ReSpecT Nets: Towards an Analysis Methodology for ReSpecT Specifications

A key feature for infrastructures providing coordination services is the ability to define the behaviour of coordination abstractions according to the requirements identified at design-time. We take as a representative for this scenario the logic-based language ReSpecT (Reaction Specification Tuples), used to program the reactive behaviour of tuple centres. ReSpecT specifications are at the core of the engineering methodology underlying the TuCSoN infrastructure, and are therefore the “conceptual place” where formal methods can be fruitfully applied to guarantee relevant system properties.In this paper we introduce ReSpecT nets, a formalism that can be used to describe reactive behaviours that can succeed and fail, and that allows for an encoding to Petri nets with inhibitor arcs. ReSpecT nets are introduced to give a core model to a fragment of the ReSpecT language, and to pave the way for devising an analysis methodology including formal verification of safety and liveness properties. In particular, we provide a semantics to ReSpecT specifications through a mapping to ReSpecT nets. The potential of this approach for the analysis of ReSpecT specifications is discussed, presenting initial results for the analysis of safety properties.     

Formal ReSpecT in the A&A Perspective

Coordination models and languages have found a new course in the context of MAS (multiagent systems). By re-interpreting results in terms of agent-oriented abstractions, new conceptual spaces are found, which extend the reach of coordination techniques far beyond their original scope. This is for instance the case of coordination media, when recasted in terms of coordination artifacts in the MAS context.In this paper, we take the well-established ReSpecT language for programming tuple centre behaviour, and adopt the A&A (agents and artifacts) meta-model as a perspective to reinterpret, revise, extend and complete it. A formal model of the so-called A&A ReSpecT language is presented, along with an example illustrating its use for MAS coordination.     

PVS#: Streamlined Tacticals for PVS

The semantics of a proof language relies on the representation of the state of a proof after a logical rule has been applied. This information, which is usually meaningless from a logical point of view, is fundamental to describe the control mechanism of the proof search provided by the language. In this paper, we present a monadic datatype to represent the state information of a proof and we illustrate its use in the PVS theorem prover. We show how this representation can be used to design a new set of powerful tacticals for PVS, called PVS#, that have a simpler and clearer semantics compared to the semantics of standard PVS tacticals.     

Virtual Organizations in Arigatoni

Arigatoni is a lightweight overlay network that deploys the Global Computing Paradigm over the Internet. Communication for over the behavioral units of the overlay is performed by a simple resource discovery protocol (RDP). Basic Global Computers Units (GC) can communicate by first registering to a brokering service and then by mutually asking and offering services.Colonies and communities are the main entities in the model. A colony is a simple virtual organization composed by exactly one leader and some set (possibly empty) of individuals. A community is a raw set of colonies and global computers (think it as a soup of colonies and global computer without a leader).We present an operational semantics via a labeled transition system, that describes the main operations necessary in the Arigatoni model to perform leader negotiation, joining/leaving a colony, linking two colonies and moving one GC from one colony to another. Our formalization results to be adequate w.r.t. the algorithm performing peer logging/delogging and colony aggregation.     

Rule-Based Programming with Diaplan

Diaplan is a language for programming with graphs and diagrams that is currently being designed and implemented by the authors. In this paper, a programming example, declaration grids, shall illustrate how Diaplan supports a functional and object-oriented style of programming. The example also indicates which features are needed beyond those discussed in previous work on the language [B. Hoffmann, Abstraction and control for shapely nested graph transformation, Fundamenta Informaticae 58 (2003) 39–56].     

Measuring a Java Test Suite Coverage Using JML Specifications

We propose in this paper a way to measure the coverage of a Java test suite by considering the JML specification associed to the Java program under test. This approach is based on extracting a predicate-based graph from the JML method specifications. We then measure the coverage of this latter w.r.t. nodes of the graph that are visited by the test suite. In addition, we propose to check whether the test suite satisfies classical condition coverage criteria. We also introduce a tool, to be used as precompiler for Java, that is in charge of measuring and reporting the coverage according to these criteria.     

Kernel-based machine learning for fast text mining in R

Recent advances in the field of kernel-based machine learning methods allow fast processing of text using string kernels utilizing suffix arrays. kernlab provides both kernel methods’ infrastructure and a large collection of already implemented algorithms and includes an implementation of suffix-array-based string kernels. Along with the use of the text mining infrastructure provided by tm these packages provide R with functionality in processing, visualizing and grouping large collections of text data using kernel methods. The emphasis is on the performance of various types of string kernels at these tasks.     

On the computational power of BlenX

We present some decidability and undecidability results for subsets of the BlenX Language, a process-calculi-based programming language developed for modelling biological processes. We show that for a core subset of the language (which considers only communication primitives) termination is decidable. Moreover, we prove that by adding either global priorities or events to this core language, we obtain Turing equivalent languages. The proof is through encodings of Random Access Machines (RAMs), a well-known Turing equivalent formalism, into our subsets of BlenX. All the encodings are shown to be correct.     

