Molecular dynamics simulations:bring biomolecular structures alive on a computer

The molecular dynamics (MD) simulations play a very important role in science today. They have been used successfully in binding free-energy calculations and rational design of drugs and vaccines. MD simulations can help visualize and understand structures and dynamics at an atomistic level when combined with molecular graphics programs. The molecular and atomistic properties can be displayed on a computer in a time-dependent way, which opens a road toward a better understanding of the relationship of structure, dynamics, and function. In this chapter, the basics of MD are explained, together with a step-by-step description of setup and running an MD simulation.

An Idea of a Computer Knowledge Bank on Medical Diagnostics

The paper is a description of information and software content of a computer knowledge bank on medical diagnostics. The classes of its users and the tasks which they can solve are described. The information content of the bank contains three ontologies: an ontology of observations in the field of medical diagnostics, an ontology of knowledge base (diseases) in medical diagnostics and an ontology of case records, and also it contains three classes of information resources for every division of medicine – observation bases, knowledge bases, and data bases (with data about patients), that correspond to these ontologies. Software content consists of editors for information of different kinds (ontologies, bases of observations, knowledge and data), and also of a program which performs medical diagnostics.

Connection of Network Sensors to Distributed Information Measurement and Control System for Education and Research

The development of the distributed information measurement and control system for optical spectral research of particle beam and plasma objects and the execution of laboratory works on Physics and Engineering Department of Petrozavodsk State University are described. At the hardware level the system is represented by a complex of the automated workplaces joined into computer network. The key element of the system is the communication server, which supports the multi-user mode and distributes resources among clients, monitors the system and provides secure access. Other system components are formed by equipment servers (CАМАC and GPIB servers, a server for the access to microcontrollers MCS-196 and others) and the client programs that carry out data acquisition, accumulation and processing and management of the course of the experiment as well. In this work the designed by the authors network interface is discussed. The interface provides the connection of measuring and executive devices to the distributed information measurement and control system via Ethernet. This interface allows controlling of experimental parameters by use of digital devices, monitoring of experiment parameters by polling of analog and digital sensors. The device firmware is written in assembler language and includes libraries for Ethernet-, IP-, TCP- и UDP-packets forming.

Generalized Nets Model of an E-Learning System Software Architecture

The paper has been presented at the International Conference Pioneers of Bulgarian Mathematics, Dedicated to Nikola Obreshko ff and Lubomir Tschakaloff , Sofi a, July, 2006.

Semantic Description of Web Services and Possibilities of BPEL4WS

The using of the upsurge of semantics web technologies gives a possibility for an increasing of the flexibility, extensibility and consistency of the existent industrial standards for modeling of web services. In the paper the types of semantic description of web services and the degree of their realization in BPEL4WS (Business Process Execution Language for Web Services) respectively on the abstract and executable level are treated. The methods for using of BPEL4WS for the purposes of semantic web services in the direction of their semi-automatic integration are suggested.

INFRAWEBS BPEL-Based Editor for Creating the Semantic Web Services Description

INFRAWEBS project [INFRAWEBS] considers usage of semantics for the complete lifecycle of Semantic Web processes, which represent complex interactions between Semantic Web Services. One of the main initiatives in the Semantic Web is WSMO framework, aiming at describing the various aspects related to Semantic Web Services in order to enable the automation of Web Service discovery, composition, interoperation and invocation. In the paper the conceptual architecture for BPEL-based INFRAWEBS editor is proposed that is intended to construct a part of WSMO descriptions of the Semantic Web Services. The semantic description of Web Services has to cover Data, Functional, Execution and QoS semantics. The representation of Functional semantics can be achieved by adding the service functionality to the process description. The architecture relies on a functional (operational) semantics of the Business Process Execution Language for Web Services (BPEL4WS) and uses abstract state machine (ASM) paradigm. This allows describing the dynamic properties of the process descriptions in terms of partially ordered transition rules and transforming them to WSMO framework.

The Use of Situation Representation when Searching for Solutions in Computer Aided Design Systems

Projects solutions reuse methodology is offered for software development. The main idea consists in connection of the system objective with the situation using the entities which describe the condition of the system in the process of the objective statement. Every situation is associated with one or several design solutions, which can be used at the development. Based on this connection the situation representing language has been created, it lets to express a problem situation using a natural language describe. The similarity measure has been built to compare situations, it is based on the similarity coefficients with adding the absent part weight.

Institute for Bulgarian Language, BAS

The paper presents the history, structure and ongoing activities of the Institute for Bulgarian Language of Bulgarian Academy of Sciences.

