Verifying Recursive Active Documents with Positive Data Tree Rewriting

This paper proposes a data tree-rewriting framework for modeling evolving documents. The framework is close to Guarded Active XML, a platform used for handling XML repositories evolving through web services. We focus on automatic verification of properties of evolving documents that can contain data from an infinite domain. We establish the boundaries of decidability, and show that verification of a {\em positive} fragment that can handle recursive service calls is decidable. We also consider bounded model-checking in our data tree-rewriting framework and show that it is \nexptime-complete

Synthesizing Program Input Grammars

We present an algorithm for synthesizing a context-free grammar encoding the language of valid program inputs from a set of input examples and blackbox access to the program. Our algorithm addresses shortcomings of existing grammar inference algorithms, which both severely overgeneralize and are prohibitively slow. Our implementation, GLADE, leverages the grammar synthesized by our algorithm to fuzz test programs with structured inputs. We show that GLADE substantially increases the incremental coverage on valid inputs compared to two baseline fuzzers

Genes for selenium dependent and independent formate dehydrogenase in the gut microbial communities of three lower, wood-feeding termites and a wood-feeding roach

The bacterial Wood-Ljungdahl pathway for CO_2-reductive acetogenesis is important for the nutritional mutualism occurring between wood-feeding insects and their hindgut microbiota. A key step in this pathway is the reduction of CO_2 to formate, catalysed by the enzyme formate dehydrogenase (FDH). Putative selenocysteine- (Sec) and cysteine- (Cys) containing paralogues of hydrogenase-linked FDH (FDH_H) have been identified in the termite gut acetogenic spirochete, Treponema primitia, but knowledge of their relevance in the termite gut environment remains limited. In this study, we designed degenerate PCR primers for FDH_H genes (fdhF) and assessed fdhF diversity in insect gut bacterial isolates and the gut microbial communities of termites and cockroaches. The insects examined herein represent three wood-feeding termite families, Termopsidae, Kalotermitidae and Rhinotermitidae (phylogenetically 'lower' termite taxa); the wood-feeding roach family Cryptocercidae (the sister taxon to termites); and the omnivorous roach family Blattidae. Sec and Cys FDH_H variants were identified in every wood-feeding insect but not the omnivorous roach. Of 68 novel alleles obtained from inventories, 66 affiliated phylogenetically with enzymes from T. primitia. These formed two subclades (37 and 29 phylotypes) almost completely comprised of Sec-containing and Cys-containing enzymes respectively. A gut cDNA inventory showed transcription of both variants in the termite Zootermopsis nevadensis (family Termopsidae). The gene patterns suggest that FDH_H enzymes are important for the CO_2-reductive metabolism of uncultured acetogenic treponemes and imply that the availability of selenium, a trace element, shaped microbial gene content in the last common ancestor of dictyopteran, wood-feeding insects, and continues to shape it to this day

Conceptual Workflow for Complex Data Integration using AXML

International audienceRelevant data for decision support systems are available everywhere and in various formats. Such data must be integrated into a unified format. Traditional data integration approaches are not adapted to handle complex data. Thus, we exploit the Active XML language for integrating complex data. Its XML part allows to unify, model and store complex data. Moreover, its services part tackles the distributed issue of data sources. Accordingly, different integration tasks are proposed as services. These services are managed via a set of active rules that are built upon metadata and events of the integration system. In this paper, we design an architecture for integrating complex data autonomously. We have also designed the workflow for data integration tasks

OptimAX: optimizing distributed continuous queries

National audienceThe system we propose to present, OptiMAX, applies the principles of distributed query optimization to the problem of distributed evaluation of continuous XML queries. OptiMAX is an optimizer for Active XML documents (AXML in short). It is implemented as a module which can be used next to an AXML peer, and it may be invoked whenever users ask queries on their AXML documents. The optimizer draws up an initial query plan, and then attempts to rewrtite it using a combination of heuristics and cost information in order to improve the plan's performance estimates. An interesting feature is that all plans are AXML documents themselves. When the optimizer has retained a plan, it hands it to the AXML peer, which evaluates it directly following the decisions taken by the optimizer

Transducer-Based Rewriting Games for Active XML

Context-free games are two-player rewriting games that are played on nested strings representing XML documents with embedded function symbols. These games were introduced to model rewriting processes for intensional documents in the Active XML framework, where input documents are to be rewritten into a given target schema by calls to external services. This paper studies the setting where dependencies between inputs and outputs of service calls are modelled by transducers, which has not been examined previously. It defines transducer models operating on nested words and studies their properties, as well as the computational complexity of the winning problem for transducer-based context-free games in several scenarios. While the complexity of this problem is quite high in most settings (ranging from NP-complete to undecidable), some tractable restrictions are also identified.Comment: Extended version of MFCS 2016 conference pape

