Peter Braun

Transforming Object Oriented Models with BOTL

Abstract In many application domains, like for example B2B, B2C, or CASE, a lot of heterogeneous applications exist which have to cooperate and exchange data. A major task of system integration is the mapping of different data models, on which the applications are built upon. In this paper, the Basic Object-oriented Transformation Language (BOTL) is introduced as a mathematically founded approach for the integration of data models. Class diagrams of the Unified Modelling Language (UML) are today established as a technique for meta modelling in the software engineering domain. Therefore, BOTL uses a UML-based notation for the definition of declarative mapping rules that allow reasoning about properties like applicability, metamodel conformance and bidirectionality of transformations.

AutoMoDe - Notations, Methods, and Tools for Model-Based Development of Automotive Software

This paper describes the first results from the AutoMoDe project (Automotive Model-based Development), where an integrated methodology for model-based development of automotive control software is being developed. The results presented include a number of problem-oriented graphical notations, based on a formally defined operational model, which are associated with system views for various degrees of abstraction. It is shown how the approach can be used for partitioning comprehensive system designs for subsequent implementation-related tasks. Recent experiences from a case study of an engine management system, specific issues related to reengineering, and the current status of CASE-tool support are also presented.

Consistent Integration of Formal Methods

The usability of formal concepts for system design depends essentially on their integration in the design process. We discuss several possible levels of integration: technical integration of tools considering APIs and tool interfaces, conceptual integration of metamodels of description formalisms combined with hard and soft constraints, semantical integration of semantics of description techniques using a common semantic model, and finally methodical integration by an embedding in the development process. We show the feasibility of such an integrated approach and its advantages presenting AutoFocus/Quest, a formal method CASE-Tool with its levels of integration. Parts of a banking system model are used as example.

Visualization of Message Passing Parallel Programs

Parallel programming is orders of magnitudes more complex than writing sequential programs. This is particularly true for programming distributed memory multiprocessor architectures based on message passing programming models. Understanding the synchronization and communication behavior of parallel programs is one of the most critical issues in programming distributed memory multiprocessors. The paper describes methods and tools for visualization and animation of the dynamic execution of parallel programs. Based on an evaluation and classification of existing visualization environments, the visualization and animation tool VISTOP (Visualization TOol for Parallel Systems) is presented as part of the integrated tool environment TOPSYS (TOols for Parallel SYStems) for programming distributed memory multiprocessors. VISTOP supports the interactive on-line visualization of message passing programs based on various views, in particular, a process graph based concurrency view for detecting synchronization and communication bugs.

Microevolution of Anthrax from a Young Ancestor (M.A.Y.A.) Suggests a Soil-Borne Life Cycle of Bacillus anthracis

During an anthrax outbreak at the Pollino National Park (Basilicata, Italy) in 2004, diseased cattle were buried and from these anthrax-foci Bacillus anthracis endospores still diffuse to the surface resulting in local accumulations. Recent data suggest that B. anthracis multiplies in soil outside the animal-host body. This notion is supported by the frequent isolation of B. anthracis from soil lacking one or both virulence plasmids. Such strains represent an evolutionary dead end, as they are likely no longer able to successfully infect new hosts. This loss of virulence plasmids is explained most simply by postulating a soil-borne life cycle of the pathogen. To test this hypothesis we investigated possible microevolution at two natural anthrax foci from the 2004 outbreak. If valid, then genotypes of strains isolated from near the surface at these foci should be on a different evolutionary trajectory from those below residing in deeper-laying horizons close to the carcass. Thus, the genetic diversity of B. anthracis isolates was compared conducting Progressive Hierarchical Resolving Assays using Nucleic Acids (PHRANA) and next generation Whole Genome Sequencing (WGS). PHRANA was not discriminatory enough to resolve the fine genetic relationships between the isolates. Conversely, WGS of nine isolates from near-surface and nine from near-carcass revealed five isolate specific SNPs, four of which were found only in different near-surface isolates. In support of our hypothesis, one surface-isolate lacked plasmid pXO1 and also harbored one of the unique SNPs. Taken together, our results suggest a limited soil-borne life cycle of B. anthracis.

Towards an integrated system model for testing and verification of automation machines

Models and documents created during the development of automation machines typically can be categorized into mechanics, electronics, and software. The functionality of an automation machine is, however, realized by the interaction of all three of these domains. So no single model covering only one development category will be able to describe the behavior of the machine thoroughly. For early planning of machine design, virtual prototypes, and especially for the formal verification of requirements an integrated functional model of the machine is required. This paper introduces a technique which can be used to model automation machines on an abstract level, including coarse-grained descriptions of mechanics, electronics and software aspects with special focus on modeling domain-specific issues such as material flow and collision response. The resulting models are detailed enough to be simulated or verified but still suitably abstract to allow fast creation and efficient simulation.

Unexpected genomic relationships between Bacillus anthracis strains from Bangladesh and Central Europe

The zoonosis anthrax caused by the bacterium Bacillus anthracis has a broad geographical distribution. Active enzootic areas are typically located away from central and northern Europe where cases of the disease occur only sporadically and in limited numbers. In contrast, a few out of the 64 districts of Bangladesh are hyper-endemic for anthrax and there the disease causes major losses in live-stock. In this study we genotyped eight strains of B. anthracis collected from the districts of Sirajganj and Tangail in 2013. All these strains belonged to canSNP group A.Br.001/002 Sterne differing only in a few of 31 tandem-repeat (MLVA)-markers. Whole genome sequences were obtained from five of these strains and compared with genomic information of B. anthracis strains originating from various geographical locations. Characteristic signatures were detected defining two Bangladesh clusters potentially useful for rapid molecular epidemiology. From this data high-resolution PCR assays were developed and subsequently tested on additional isolates from Bangladesh and Central Europe. Remarkably, this comparative genomic analysis focusing on SNP-discovery revealed a close genetic relationship between these strains from Bangladesh and historic strains collected between 1991 and 2008 in The Netherlands and Germany, respectively. Possible explanations for these phylogenetic relationships are discussed.

Genome Sequence of Bacillus anthracis Isolated from an Anthrax Burial Site in Pollino National Park, Basilicata Region (Southern Italy)

ABSTRACT A Bacillus anthracis strain was isolated from a burial-site in Pollino National Park where a bovine died of anthrax and was buried in 2004. We report the first genome sequence of B. anthracis isolated in the Basilicata region (southern Italy), which is the highest risk area of anthrax infection in Italy.

Genome Sequence of Bacillus anthracis Strain Tangail-1 from Bangladesh

ABSTRACT Soil was collected in July 2013 at a site where a cow infected with anthrax had been the month before. Selective culturing yielded Bacillus anthracis strain Tangail-1. Here, we report the draft genome sequence of this Bacillus anthracis isolate that belongs to the canonical A.Br.001/002 clade.