Search results for: software metrics.
1386 A Simple User Administration View of Computing Clusters
Authors: Valeria M. Bastos, Myrian A. Costa, Matheus Ambrozio, Nelson F. F. Ebecken
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In this paper a very simple and effective user administration view of computing clusters systems is implemented in order of friendly provide the configuration and monitoring of distributed application executions. The user view, the administrator view, and an internal control module create an illusionary management environment for better system usability. The architecture, properties, performance, and the comparison with others software for cluster management are briefly commented.Keywords: Big data, computing clusters, administration view, user view.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 15491385 A Research on Determining the Viability of a Job Board Website for Refugees in Kenya
Authors: Prince Mugoya, Collins Oduor Ondiek, Patrick Kanyi Wamuyu
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Refugee Job Board Website is a web-based application that provides a platform for organizations to post jobs specifically for refugees. Organizations upload job opportunities and refugees can view them on the website. The website also allows refugees to input their skills and qualifications. The methodology used to develop this system is a waterfall (traditional) methodology. Software development tools include Brackets which will be used to code the website and PhpMyAdmin to store all the data in a database.
Keywords: Information technology, refugee, skills, utilization, economy, jobs.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 7511384 Load Forecasting in Microgrid Systems with R and Cortana Intelligence Suite
Authors: F. Lazzeri, I. Reiter
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Energy production optimization has been traditionally very important for utilities in order to improve resource consumption. However, load forecasting is a challenging task, as there are a large number of relevant variables that must be considered, and several strategies have been used to deal with this complex problem. This is especially true also in microgrids where many elements have to adjust their performance depending on the future generation and consumption conditions. The goal of this paper is to present a solution for short-term load forecasting in microgrids, based on three machine learning experiments developed in R and web services built and deployed with different components of Cortana Intelligence Suite: Azure Machine Learning, a fully managed cloud service that enables to easily build, deploy, and share predictive analytics solutions; SQL database, a Microsoft database service for app developers; and PowerBI, a suite of business analytics tools to analyze data and share insights. Our results show that Boosted Decision Tree and Fast Forest Quantile regression methods can be very useful to predict hourly short-term consumption in microgrids; moreover, we found that for these types of forecasting models, weather data (temperature, wind, humidity and dew point) can play a crucial role in improving the accuracy of the forecasting solution. Data cleaning and feature engineering methods performed in R and different types of machine learning algorithms (Boosted Decision Tree, Fast Forest Quantile and ARIMA) will be presented, and results and performance metrics discussed.
Keywords: Time-series, features engineering methods for forecasting, energy demand forecasting, Azure machine learning.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 12791383 Robust Control Design and Analysis Using SCILAB for a Mass-Spring-Damper System
Authors: Yoonsoo Kim
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This paper introduces an open-source software package SCILAB [1], an alternative of MATLAB [2], which can be used for robust control design and analysis of a typical mass-spring-damper (MSD) system. Using the previously published ideas in [3,4], this popular mechanical system is considered to provide another example of usefulness of SCILAB for advanced control design.
Keywords: Robust Control, SCILAB, Mass-Spring-Damper(MSD).
