Monthly Archives: November 2008

Testing Software Based on Design by Contract

Diana Berberova, Boyan Bontchev

Abstract: In the last decade, several proposals have been done for construction of aspect-oriented system for testing software products. The article presents results from design and development of a new aspect-oriented system for testing software created in Java 5 as an open source project named CodeGontract, by using Design by Contract methodology. The system provides means of describing contracts and conditions during the design of software systems that should be satisfied during the system work process. Various conditions used in the contracts are able to be defined by means of preconditions, post-conditions and invariants. In order to describe these conditions in con- tracts, Java annotations are used. When using the CodeContract system, contracts should be cre- ated during the development of software application. Then runtime checks of contracts are exe- cuted during the testing of the software application.

Keywords: design by contract, testing, aspect-oriented programming.

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A Genetic Algorithm for Project Planning Problem

Milena Karova, Julka Petkova, Vassil Smarkov

Abstract: This paper presents implementation of Genetic Algorithms in Project Planning and Project Scheduling Problem. There are strict requirements to timeframes and budpet cost for projects. Project management causes !he problem of efficient resource assignment, activity, time constraints and relationships between activities. Genetic Algorithm uses random presentation of chromosome and two types of crossover.” uniform and arithmetic. The approach is tested on a set of randomly generated problems.

Key words: genetic operators, planning, project management, scheduling

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CPLD Fuzzy Elastic Strain Probe Loading Controller

Yassen Gorbounov, Radoslav Rusinov, Constantin Pavlitov, Alexandar  Alexandrov,  Kliment Hadjov, Dimitar Dontchev

Abstract: The paper is focused on the application of Verilog Hardware Description  Language (HDL) for implementation of parallel processing algorithms in electromechanical systems. A dedicated fuzzy controller for a DC motor drive is considered that is implemented on the basis of Xilinx CoolRunner II Complex Programmable Logic Device (CPLD). The controller is the main part of an automated system for elastic strain loading of etalon probes. The application of a CPLD is determined by the necessity of independent parallel  running algorithms. These are the detection and correction algorithms of the high precision linear incremental quadrature optical encoder that is used in the position feedback loop, the speed measurement algorithm, the fuzzy controller and the output generation algorithm used to produce Pulse Width Modulation (PWM) sipna/s which directly control the motor power driver.

Key words: CPLD, Electromechanical Systems, Fuzzy Logic, Motor Control, Parallel Processing, Verilog HDL

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Understanding of Interferon-Gamma Binding

Leander Litov, Peicho Petkov, Petko Petkov, Stoyan Markov, Nevena llieva

Abstract:An investigation using MD simulations of interaction of human interferon-gamma and both its known ligands (its extracellular receptor and heparin derived oligosacchorides) were carried out. The significance of the positive charge, localized in the peptide’s C-terminus, in the interaction with its receptor is emphasized.

Keywords: human interferon gamma, human interferon gamma receptor, heparin, heparan sulfate, MD simulations, GROMACS.

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Design and Implementation of Graphs with C#

Mariana Goranova

Abstract:This paper proposes a programming framework for graph data structures and graph algorithms. .NET Framework Class Library (FCL) does not encapsulate graph data type. The goal of the paper is to find the most abstract formulation of graph algorithms and then implementing efficient representation of them. The new features of C#, such as generics, iterators, lambda expressions and query expressions simplify the overall programming model and enable its structure to be described and checked more accurately.

Key words: graph, adjacency list, iterator design pattern, CN, .NET Framework.

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Shared Memory Design for Multicore Systems

Peter Manoilov

Abstract:In the article the effectiveness of shared memory blocks with various orpaniza/ion and architecture in multicore systems on FPGA is investigated. A method of quad-port memory imple- mentation on FPGA, using the existing dual-pon RAM FPGA cells and adding a doubled clock is shown. Some of  important results of the investigations multicore speed-up as function of core number and memory port number are commented.

Keywords: multicore system, shared memory, FPGA , quad-port RAM

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DALIGRES – A Graph Query Tool to Unravel the Life Science Database Maze

Matthias Lange, Matthias Klapperstuck, Karl Spies, Uwe Scholz

Abstract: The knowledge found in the Web, in particular in life-science databases, are a major resource in molecular biology dry lab research. To support the interpretation of measured facts from the wet lab, like transcriptional activity, DNA sequences or protein masses, the functional context has to be determined. This is done using dry lab research, which is dependent on existing biological knowledge. In general, biological knowled9t3 is worldwide represented in a network of databases.

In this paper we present methods and tools for knowledge extraction from life science databases, which prevents the scientists from expensive web na\/igation and allows a large scale automated database exploration. Using computed data linkage graphs (DLG), we present a query language to extract interlinked biological knowledge.

Based  on  the software  tool DALIGRES  which enables  the joining  of  millions  of  data points  over hundreds of databases, we computed data networks of protein knowledge, which interconnect me- tabolic,  disease,  enzyme  and  gene  function  data.  Availability.’  The  data  linkage  graphs  (XML  or TGF format), the  integrated  database  schema  (CML or  GRAPH-ML)  and the  DALIGPES  tool can be downloaded  from the following  URL.” http.”//pgrc.ipk-gatersleben.de/dlg/

Keywords: bioinformatics, database networks, database integration, prap/› queries

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Secure Partial Reconfiguration of FPGAs

Betim Quo, Fisnik Kraja

Abstract: SRAM FPGAs are configured by loading application-specific configuration data into an internal confipura/ion memory. The necessity of configuration on each power up makes it easi’er for attackers to clone, reverse engineer, or tamper the bit-stream during configuration. Bit-stream encryption is the most effective and practical solution to improve the security of SRAM FPGAs and protecting the configuration data. One of the drawbacks of thIS solutlDfl IS that it is not possible to use partial reconfiguration and read-back when the device is configured with an encrypted bit- stream. This paper investigates a method to perform a secure partial reconfiguration and improve the security of SRAM FPGAs through exploiting a configuration controller that enables an FPGA to dynamically reconfigure itself under the control of an embedded processor core.

Key words: Design Security, FPGA Bitstream, Dynamic Partial Reconfiguration, FPGA

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Methods for Determining Protein Structure Similarity

Stoicho Stoichev, Dobrinka Petrova

Abstract: Different  methods for protein structure comparison are presented in this paper. The methods are grouped by their level of protein structure representation. The described models present the structure of proteins from the low atomic level to the level of secondary structure elements. The estimation of these methods is made according to three criteria.‘ complexity, accuracy and biological significance of the method and the final results.

Keywords: protein structure comparison, protein structure, algorithmic complexity.

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