Quantitative online prediction of peptide binding to the major histocompatibility complex

With its implications for vaccine discovery, the accurate prediction of T cell epitopes is one of the key aspirations of computational vaccinology. We have developed a robust multivariate statistical method, based on partial least squares, for the quantitative prediction of peptide binding to major histocompatibility complexes (MHC), the principal checkpoint on the antigen presentation pathway. As a service to the immunobiology community, we have made a Perl implementation of the method available via a World Wide Web server. We call this server MHCPred. Access to the server is freely available from the URL: http://www.jenner.ac.uk/MHCPred. We have exemplified our method with a model for peptides binding to the common human MHC molecule HLA-B*3501.

A Semantic-Oriented Architecture of a Functional Module for Personalized and Adaptive Access to the Knowledge in a Multimedia Digital Library

This article presents the principal results of the doctoral thesis “Semantic-oriented Architecture and Models for Personalized and Adaptive Access to the Knowledge in Multimedia Digital Library” by Desislava Ivanova Paneva-Marinova (Institute of Mathematics and Informatics), successfully defended before the Specialised Academic Council for Informatics and Mathematical Modelling on 27 October, 2008.

A Survey on the Integration of Enterprise Applications as a Service

The present paper discusses the process of multi-lateral integration of the business applications, which requires the construction of a common infra-structure, acquires the format of a service and leads to release of the individual construction of a private infra-structure by every participant in the process.

webComputing Service Framework

Presented is webComputing – a general framework of mathematically oriented services including remote access to hardware and software resources for mathematical computations, and web interface to dynamic interactive computations and visualization in a diversity of contexts: mathematical research and engineering, computer-aided mathematical/technical education and distance learning. webComputing builds on the innovative webMathematica technology connecting technical computing system Mathematica to a web server and providing tools for building dynamic and interactive web-interface to Mathematica-based functionality. Discussed are the conception and some of the major components of webComputing service: Scientific Visualization, Domain- Specific Computations, Interactive Education, and Authoring of Interactive Pages.

A WEB-System for Computer Experiments in the Field of Program Transformations

The paper presents basic notions and scientific achievements in the field of program transformations, describes usage of these achievements both in the professional activity (when developing optimizing and unparallelizing compilers) and in the higher education. It also analyzes main problems in this area. The concept of control of program transformation information is introduced in the form of specialized knowledge bank on computer program transformations to support the scientific research, education and professional activity in the field. The tasks that are solved by the knowledge bank are formulated. The paper is intended for experts in the artificial intelligence, optimizing compilation, postgraduates and senior students of corresponding specialties; it may be also interesting for university lecturers and instructors.

Ontology-based Classification of News in an Electronic Newspaper

This paper deals with the classification of news items in ePaper, a prototype system of a future personalized newspaper service on a mobile reading device. The ePaper system aggregates news items from various news providers and delivers to each subscribed user (reader) a personalized electronic newspaper, utilizing content-based and collaborative filtering methods. The ePaper can also provide users "standard" (i.e., not personalized) editions of selected newspapers, as well as browsing capabilities in the repository of news items. This paper concentrates on the automatic classification of incoming news using hierarchical news ontology. Based on this classification on one hand, and on the users' profiles on the other hand, the personalization engine of the system is able to provide a personalized paper to each user onto her mobile reading device.

Multiscale modelling:approaches and challenges

Multiscale systems that are characterized by a great range of spatial–temporal scales arise widely in many scientific domains. These range from the study of protein conformational dynamics to multiphase processes in, for example, granular media or haemodynamics, and from nuclear reactor physics to astrophysics. Despite the diversity in subject areas and terminology, there are many common challenges in multiscale modelling, including validation and design of tools for programming and executing multiscale simulations. This Theme Issue seeks to establish common frameworks for theoretical modelling, computing and validation, and to help practical applications to benefit from the modelling results. This Theme Issue has been inspired by discussions held during two recent workshops in 2013: ‘Multiscale modelling and simulation’ at the Lorentz Center, Leiden (http://www.lorentzcenter.nl/lc/web/2013/569/info.php3?wsid=569&venue=Snellius), and ‘Multiscale systems: linking quantum chemistry, molecular dynamics and microfluidic hydrodynamics’ at the Royal Society Kavli Centre. The objective of both meetings was to identify common approaches for dealing with multiscale problems across different applications in fluid and soft matter systems. This was achieved by bringing together experts from several diverse communities.

One Approach to Knowledge Mapping for International Student Portal

* The work is partly supported by RFFI grant 08-07-00062-a

Modernizing Legacy Physics Applications for Reuse in Web and SOA

This paper concerns the application of recent information technologies for creating a software system for numerical simulations in the domain of plasma physics and in particular metal vapor lasers. The presented work is connected with performing modernization of legacy physics software for reuse on the web and inside a Service-Oriented Architecture environment. Applied and described is the creation of Java front-ends of legacy C++ and FORTRAN codes. Then the transformation of some of the scientific components into web services, as well as the creation of a web interface to the legacy application, is presented. The use of the BPEL language for managing scientific workflows is also considered.