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 39441382 The Leaves of a Tree
Authors: Zhu Jiaming, Yu Mengna
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In this article, models based on quantitative analysis, physical geometry and regression analysis are established, by using analytic hierarchy process analysis, fuzzy cluster analysis, fuzzy photographic and data fitting. The reasons of various leaf shapes among different species and the differences between the leaf shapes on same tree have been solved by using software, such as Eviews, VB and Matlab. We also successfully estimate the leaf mass of a tree and the correlation with the tree profile.Keywords: Leaf shape; Mass; Fuzzy cluster; Regression analysis; Eviews; Matlab
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 15891381 Software Technology Behind Computer Accounting
Authors: M. Župan, V. Budimir
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The main problems of data centric and open source project are large number of developers and changes of core framework. Model-View-Control (MVC) design pattern significantly improved the development and adjustments of complex projects. Entity framework as a Model layer in MVC architecture has simplified communication with the database. How often are the new technologies used and whether they have potentials for designing more efficient Enterprise Resource Planning (ERP) system that will be more suited to accountants?Keywords: Accounting, Enterprise Resource Planning, Model- View-Control, Object Role Modeling, Open Source
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 18801380 Complexity of Component-based Development of Embedded Systems
Authors: M. Zheng, V. S. Alagar
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The paper discusses complexity of component-based development (CBD) of embedded systems. Although CBD has its merits, it must be augmented with methods to control the complexities that arise due to resource constraints, timeliness, and run-time deployment of components in embedded system development. Software component specification, system-level testing, and run-time reliability measurement are some ways to control the complexity.Keywords: Components, embedded systems, complexity, softwaredevelopment, traffic controller system.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 14861379 Analysis of Direct Current Motor in LabVIEW
Authors: E. Ramprasath, P. Manojkumar, P. Veena
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DC motors have been widely used in the past centuries which are proudly known as the workhorse of industrial systems until the invention of the AC induction motors which makes a huge revolution in industries. Since then, the use of DC machines has been decreased due to enormous factors such as reliability, robustness and complexity but it lost its fame due to the losses. In this paper a new methodology is proposed to construct a DC motor through the simulation in LabVIEW to get an idea about its real time performances, if a change in parameter might have bigger improvement in losses and reliability.Keywords: Direct Current motor, LabVIEW software, modelling and analysis, overall characteristics of Direct Current motor.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 30591378 Multi-Sensor Image Fusion for Visible and Infrared Thermal Images
Authors: Amit Kr. Happy
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This paper is motivated by the importance of multi-sensor image fusion with specific focus on Infrared (IR) and Visible image (VI) fusion for various applications including military reconnaissance. Image fusion can be defined as the process of combining two or more source images into a single composite image with extended information content that improves visual perception or feature extraction. These images can be from different modalities like Visible camera & IR Thermal Imager. While visible images are captured by reflected radiations in the visible spectrum, the thermal images are formed from thermal radiation (IR) that may be reflected or self-emitted. A digital color camera captures the visible source image and a thermal IR camera acquires the thermal source image. In this paper, some image fusion algorithms based upon Multi-Scale Transform (MST) and region-based selection rule with consistency verification have been proposed and presented. This research includes implementation of the proposed image fusion algorithm in MATLAB along with a comparative analysis to decide the optimum number of levels for MST and the coefficient fusion rule. The results are presented, and several commonly used evaluation metrics are used to assess the suggested method's validity. Experiments show that the proposed approach is capable of producing good fusion results. While deploying our image fusion algorithm approaches, we observe several challenges from the popular image fusion methods. While high computational cost and complex processing steps of image fusion algorithms provide accurate fused results, but they also make it hard to become deployed in system and applications that require real-time operation, high flexibility and low computation ability. So, the methods presented in this paper offer good results with minimum time complexity.
Keywords: Image fusion, IR thermal imager, multi-sensor, Multi-Scale Transform.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 4111377 Wireless Communicated Smart Wind Sensor
Authors: Zdenek Bohuslavek
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Development of microprocessor controlled sensor for measurement of wind speed and direction is the aim of this study. Electrical circuits and software were developed to the existing electromechanical part of the sensor TM-W2 becoming the properties of so-called smart sensor. The measured data about wind speed (sensitivity 0.01 m/s) and direction (0-360° by step 10°) are transmitted as 16-bit information. The connection between sensor and control unit is realized by radio communication (FM 433 MHz). Transition range is 220 m if used Quad type antenna. This concept provides substitution of actual cable systems by wireless ones.
