furthermore obtained a complete picture of the compartmentation of thioredoxin- and glutaredoxin-like proteins. Notably, for the two major antioxidant redox-enzymes – glutathione reductase and thioredoxin reductase – Plasmodium makes use of alternative-translation-initiation (ATI) to achieve differential targeting. Dual localization of proteins effected by ATI is likely to occur also in other Apicomplexa and might open new avenues for therapeutic intervention

Brownian motors: noisy transport far from equilibrium

Transport phenomena in spatially periodic systems far from thermal equilibrium are considered. The main emphasize is put on directed transport in so-called Brownian motors (ratchets), i.e. a dissipative dynamics in the presence of thermal noise and some prototypical perturbation that drives the system out of equilibrium without introducing a priori an obvious bias into one or the other direction of motion. Symmetry conditions for the appearance (or not) of directed current, its inversion upon variation of certain parameters, and quantitative theoretical predictions for specific models are reviewed as well as a wide variety of experimental realizations and biological applications, especially the modeling of molecular motors. Extensions include quantum mechanical and collective effects, Hamiltonian ratchets, the influence of spatial disorder, and diffusive transport.Comment: Revised version (Aug. 2001), accepted for publication in Physics Report

Determination of glycan structure from tandem mass spectra

Abstract—Glycans are molecules made from simple sugars that form complex tree structures. Glycans constitute one of the most important protein modifications and identification of glycans remains a pressing problem in biology. Unfortunately, the structure of glycans is hard to predict from the genome sequence of an organism. In this paper, we consider the problem of deriving the topology of a glycan solely from tandem mass spectrometry (MS) data. We study, how to generate glycan tree candidates that sufficiently match the sample mass spectrum, avoiding the combinatorial explosion of glycan structures. Unfortunately, the resulting problem is known to be computationally hard. We present an efficient exact algorithm for this problem based on fixed-parameter algorithmics that can process a spectrum in a matter of seconds. We also report some preliminary results of our method on experimental data, combining it with a preliminary candidate evaluation scheme. We show that our approach is fast in applications, and that we can reach very well de novo identification results. Finally, we show how to count the number of glycan topologies for a fixed size or a fixed mass. We generalize this result to count the number of (labeled) trees with bounded out degree, improving on results obtained using Pólya’s enumeration theorem. Index Terms—Computational mass spectrometry, glycans, parameterized algorithms, exact algorithms, counting trees. Ç