Computer Processing of Medieval Slavic Sources in the Institute of Literature at BAS Repertorium Project (1994–2004)

Mixed-content miscellanies (very frequent in the Byzantine and mediaeval Slavic written heritage) are usually defined as collections of works with non-occupational, non-liturgical application, and texts in them are selected and arranged according to no identifiable principle. It is a “readable” type of miscellanies which were compiled mainly on the basis of the cognitive interests of compilers and readers. Just like the occupational ones, they also appeared to satisfy public needs but were intended for individual usage. My textological comparison had shown that mixed- content miscellanies often showed evidence of a stable content – some of them include the same constituent works in the same order, regardless that the manuscripts had no obvious genetic relationship. These correspondences were sufficiently numerous and distinctive that they could not be merely fortuitous, and the only sensible interpretation was that even when the operative organizational principle was not based on independently identifiable criteria, such as the church calendar, liturgical function, or thematic considerations, mixed-content miscellanies (or, at least, portions of their contents) nonetheless fell into types. In this respect, the apparent free selection and arrangement of texts in mixed-content miscellanies turns out to be illusory. The problem was – as the corpus of manuscripts that I and my colleagues needed to examine grew – our ability to keep track of the structure of each one, and to identify structural correspondences among manuscripts within the corpus, diminished. So, at the end of 1993 I addressed a letter to Prof. David Birnbaum (University of Pittsburgh, PA) with a request to help me to solve the problem. He and my colleague Andrey Boyadzhiev (Sofia University) pointed out to me that computers are well suited to recording, processing, and analyzing large amounts of data, and to identifying patterns within the data, and their proposal was that we try to develop a computer system for description of manuscripts, for their analysis and of course, for searching the data. Our collaboration in this project is now ten years old, and our talk today presents an overview of that collaboration.

Politeness in computer-mediated discourse of a virtual team

Drawing on the newest findings of politeness research, this paper proposes an interactionally grounded approach to computer-mediated discourse (CMD). Through the analysis of naturally occurring text-based synchronous interactions of a virtual team the paper illustrates that the interactional politeness approach can account for linguistic phenomena not yet fully explored in computer-mediated discourse analysis. Strategies used for compensating for the lack of audio-visual information in computer-mediated communication, strategies to compensate for the technological constraints of the medium, and strategies to aid interaction management are examined from an interactional politeness viewpoint and compared to the previous findings of CMD analysis. The conclusion of this preliminary research suggests that the endeavour to communicate along the lines of politeness norms in a work-based virtual environment contradicts some of the previous findings of CMD research (unconventional orthography, capitalization, economizing), and that other areas (such as emoticons, backchannel signals and turn-taking strategies) need to be revisited and re-examined from an interactional perspective to fully understand how language functions in this merely text-based environment.

A Metaontology for Medical Diagnostics of Acute Diseases. Part 1. An Informal Description and Definitions of Basic Terms

The aim of this article is to describe formally a metaontology for medical diagnostics of acute diseases in the language of applied logic. The article includes an informal description of the metaontology, and the part of its model which contains the definitions for basic terms of knowledge and situations and also their integrity restrictions in the form of ontological agreements.

A Metaontology for Medical Diagnostics of Acute Diseases. Part 2. A Formal Description of Cause-and-effect Relations

This article is the continuation of the formal description of the metaontology for medical diagnostics in the language of applied logic. It contains a description of interrelations between terms of knowledge and reality in the form of ontological agreements.

A Metaontology for Medical Diagnostics of Acute Diseases. Part 3. A Formal Description of the Causes of Signs’ Values and of Diseases

This article is the final part of the formal description of the metaontology for medical diagnostics in the language of applied logic. It contains a description of the causes of signs’ values and of the causes of diseases.

Methodology for Language Analysis and Generation in Closed Domains: Pharmaceutical Leaflet

The best results in the application of computer science systems to automatic translation are obtained in word processing when texts pertain to specific thematic areas, with structures well defined and a concise and limited lexicon. In this article we present a plan of systematic work for the analysis and generation of language applied to the field of pharmaceutical leaflet, a type of document characterized by format rigidity and precision in the use of lexicon. We propose a solution based in the use of one interlingua as language pivot between source and target languages; we are considering Spanish and Arab languages in this case of application.

Computer-aided System of Semantic Text Analysis of a Technical Specification

The given work is devoted to development of the computer-aided system of semantic text analysis of a technical specification. The purpose of this work is to increase efficiency of software engineering based on automation of semantic text analysis of a technical specification. In work it is offered and investigated the model of the analysis of the text of the technical project is submitted, the attribute grammar of a technical specification, intended for formalization of limited Russian is constructed with the purpose of analysis of offers of text of a technical specification, style features of the technical project as class of documents are considered, recommendations on preparation of text of a technical specification for the automated processing are formulated. The computer-aided system of semantic text analysis of a technical specification is considered. This system consists of the following subsystems: preliminary text processing, the syntactic and semantic analysis and construction of software models, storage of documents and interface.