Optimizing Repetitive Computations of Database Triggers Within a Transaction

Projet RODINWe study the problem of optimizing costly repetitive evaluations of database triggers within a transaction. We first show that well known incremental rule evaluation algorithms such as RETE or TREAT are inappropriate for that because they do not consider how repetitive triggerings of rules can be caused by the structure of transaction programs. Therefore, their decision of precomputing and caching some expressions in rule conditions for a later reuse can be erroneous. We assume that transaction programs are represented by their flow graph. We then propose an algorithm that, given a transaction's flow graph, and a set of triggers, constructs a compact data structure called a triggering graph. First, for each possible transaction execution, this graph indicates which rules may be triggered. Second, for every rule $r$ capable of being triggered and fired several times, the graph represents the real «influence» of both the transaction and the rules on $r$. This provides the necessary information for deciding which subexpressions of $r$ are most profitable to cache for the considered transaction

An Adaptative algorithm for incremental evaluation of production rules in databases

Projet RODINSeveral incremental algorithms have been proposed ro evaluate database production rule programs. They all derive from existing incremental algorithms, lke RETE and TREAT, developed for rule-based systems in the framework of artificial intelligence. In this paper, we address a specific but crucial problem that arises with these incremental algorithms : how much data should be profitably materialized and maintained in order to speed-up program evaluation ?. We show that the answer exposes to a well known space-time tradeoff. Our major contribution is to propose and adaptive algorithm that takes as input a program of rules and returns for each rule, the set of most profitable relational expressions that should be maintained in order to obtain a good space-time compromise. A notable feature of our algorithm is that it works for both set-oriented and instance-oriented rules. We compare our algorithms with existing incremental algorithms for database production rule programs

Analyzing Repetitive Evaluations of Active Rules Within a Transaction

Projet RODINAn active database system automatically triggers rules in response to certain events occuring. Events are issued by transactions or action parts of rules. Repeated executions of rules can be caused by the structure of the initial triggering transaction program and by the structure and execution semantics of rules. Repeated calculations of rules may incur costly redundant computations in rule conditions or actions. The central contribution of this paper is to propose technics for analyzing the behaviour of a transaction and a set of rules triggered by this transaction in order to derive: (i) if a given rule is processed more than once, and (ii) a fine indication of the database changes that may occur between two consecutive executions of the rule. Knowing these changes, it is possible to use existing algorithms that compute useful intermediate expressions in a rule that can be cached and incrementally maintained in order to avoid redundant computations. A notable property of our analysis technics is that they are parametrized by a few essential semantics parameters that define the execution semantics of an active rule language. Thus, our analysis apply to a large class of existing active rule systems

Dynamic Scheduling of Complex Distributed Queries

Projet RODINRésumé disponible dans le fichier PD

Efficient Matching Algorithms for Publish and Subscribe Systems

Projet CARAVELPublish/Subscribe is the paradigm in which users express long-term interests («subscriptions») and some external agent (perhaps other users) «publishes» events (e.g., offers). The job of Publish/Subscribe software is to send events to the owners of subscriptions satisfied by those events. For example, a user subscription may consist of an interest in an airplane of a certain type, not to exceed a certain price. A published event may consist of an offer of an airplane with certain properties including price. A subscriptio- n closely resembles a trigger in that it is a long-lived conditional query associated with an action (usually, informing the subscriber). However, it is less general than a trigger so novel data structures and implementations may enable the creation of scalable, high performance publish-subscribe systems. This paper describes an attempt at the construction of such algorithm- s and its implementation. Using a combination of data structures, application-- specific caching policies, and application-specific query processing our system can handle 600 events per second on 6 million subscriptions consisting of conjunctions of (attribute, comparison operator, value) predicates

mazF, a novel counter-selectable marker for unmarked chromosomal manipulation in Bacillus subtilis

Here, we present a novel method for the directed genetic manipulation of the Bacillus subtilis chromosome free of any selection marker. Our new approach employed the Escherichia coli toxin gene mazF as a counter-selectable marker. The mazF gene was placed under the control of an isopropyl-β-d-thiogalactopyranoside (IPTG)-inducible expression system and associated with a spectomycin-resistance gene to form the MazF cassette, which was flanked by two directly-repeated (DR) sequences. A double-crossover event between the linearized delivery vector and the chromosome integrated the MazF cassette into a target locus and yielded an IPTG-sensitive strain with spectomycin-resistance, in which the wild-type chromosome copy had been replaced by the modified copy at the targeted locus. Another single-crossover event between the two DR sequences led to the excision of the MazF cassette and generated a strain with IPTG resistance, thereby realizing the desired alteration to the chromosome without introducing any unwanted selection markers. We used this method repeatedly and successfully to inactivate a specific gene, to introduce a gene of interest and to realize the in-frame deletion of a target gene in the same strain. As there is no prerequisite strain for this method, it will be a powerful and universal tool

Molecular dissection of translation termination mechanism identifies two new critical regions in eRF1

Translation termination in eukaryotes is completed by two interacting factors eRF1 and eRF3. In Saccharomyces cerevisiae, these proteins are encoded by the genes SUP45 and SUP35, respectively. The eRF1 protein interacts directly with the stop codon at the ribosomal A-site, whereas eRF3—a GTPase protein—probably acts as a proofreading factor, coupling stop codon recognition to polypeptide chain release. We performed random PCR mutagenesis of SUP45 and screened the library for mutations resulting in increased eRF1 activity. These mutations led to the identification of two new pockets in domain 1 (P1 and P2) involved in the regulation of eRF1 activity. Furthermore, we identified novel mutations located in domains 2 and 3, which confer stop codon specificity to eRF1. Our findings are consistent with the model of a closed-active conformation of eRF1 and shed light on two new functional regions of the protein

A Viable Hypomorphic Allele of the Essential IMP3 Gene Reveals Novel Protein Functions in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, the essential IMP3 gene encodes a component of the SSU processome, a large ribonucleoprotein complex required for processing of small ribosomal subunit RNA precursors. Mutation of the IMP3 termination codon to a sense codon resulted in a viable mutant allele producing a C-terminal elongated form of the Imp3 protein. A strain expressing the mutant allele displayed ribosome biogenesis defects equivalent to IMP3 depletion. This hypomorphic allele represented a unique opportunity to investigate and better understand the Imp3p functions. We demonstrated that the +1 frameshifting was increased in the mutant strain. Further characterizations revealed involvement of the Imp3 protein in DNA repair and telomere length control, pointing to a functional relationship between both pathways and ribosome biogenesis