HyPaLib: a database of RNAs and RNA structural elements defined by hybrid patterns

The database, called HyPaLib (for Hybrid Pattern Library), contains annotated structural elements characteristic for certain classes of structural and/or functional RNAs. These elements are described in a language specifically designed for this purpose. The language allows convenient specification of hybrid patterns, i.e. motifs consisting of sequence features and structural elements together with sequence similarity and thermodynamic constraints. We are currently developing software tools that allow a user to search sequence databases for any pattern in HyPaLib, thus providing functionality which is similar to PROSITE, but dedicated to the more complex patterns in RNA sequences. HyPaLib is available at http://bibiserv.techfak.uni-bielefeld.de/HyPa/.

One Approach to the Problem Solution of Specialized Software Development for Subject Search

In the article relevance of system development for subject search using computational linguistics is considered. The basic principles of system functioning are defined. The principle of grammar development for information retrieval from the partially structured text in a natural language is considered. The ranging principle of results of information search is defined.

SubCM: A tool for improved visibility of software change in an industrial setting

Software Configuration Management is the discipline of managing large collections of software development artefacts from which software products are built. Software configuration management tools typically deal with artefacts at fine levels of granularity - such as individual source code files - and assist with coordination of changes to such artefacts. This paper describes a lightweight tool, designed to be used on top of a traditional file-based configuration management system. The add-on tool support enables users to flexibly define new hierarchical views of product structure, independent of the underlying artefact-repository structure. The tool extracts configuration and change data with respect to the user-defined hierarchy, leading to improved visibility of how individual subsystems have changed. The approach yields a range of new capabilities for build managers, and verification and validation teams. The paper includes a description of our experience using the tool in an organization that builds large embedded software systems.

A probabilistic switch model of information flow in social networks: Application for virtual circuits to organizational design

Network building and exchange of information by people within networks is crucial to the innovation process. Contrary to older models, in social networks the flow of information is noncontinuous and nonlinear. There are critical barriers to information flow that operate in a problematic manner. New models and new analytic tools are needed for these systems. This paper introduces the concept of virtual circuits and draws on recent concepts of network modelling and design to introduce a probabilistic switch theory that can be described using matrices. It can be used to model multistep information flow between people within organisational networks, to provide formal definitions of efficient and balanced networks and to describe distortion of information as it passes along human communication channels. The concept of multi-dimensional information space arises naturally from the use of matrices. The theory and the use of serial diagonal matrices have applications to organisational design and to the modelling of other systems. It is hypothesised that opinion leaders or creative individuals are more likely to emerge at information-rich nodes in networks. A mathematical definition of such nodes is developed and it does not invariably correspond with centrality as defined by early work on networks.

Test strategies on functionally partitioned module-based programmable architecture for base-band processing

A specialised reconfigurable architecture for telecommunication base-band processing is augmented with testing resources. The routing network is linked via virtual wire hardware modules to reduce the area occupied by connecting buses. The number of switches within the routing matrices is also minimised, which increases throughput without sacrificing flexibility. The testing algorithm was developed to systematically search for faults in the processing modules and the flexible high-speed routing network within the architecture. The testing algorithm starts by scanning the externally addressable memory space and testing the master controller. The controller then tests every switch in the route-through switch matrix by making loops from the shared memory to each of the switches. The local switch matrix is also tested in the same way. Next the local memory is scanned. Finally, pre-defined test vectors are loaded into local memory to check the processing modules. This algorithm scans all possible paths within the interconnection network exhaustively and reports all faults. Strategies can be inserted to bypass minor faults