TiReX: Replica-exchange molecular dynamics using Tinker

We present a driver program for performing replica-exchange molecular dynamics simulations with the Tinker package. Parallelization is based on the Message Passing Interface, with every replica assigned to a separate process. The algorithm is not communication intensive, which makes the program suitable for running even on loosely coupled cluster systems. Particular attention is paid to the practical aspects of analyzing the program output.

Program summary

Program title: TiReXCatalogue identifier: AEEK_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEK_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 43 385No. of bytes in distributed program, including test data, etc.: 502 262Distribution format: tar.gzProgramming language: Fortran 90/95Computer: Most UNIX machinesOperating system: LinuxHas the code been vectorized or parallelized?: parallelized with MPIClassification: 16.13External routines: TINKER version 4.2 or 5.0, built as a libraryNature of problem: Replica-exchange molecular dynamics.Solution method: Each replica is assigned to a separate process; temperatures are swapped between replicas at regular time intervals.Running time: The sample run may take up to a few minutes.     

Software specification using the special language

This paper presents a tutorial overview of special, a formal specification and assertion language created by SRI International as part of their hierarchical design methodology. The language is based on a formal model of system behavior and is supported by language processors that assist in the interactive development of specifications. special is a strongly typed language that models data and programs as abstract resources known as objects. Collections of modules known as abstract machines are the major building blocks of a software specification in special. The technical foundations of special and the components of a special specification are described. A sample specification is detailed in an appendix.     

Merging the autoview image processing language with prolog

A new computer language, called provision, is defined. It combines features of both prolog (for artificial intelligence) and autoview (for image processing). Predicates for image processing, controlling cameras, illumination sources, optics, a video multiplexor and simple robotic devices are all integrated with PROLOG2, an extension of standard core prolog. The result is a powerful medium for expressing a wide range of algorithms for the visual control of robots and advanced industrial inspection. Several provision applications (i.e. ‘programs’) are presented.     

Revised and extended Utilities for the Ratip package

During the last years, the Ratip package has been found useful for calculating the excitation and decay properties of free atoms. Based on the (relativistic) multiconfiguration Dirac-Fock method, this program is used to obtain accurate predictions of atomic properties and to analyze many recent experiments. The daily work with this package made an extension of its Utilities [S. Fritzsche, Comput. Phys. Comm. 141 (2001) 163] desirable in order to facilitate the data handling and interpretation of complex spectra. For this purpose, we make available an enlarged version of the Utilities which mainly supports the comparison with experiment as well as large Auger computations. Altogether 13 additional tasks have been appended to the program together with a new menu structure to improve the interactive control of the program.

Program summary

Title of program: RATIPCatalogue identifier: ADPD_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADPD_v2_0Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandLicensing provisions: noneReference in CPC to previous version: S. Fritzsche, Comput. Phys. Comm. 141 (2001) 163Catalogue identifier of previous version: ADPDAuthors of previous version: S. Fritzsche, Department of Physics, University of Kassel, Heinrich-Plett-Strasse 40, D-34132 Kassel, GermanyDoes the new version supersede the original program?: yesComputer for which the new version is designed and others on which it has been tested: IBM RS 6000, PC Pentium II-IVInstallations: University of Kassel (Germany), University of Oulu (Finland)Operating systems: IBM AIX, Linux, UnixProgram language used in the new version: ANSI standard Fortran 90/95Memory required to execute with typical data: 300 kBNo. of bits in a word: All real variables are parameterized by a selected kind parameter and, thus, can be adapted to any required precision if supported by the compiler. Currently, the kind parameter is set to double precision (two 32-bit words) as used also for other components of the Ratip package [S. Fritzsche, C.F. Fischer, C.Z. Dong, Comput. Phys. Comm. 124 (2000) 341; G. Gaigalas, S. Fritzsche, Comput. Phys. Comm. 134 (2001) 86; S. Fritzsche, Comput. Phys. Comm. 141 (2001) 163; S. Fritzsche, J. Elec. Spec. Rel. Phen. 114-116 (2001) 1155]No. of lines in distributed program, including test data, etc.:231 813No. of bytes in distributed program, including test data, etc.: 3 977 387Distribution format: tar.gzip fileNature of the physical problem: In order to describe atomic excitation and decay properties also quantitatively, large-scale computations are often needed. In the framework of the Ratip package, the Utilities support a variety of (small) tasks. For example, these tasks facilitate the file and data handling in large-scale applications or in the interpretation of complex spectra.Method of solution: The revised Utilities now support a total of 29 subtasks which are mainly concerned with the manipulation of output data as obtained from other components of the Ratip package. Each of these tasks are realized by one or several subprocedures which have access to the corresponding modules of the main components. While the main menu defines seven groups of subtasks for data manipulations and computations, a particular task is selected from one of these group menus. This allows to enlarge the program later if technical support for further tasks will become necessary. For each selected task, an interactive dialog about the required input and output data as well as a few additional information are printed during the execution of the program.Reasons for the new version: The requirement for enlarging the previous version of the Utilities [S. Fritzsche, Comput. Phys. Comm. 141 (2001) 163] arose from the recent application of the Ratip package for large-scale radiative and Auger computations. A number of new subtasks now refer to the handling of Auger amplitudes and their proper combination in order to facilitate the interpretation of complex spectra. A few further tasks, such as the direct access to the one-electron matrix elements for some given set of orbital functions, have been found useful also in the analysis of data.Summary of revisions: extraction and handling of atomic data within the framework of Ratip. With the revised version, we now ‘add’ another 13 tasks which refer to the manipulation of data files, the generation and interpretation of Auger spectra, the computation of various one- and two-electron matrix elements as well as the evaluation of momentum densities and grid parameters. Owing to the rather large number of subtasks, the main menu has been divided into seven groups from which the individual tasks can be selected very similarly as before.Typical running time: The program responds promptly for most of the tasks. The responding time for some tasks, such as the generation of a relativistic momentum density, strongly depends on the size of the corresponding data files and the number of grid points.Unusual features of the program: A total of 29 different tasks are supported by the program. Starting from the main menu, the user is guided interactively through the program by a dialog and a few additional explanations. For each task, a short summary about its function is displayed before the program prompts for all the required input data.     