Peer Data Management

Peer Data Management (PDM) deals with the management of structured data in unstructured peer-to-peer (P2P) networks. Each peer can store data locally and define relationships between its data and the data provided by other peers. Queries posed to any of the peers are then answered by also considering the information implied by those mappings. The overall goal of PDM is to provide semantically well-founded integration and exchange of heterogeneous and distributed data sources. Unlike traditional data integration systems, peer data management systems (PDMSs) thereby allow for full autonomy of each member and need no central coordinator. The promise of such systems is to provide flexible data integration and exchange at low setup and maintenance costs. However, building such systems raises many challenges. Beside the obvious scalability problem, choosing an appropriate semantics that can deal with arbitrary, even cyclic topologies, data inconsistencies, or updates while at the same time allowing for tractable reasoning has been an area of active research in the last decade. In this survey we provide an overview of the different approaches suggested in the literature to tackle these problems, focusing on appropriate semantics for query answering and data exchange rather than on implementation specific problems

ThermoPhyl : a software tool for selecting phylogenetically optimized conventional and quantitative-PCR taxon-targeted assays for use with complex samples

The ability to specifically and sensitively target genotypes of interest is critical for the success of many PCR-based analyses of environmental or clinical samples that contain multiple templates.Next-generation sequence data clearly show that such samples can harbour hundreds to thousands of operational taxonomic units; a richness which precludes the manual evaluation of candidate assay specificity and sensitivity using multiple sequence alignments. To solve this problem we have developed and validated a free software tool which automates the identification of PCR assays targeting specific genotypes in complex samples. ThermoPhyl uses user-defined target and non-target sequence databases to assess the phylogenetic sensitivity and specificity of thermodynamically optimised candidate assays derived from primer design software packages. ThermoPhyl takes its name from its central premise of testing Thermodynamically optimal assays for Phylogenetic specificity and sensitivity and can be used for two primer (traditional PCR) or two primers with an internal probe (e.g. TaqMan® qPCR) applications and potentially for oligonucleotide probes.Here we describe the use of ThermoPhyl for traditional PCR and qPCR assays. PCR assays selected using ThermoPhyl were validated using 454 pyrosequencing of a traditional specific PCR assay and with a set of four genotype-specific qPCR assays applied to estuarine sediment samples

A Generic Approach and Framework for Managing Complex Information

Several application domains, such as healthcare, incorporate domain knowledge into their day-to-day activities to standardise and enhance their performance. Such incorporation produces complex information, which contains two main clusters (active and passive) of information that have internal connections between them. The active cluster determines the recommended procedure that should be taken as a reaction to specific situations. The passive cluster determines the information that describes these situations and other descriptive information plus the execution history of the complex information. In the healthcare domain, a medical patient plan is an example for complex information produced during the disease management activity from specific clinical guidelines. This thesis investigates the complex information management at an application domain level in order to support the day-to-day organization activities. In this thesis, a unified generic approach and framework, called SIM (Specification, Instantiation and Maintenance), have been developed for computerising the complex information management. The SIM approach aims at providing a conceptual model for the complex information at different abstraction levels (generic and entity-specific). In the SIM approach, the complex information at the generic level is referred to as a skeletal plan from which several entity-specific plans are generated. The SIM framework provides comprehensive management aspects for managing the complex information. In the SIM framework, the complex information goes through three phases, specifying the skeletal plans, instantiating entity-specific plans, and then maintaining these entity-specific plans during their lifespan. In this thesis, a language, called AIM (Advanced Information Management), has been developed to support the main functionalities of the SIM approach and framework. AIM consists of three components: AIMSL, AIM ESPDoc model, and AIMQL. The AIMSL is the AIM specification component that supports the formalisation process of the complex information at a generic level (skeletal plans). The AIM ESPDoc model is a computer-interpretable model for the entity-specific plan. AIMQL is the AIM query component that provides support for manipulating and querying the complex information, and provides special manipulation operations and query capabilities, such as replay query support. The applicability of the SIM approach and framework is demonstrated through developing a proof-of-concept system, called AIMS, using the available technologies, such as XML and DBMS. The thesis evaluates the the AIMS system using a clinical case study, which has applied to a medical test request application