FlexSIG-Flexible software inspection groupware

The objective of this research is to design and build a groupware system which will allow members of a distributed group more flexibility in performing software inspection. Software inspection, which is part of non-execution based testing in software development, is a group activity. The groupware system aims to provide a system that will improve acceptability of groupware and improve software quality by providing a software inspection tool that is flexible and adaptable. The groupware system provide a flexible structure for software inspection meetings. The groupware system will extend the structure of the software inspection meeting itself, allowing software inspection meetings to use all four quadrant of the space-time matrix: face-to-face, distributed synchronous, distributed asynchronous, and same place-different time. This will open up new working possibilities. The flexibility and adaptability of the system allows work to switch rapidly between synchronous and asynchronous interaction. A model for a flexible groupware system was developed. The model was developed based on review of the literature and questionnaires. A prototype based on the model was built using java and WWW technology. To test the effectiveness of the system, an evaluation was conducted. Questionnaires was used to gather response from the users. The evaluations ascertained that the model developed is flexible and adaptable to the different working modes, and the system is capable of supporting several different models of the software inspection process.

The design of fault tolerant software for loosely coupled distributed systems

Requirements for systems to continue to operate satisfactorily in the presence of faults has led to the development of techniques for the construction of fault tolerant software. This thesis addresses the problem of error detection and recovery in distributed systems which consist of a set of communicating sequential processes. A method is presented for the `a priori' design of conversations for this class of distributed system. Petri nets are used to represent the state and to solve state reachability problems for concurrent systems. The dynamic behaviour of the system can be characterised by a state-change table derived from the state reachability tree. Systematic conversation generation is possible by defining a closed boundary on any branch of the state-change table. By relating the state-change table to process attributes it ensures all necessary processes are included in the conversation. The method also ensures properly nested conversations. An implementation of the conversation scheme using the concurrent language occam is proposed. The structure of the conversation is defined using the special features of occam. The proposed implementation gives a structure which is independent of the application and is independent of the number of processes involved. Finally, the integrity of inter-process communications is investigated. The basic communication primitives used in message passing systems are seen to have deficiencies when applied to systems with safety implications. Using a Petri net model a boundary for a time-out mechanism is proposed which will increase the integrity of a system which involves inter-process communications.

Optical grooming switch with regenerative functionality for transparent interconnection of networks

We demonstrate a regenerative optical grooming switch for buffer-less interconnection of metro/access and metro/core ring networks with switching functionality in time, space and wavelength domain. Key functionalities of the router are the traffic aggregation with time-slot interchanging (TSI) functionality, the WDM-to-ODTM multiplexing and the OTDM-to-WDM demultiplexing of high-speed channel into lower bit-rate tributaries as well as multi-wavelength all-optical 2R regeneration of several higher-speed signals. BER and Q-factor measurements of different switching scenarios show excellent performance with no error floor and Q-factors above 21 dB.

An all-optical grooming switch for interconnecting access and metro ring networks

A regenerative all-optical grooming switch for interconnecting 130 Gbit/s on-off keying (OOK) metro/core ring and 43 Gbit/s-OOK metro/access ring networks with switching functionality in time, space, and wavelength domains is demonstrated. Key functionalities of the switch are traffic aggregation with time-slot interchanging functionality, optical time division multiplexing (OTDM) to wavelength division multiplexing (WDM) demultiplexing, and multi-wavelength 2R regeneration. Laboratory and field demonstrations show the excellent performance of the new concept with error-free signal transmission and Q-factors above 20 dB.

Polynomial function intervals for floating-point software verification

The focus of our work is the verification of tight functional properties of numerical programs, such as showing that a floating-point implementation of Riemann integration computes a close approximation of the exact integral. Programmers and engineers writing such programs will benefit from verification tools that support an expressive specification language and that are highly automated. Our work provides a new method for verification of numerical software, supporting a substantially more expressive language for specifications than other publicly available automated tools. The additional expressivity in the specification language is provided by two constructs. First, the specification can feature inclusions between interval arithmetic expressions. Second, the integral operator from classical analysis can be used in the specifications, where the integration bounds can be arbitrary expressions over real variables. To support our claim of expressivity, we outline the verification of four example programs, including the integration example mentioned earlier. A key component of our method is an algorithm for proving numerical theorems. This algorithm is based on automatic polynomial approximation of non-linear real and real-interval functions defined by expressions. The PolyPaver tool is our implementation of the algorithm and its source code is publicly available. In this paper we report on experiments using PolyPaver that indicate that the additional expressivity does not come at a performance cost when comparing with other publicly available state-of-the-art provers. We also include a scalability study that explores the limits of PolyPaver in proving tight functional specifications of progressively larger randomly generated programs. © 2014 Springer International Publishing Switzerland.

