Testbed for the Pellet Launching System for JT-60SA

As part of the European contribution to the large size superconducting tokamak project JT-60SA, a new Pellet Launching System (PLS) is designed and built. The aims of the PLS are to provide efficient fuelling to the plasma and to control and mitigate Edge Localised Modes (ELMs). Two pellet sources, one for fuelling pellets, one for pacing pellets, are delivering pellets to a centrifuge launcher. The centrifuge enables precise launch of pellets according to already proven control schemes. Furthermore, this system opens a way towards a test bed for the EU-DEMO fuelling system. The new PLS has to be completed and commissioned first at the IPP Garching pellet lab and then to be shipped to QST Naka site after having demonstrated its performance. This dedicated test bed has been set up, providing suitable vacuum conditions to operate the PLS in similar conditions (except magnetic field and radiation). Maximum hydrogen throughput is about 400 mbar·L/s per pellet source. Safety issues must be considered for hydrogen inventory of pellet sources (∼100 bar·L each). In a first step, the pellet sources will be put on a test vessel providing inherent safety by a huge volume (10 m³) which makes sure that the hydrogen concentration is below 1% under all circumstances. A hydrogen safety survey prior to assembly confirmed the concept to be followed by an assessment after the installation in order to get the required license for operation. The PLS as a whole, for the time being equipped with two pellet sources, is to be certified according to explosion prevention rules (ATEX) as a product to be shipped to Naka site. To obtain this, an appropriate declaration of explosion zones inside the vacuum system and the use of suitable and certified equipment is mandatory. Such, the integration of this system can be planned and assessed on a clear technical and regulatory basis

Faster Algorithms for Weighted Recursive State Machines

Pushdown systems (PDSs) and recursive state machines (RSMs), which are linearly equivalent, are standard models for interprocedural analysis. Yet RSMs are more convenient as they (a) explicitly model function calls and returns, and (b) specify many natural parameters for algorithmic analysis, e.g., the number of entries and exits. We consider a general framework where RSM transitions are labeled from a semiring and path properties are algebraic with semiring operations, which can model, e.g., interprocedural reachability and dataflow analysis problems. Our main contributions are new algorithms for several fundamental problems. As compared to a direct translation of RSMs to PDSs and the best-known existing bounds of PDSs, our analysis algorithm improves the complexity for finite-height semirings (that subsumes reachability and standard dataflow properties). We further consider the problem of extracting distance values from the representation structures computed by our algorithm, and give efficient algorithms that distinguish the complexity of a one-time preprocessing from the complexity of each individual query. Another advantage of our algorithm is that our improvements carry over to the concurrent setting, where we improve the best-known complexity for the context-bounded analysis of concurrent RSMs. Finally, we provide a prototype implementation that gives a significant speed-up on several benchmarks from the SLAM/SDV project

Fit for what?: towards explaining Battlegroup inaction

The thrust of this paper concerns the case of the European Battlegroup (BG) non-deployment in late 2008, when the United Nations requested European military support for the United Nations Organisation Mission peacekeeping force in the Democratic Republic of the Congo (DRC). The argument is built on the fact that when, in official documents, the EU approaches the European security and ESDP/CSDP's military crisis management policy and interventions, it makes strong references to the United Nations and the UN Charter Chapter VII's mandate of restoring international peace and security. Such references make it seem that supporting the UN when it deals with threats and crises is a primary concern of the EU and the member states. These allusions lead to the main contention of this paper, that there is much ambivalence in these indications. The paper develops its argument from one key hypothesis; namely, that the non-deployment of a European BG in the DRC, at the end of 2008, constitutes a useful case study for detecting a number of ambiguities of the EU in respect of its declarations in the official documents establishing the European military crisis management intervention structure

Fast index based algorithms and software for matching position specific scoring matrices

BACKGROUND: In biological sequence analysis, position specific scoring matrices (PSSMs) are widely used to represent sequence motifs in nucleotide as well as amino acid sequences. Searching with PSSMs in complete genomes or large sequence databases is a common, but computationally expensive task. RESULTS: We present a new non-heuristic algorithm, called ESAsearch, to efficiently find matches of PSSMs in large databases. Our approach preprocesses the search space, e.g., a complete genome or a set of protein sequences, and builds an enhanced suffix array that is stored on file. This allows the searching of a database with a PSSM in sublinear expected time. Since ESAsearch benefits from small alphabets, we present a variant operating on sequences recoded according to a reduced alphabet. We also address the problem of non-comparable PSSM-scores by developing a method which allows the efficient computation of a matrix similarity threshold for a PSSM, given an E-value or a p-value. Our method is based on dynamic programming and, in contrast to other methods, it employs lazy evaluation of the dynamic programming matrix. We evaluated algorithm ESAsearch with nucleotide PSSMs and with amino acid PSSMs. Compared to the best previous methods, ESAsearch shows speedups of a factor between 17 and 275 for nucleotide PSSMs, and speedups up to factor 1.8 for amino acid PSSMs. Comparisons with the most widely used programs even show speedups by a factor of at least 3.8. Alphabet reduction yields an additional speedup factor of 2 on amino acid sequences compared to results achieved with the 20 symbol standard alphabet. The lazy evaluation method is also much faster than previous methods, with speedups of a factor between 3 and 330. CONCLUSION: Our analysis of ESAsearch reveals sublinear runtime in the expected case, and linear runtime in the worst case for sequences not shorter than | [Formula: see text] |(m )+ m - 1, where m is the length of the PSSM and [Formula: see text] a finite alphabet. In practice, ESAsearch shows superior performance over the most widely used programs, especially for DNA sequences. The new algorithm for accurate on-the-fly calculations of thresholds has the potential to replace formerly used approximation approaches. Beyond the algorithmic contributions, we provide a robust, well documented, and easy to use software package, implementing the ideas and algorithms presented in this manuscript