Fast Information Retrieval in the Open Grid Service Architecture

This is an extended version of an article presented at the Second International Conference on Software, Services and Semantic Technologies, Sofia, Bulgaria, 11–12 September 2010.

The challenges of representing human behaviour in simulation models:some case examples from supply chain, evacuation modelling and rail disruption

As more of the economy moves from traditional manufacturing to the service sector, the nature of work is becoming less tangible and thus, the representation of human behaviour in models is becoming more important. Representing human behaviour and decision making in models is challenging, both in terms of capturing the essence of the processes, and also the way that those behaviours and decisions are or can be represented in the models themselves. In order to advance understanding in this area, a useful first step is to evaluate and start to classify the various types of behaviour and decision making that are required to be modelled. This talk will attempt to set out and provide an initial classification of the different types of behaviour and decision making that a modeller might want to represent in a model. Then, it will be useful to start to assess the main methods of simulation in terms of their capability in representing these various aspects. The three main simulation methods, System Dynamics, Agent Based Modelling and Discrete Event Simulation all achieve this to varying degrees. There is some evidence that all three methods can, within limits, represent the key aspects of the system being modelled. The three simulation approaches are then assessed for their suitability in modelling these various aspects. Illustration of behavioural modelling will be provided from cases in supply chain management, evacuation modelling and rail disruption.

BOWL:augmenting the semantic web with beliefs

As the Semantic Web is an open, complex and constantly evolving medium, it is the norm, but not exception that information at different sites is incomplete or inconsistent. This poses challenges for the engineering and development of agent systems on the Semantic Web, since autonomous software agents need to understand, process and aggregate this information. Ontology language OWL provides core language constructs to semantically markup resources on the Semantic Web, on which software agents interact and cooperate to accomplish complex tasks. However, as OWL was designed on top of (a subset of) classic predicate logic, it lacks the ability to reason about inconsistent or incomplete information. Belief-augmented Frames (BAF) is a frame-based logic system that associates with each frame a supporting and a refuting belief value. In this paper, we propose a new ontology language Belief-augmented OWL (BOWL) by integrating OWL DL and BAF to incorporate the notion of confidence. BOWL is paraconsistent, hence it can perform useful reasoning services in the presence of inconsistencies and incompleteness. We define the abstract syntax and semantics of BOWL by extending those of OWL. We have proposed reasoning algorithms for various reasoning tasks in the BOWL framework and we have implemented the algorithms using the constraint logic programming framework. One example in the sensor fusion domain is presented to demonstrate the application of BOWL.

Majestic Gamification:a case study in the adoption of a service innovation

Purpose: A case study is presented concerning a gamified awards system designed to encourage software users to explore a suite of tools, and to share their expertise level in profile pages. Majestic is a high-tech business based in the West Midlands (UK) w hich offers a Link Intelligence database using a Software as a Service (SaaS) business model. Customers leverage the database for tasks including Search Engine Optimisation (SEO) by using a suite of web-based tools. Getting to know all the tools and how they can be deployed to good effect represents a considerable learning challenge, and Majestic were aware that. Design/methodology/approach: We present the development of Majestic Awards as a case study highlighting the most important design decisions. Then we reflect on the development process as an example of innovation adoption, thereby identifying resources and cu ltura l factors which were critical in ensuring the success of the project. Findings: The gamified awards system makes learning the tools an enjoyable, explorative experience. Success factors included identifying a clear business goal, the process/ project f it, senior management buy in, and identifying the knowledge and resources to resolve t echnical issues. Originality/value: Prior to gamification of the system, only the most expert users regu larly utilized all the tools. The user base is now more knowl edgable about the system and some users choose to use the system to publicize their expertise.

Representing supply chain events on the Web of data

The Electronic Product Code Information Service (EPCIS) is an EPCglobal standard, that aims to bridge the gap between the physical world of RFID1 tagged artifacts, and information systems that enable their tracking and tracing via the Electronic Product Code (EPC). Central to the EPCIS data model are "events" that describe specific occurrences in the supply chain. EPCIS events, recorded and registered against EPC tagged artifacts, encapsulate the "what", "when", "where" and "why" of these artifacts as they flow through the supply chain. In this paper we propose an ontological model for representing EPCIS events on the Web of data. Our model provides a scalable approach for the representation, integration and sharing of EPCIS events as linked data via RESTful interfaces, thereby facilitating interoperability, collaboration and exchange of EPC related data across enterprises on a Web scale.

Architecture of remote monitoring and diagnosis system based on service-oriented architecture(SOA)

In view of the increasingly complexity of services logic and functional requirements, a new system architecture based on SOA was proposed for the equipment remote monitoring and diagnosis system. According to the design principles of SOA, different levels and different granularities of services logic and functional requirements for remote monitoring and diagnosis system were divided, and a loosely coupled web services system was built. The design and implementation schedule of core function modules for the proposed architecture were presented. A demo system was used to validate the feasibility of the proposed architecture.