A Small Settings Case Study using TSPi in a Software Project

This article introduces a small setting case study about the benefits of using TSPi in a software project. An adapted process from the current process based on the TSPi was defined. The pilot project had schedule and budget constraints. The process began by gathering historical data from previous projects in order to get a measurement repository. The project was launched with the following goals: increase the productivity, reduce the test time and improve the product quality. Finally, the results were analysed and the goals were verified.

Traceability Management Architectures Supporting Total Traceability in the Context of Software Engineering

In the area of Software Engineering, traceability is defined as the capability to track requirements, their evolution and transformation in different components related to engineering process, as well as the management of the relationships between those components. However the current state of the art in traceability does not keep in mind many of the elements that compose a product, specially those created before requirements arise, nor the appropriated use of traceability to manage the knowledge underlying in order to be handled by other organizational or engineering processes. In this work we describe the architecture of a reference model that establishes a set of definitions, processes and models which allow a proper management of traceability and further uses of it, in a wider context than the one related to software development.

A Software Platform for Educational Board Games

Educational games such as quizzes, quests, puzzles, mazes and logical problems may be modeled as multimedia board games. In the scope of the ADOPTA project1 being under development at the Faculty of Mathematics and Informatics at Sofia University, a formal model for presentation of such educational board games was invented and elaborated. Educational games can be modeled as special board mini-games, with a board of any form and any types of positions. Over defined positions, figures (objects) with certain properties are placed and, next, there are to be defined formal rules for manipulation of these figures and resulted effects. The model has been found to be general enough in order to allow description and execution control of more complex logical problems to be solved by several actions delivered to/by the player according some formal rules and context conditions and, in general, of any learning activities and their workflow. It is used as a base for creation of a software platform providing facilities for easy construction of multimedia board games and their execution. The platform consists of game designer (i.e., a game authoring tool) and game run-time controller communicating each other through game repository. There are created and modeled many examples of educational board games appropriate for didactic purposes, self evaluations, etc., which are supposed to be designed easily by authors with no IT skills and experience. By means of game metadata descriptions, these games are going be included into narrative storyboards and, next, delivered to learners with appropriate profile according their learning style, preferences, etc. Moreover, usage of artificial intelligence agents is planned as well – once as playing virtual opponents of the player or, otherwise, being virtual advisers of the gamer helping him/her in finding the right problem solution within given domain such as discovering a treasure using a location map, finding best tour in a virtual museum, guessing an unknown word in a hangman game, and many others.

Design, synthesis and thermal behaviour of a series of well-defined clickable and triggerable sulfonate polymers

In the printing industry, the exploitation of triggerable materials that can have their surface properties altered on application of a post-deposition external stimulus has been crucial for the production of robust layers and patterns. To this end, herein, a series of clickable poly(R-alkyl p-styrene sulfonate) homopolymers, with systematically varied thermally-labile protecting groups, has been synthesised via reversible addition-fragmentation chain transfer (RAFT) polymerisation. The polymer range has been designed to offer varied post-deposition thermal treatment to switch them from hydrophobic to hydrophilic. Suitable RAFT conditions have been identified to produce well-defined homopolymers (Đ, Mw/Mn < 1.11 in all cases) at high monomer conversions (>80% for all but one monomer) with controllable molar mass. Poly(p-styrene sulfonate) with an isobutyl protecting group has been shown to be the most readily thermolysed polymer that remains stable at room temperature, and was thus investigated further by incorporation into a diblock copolymer, P3HT-b-PiBSS, by click chemistry. The strategy for preparation of thermal modifiable block copolymers exploiting R-protected p-styrene sulfonates and azide-alkyne click chemistry presented herein allows the design of new, roll-to-roll processable materials for potential application in the printing industry, particularly organic electronics.