ACTAS : A System Design for Associative and Commutative Tree Automata Theory

ACTAS is an integrated system for manipulating associative and commutative tree automata (AC-tree automata for short), that has various functions such as for Boolean operations of AC-tree automata, computing rewrite descendants, and solving emptiness and membership problems. In order to deal with high-complexity problems in reasonable time, over- and under-approximation algorithms are also equipped. Such functionality enables us automated verification of safety property in infinite state models, that is helpful in the domain of, e.g. network security, in particular, for security problems of cryptographic protocols allowing an equational property. In runtime of model construction, a tool support for analysis of state space expansion is provided. The intermediate status of the computation is displayed in numerical data table, and also the line graphs are generated. Besides, a graphical user interface of the system provides us a user-friendly environment for handy use.     

Bandwidth on AT-free graphs

We study the classical Bandwidth problem from the viewpoint of parametrised algorithms. Given a graph G=(V,E) and a positive integer k, the Bandwidth problem asks whether there exists a bijective function β:{1,…,∣V∣}→V such that for every edge uv∈E, ∣β⁻¹(u)−β⁻¹(v)∣≤k. It is known that under standard complexity assumptions, no algorithm for Bandwidth with running time of the form f(k)n^O(1) exists, even when the input is restricted to trees. We initiate the search for classes of graphs where such algorithms do exist. We present an algorithm with running time n⋅2^O(klogk) for Bandwidth on AT-free graphs, a well-studied graph class that contains interval, permutation, and cocomparability graphs. Our result is the first non-trivial algorithm that shows fixed-parameter tractability of Bandwidth on a graph class on which the problem remains NP-complete.     

A component- and push-based architectural style for ajax applications

A new breed of web application, dubbed ajax, is emerging in response to a limited degree of interactivity in large-grain stateless Web interactions. At the heart of this new approach lies a single page interaction model that facilitates rich interactivity. Also push-based solutions from the distributed systems are being adopted on the web for ajax applications. The field is, however, characterized by the lack of a coherent and precisely described set of architectural concepts. As a consequence, it is rather difficult to understand, assess, and compare the existing approaches. We have studied and experimented with several ajax frameworks trying to understand their architectural properties. In this paper, we summarize four of these frameworks and examine their properties and introduce the spiar architectural style which captures the essence of ajax applications. We describe the guiding software engineering principles and the constraints chosen to induce the desired properties. The style emphasizes user interface component development, intermediary delta-communication between client/server components, and push-based event notification of state changes through the components, to improve a number of properties such as user interactivity, user-perceived latency, data coherence, and ease of development. In addition, we use the concepts and principles to discuss various open issues in ajax frameworks and application development.     

Mobile data collection in sensor networks: The TinyLime middleware

In this paper we describe TinyLime, a novel middleware for wireless sensor networks that departs from the traditional setting where sensor data is collected by a central monitoring station, and enables instead multiple mobile monitoring stations to access the sensors in their proximity and share the collected data through wireless links. This intrinsically context-aware setting is demanded by applications where the sensors are sparse and possibly isolated, and where on-site, location-dependent data collection is required. An extension of the Lime middleware for mobile ad hoc networks, TinyLime makes sensor data available through a tuple space interface, providing the illusion of shared memory between applications and sensors. Data aggregation capabilities and a power-savvy architecture complete the middleware features. The paper presents the model and application programming interface of TinyLime, together with its implementation for the Crossbow MICA2 sensor platform.     

A verified Common Lisp implementation of Buchberger’s algorithm in ACL2

In this article, we present the formal verification of a Common Lisp implementation of Buchberger’s algorithm for computing Gröbner bases of polynomial ideals. This work is carried out in ACL2, a system which provides an integrated environment where programming (in a pure functional subset of Common Lisp) and formal verification of programs, with the assistance of a theorem prover, are possible. Our implementation is written in a real programming language and it is directly executable within the ACL2 system or any compliant Common Lisp system. We provide here snippets of real verified code, discuss the formalization details in depth, and present quantitative data about the proof effort.