Lexical deconstruction—review of Giegerich, H., Lexical structures: Compounding and the modules of grammar, Edinburgh Studies in Theoretical Linguistics, vol. 1

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Practical methods for constructing suffix trees

Sequence datasets are ubiquitous in modern life-science applications, and querying sequences is a common and critical operation in many of these applications. The suffix tree is a versatile data structure that can be used to evaluate a wide variety of queries on sequence datasets, including evaluating exact and approximate string matches, and finding repeat patterns. However, methods for constructing suffix trees are often very time-consuming, especially for suffix trees that are large and do not fit in the available main memory. Even when the suffix tree fits in memory, it turns out that the processor cache behavior of theoretically optimal suffix tree construction methods is poor, resulting in poor performance. Currently, there are a large number of algorithms for constructing suffix trees, but the practical tradeoffs in using these algorithms for different scenarios are not well characterized.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47869/1/778_2005_Article_154.pd

Discovering temporal regularities in retail customers’ shopping behavior

In this paper we investigate the regularities characterizing the temporal purchasing behavior of the customers of a retail market chain. Most of the literature studying purchasing behavior focuses on what customers buy while giving few importance to the temporal dimension. As a consequence, the state of the art does not allow capturing which are the temporal purchasing patterns of each customers. These patterns should describe the customerâ\u80\u99s temporal habits highlighting when she typically makes a purchase in correlation with information about the amount of expenditure, number of purchased items and other similar aggregates. This knowledge could be exploited for different scopes: set temporal discounts for making the purchases of customers more regular with respect the time, set personalized discounts in the day and time window preferred by the customer, provide recommendations for shopping time schedule, etc. To this aim, we introduce a framework for extracting from personal retail data a temporal purchasing profile able to summarize whether and when a customer makes her distinctive purchases. The individual profile describes a set of regular and characterizing shopping behavioral patterns, and the sequences in which these patterns take place. We show how to compare different customers by providing a collective perspective to their individual profiles, and how to group the customers with respect to these comparable profiles. By analyzing real datasets containing millions of shopping sessions we found that there is a limited number of patterns summarizing the temporal purchasing behavior of all the customers, and that they are sequentially followed in a finite number of ways. Moreover, we recognized regular customers characterized by a small number of temporal purchasing behaviors, and changing customers characterized by various types of temporal purchasing behaviors. Finally, we discuss on how the profiles can be exploited both by customers to enable personalized services, and by the retail market chain for providing tailored discounts based on temporal purchasing regularity

SeqAn An efficient, generic C++ library for sequence analysis

<p>Abstract</p> <p>Background</p> <p>The use of novel algorithmic techniques is pivotal to many important problems in life science. For example the sequencing of the human genome <abbrgrp><abbr bid="B1">1</abbr></abbrgrp> would not have been possible without advanced assembly algorithms. However, owing to the high speed of technological progress and the urgent need for bioinformatics tools, there is a widening gap between state-of-the-art algorithmic techniques and the actual algorithmic components of tools that are in widespread use.</p> <p>Results</p> <p>To remedy this trend we propose the use of SeqAn, a library of efficient data types and algorithms for sequence analysis in computational biology. SeqAn comprises implementations of existing, practical state-of-the-art algorithmic components to provide a sound basis for algorithm testing and development. In this paper we describe the design and content of SeqAn and demonstrate its use by giving two examples. In the first example we show an application of SeqAn as an experimental platform by comparing different exact string matching algorithms. The second example is a simple version of the well-known MUMmer tool rewritten in SeqAn. Results indicate that our implementation is very efficient and versatile to use.</p> <p>Conclusion</p> <p>We anticipate that SeqAn greatly simplifies the rapid development of new bioinformatics tools by providing a collection of readily usable, well-designed algorithmic components which are fundamental for the field of sequence analysis. This leverages not only the implementation of new algorithms, but also enables a sound analysis and comparison of existing algorithms.</p