Keywords: smart wind sensor, anemometer, wind speed, wireless communication
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 19551376 Renewable Energy Trends Analysis: A Patents Study
Authors: Sepulveda Juan
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This article explains the elements and considerations taken into account when implementing and applying patent evaluation and scientometric study in the identifications of technology trends, and the tools that led to the implementation of a software application for patent revision. Univariate analysis helped recognize the technological leaders in the field of energy, and steered the way for a multivariate analysis of this sample, which allowed for a graphical description of the techniques of mature technologies, as well as the detection of emerging technologies. This article ends with a validation of the methodology as applied to the case of fuel cells.Keywords: Energy, technology mapping, patents.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 21721375 Price Prediction Line, Investment Signals and Limit Conditions Applied for the German Financial Market
Authors: Cristian Păuna
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In the first decades of the 21st century, in the electronic trading environment, algorithmic capital investments became the primary tool to make a profit by speculations in financial markets. A significant number of traders, private or institutional investors are participating in the capital markets every day using automated algorithms. The autonomous trading software is today a considerable part in the business intelligence system of any modern financial activity. The trading decisions and orders are made automatically by computers using different mathematical models. This paper will present one of these models called Price Prediction Line. A mathematical algorithm will be revealed to build a reliable trend line, which is the base for limit conditions and automated investment signals, the core for a computerized investment system. The paper will guide how to apply these tools to generate entry and exit investment signals, limit conditions to build a mathematical filter for the investment opportunities, and the methodology to integrate all of these in automated investment software. The paper will also present trading results obtained for the leading German financial market index with the presented methods to analyze and to compare different automated investment algorithms. It was found that a specific mathematical algorithm can be optimized and integrated into an automated trading system with good and sustained results for the leading German Market. Investment results will be compared in order to qualify the presented model. In conclusion, a 1:6.12 risk was obtained to reward ratio applying the trigonometric method to the DAX Deutscher Aktienindex on 24 months investment. These results are superior to those obtained with other similar models as this paper reveal. The general idea sustained by this paper is that the Price Prediction Line model presented is a reliable capital investment methodology that can be successfully applied to build an automated investment system with excellent results.
Keywords: Algorithmic trading, automated investment system, DAX Deutscher Aktienindex.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 6791374 Rigorous Electromagnetic Model of Fourier Transform Infrared (FT-IR) Spectroscopic Imaging Applied to Automated Histology of Prostate Tissue Specimens
Authors: Rohith K Reddy, David Mayerich, Michael Walsh, P Scott Carney, Rohit Bhargava
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Fourier transform infrared (FT-IR) spectroscopic imaging is an emerging technique that provides both chemically and spatially resolved information. The rich chemical content of data may be utilized for computer-aided determinations of structure and pathologic state (cancer diagnosis) in histological tissue sections for prostate cancer. FT-IR spectroscopic imaging of prostate tissue has shown that tissue type (histological) classification can be performed to a high degree of accuracy [1] and cancer diagnosis can be performed with an accuracy of about 80% [2] on a microscopic (≈ 6μm) length scale. In performing these analyses, it has been observed that there is large variability (more than 60%) between spectra from different points on tissue that is expected to consist of the same essential chemical constituents. Spectra at the edges of tissues are characteristically and consistently different from chemically similar tissue in the middle of the same sample. Here, we explain these differences using a rigorous electromagnetic model for light-sample interaction. Spectra from FT-IR spectroscopic imaging of chemically heterogeneous samples are different from bulk spectra of individual chemical constituents of the sample. This is because spectra not only depend on chemistry, but also on the shape of the sample. Using coupled wave analysis, we characterize and quantify the nature of spectral distortions at the edges of tissues. Furthermore, we present a method of performing histological classification of tissue samples. Since the mid-infrared spectrum is typically assumed to be a quantitative measure of chemical composition, classification results can vary widely due to spectral distortions. However, we demonstrate that the selection of localized metrics based on chemical information can make our data robust to the spectral distortions caused by scattering at the tissue boundary.Keywords: Infrared, Spectroscopy, Imaging, Tissue classification
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 16251373 AMBICOM: An Ambient Computing Middleware Architecture for Heterogeneous Environments
Authors: Ekrem Aksoy, Nihat Adar, Selçuk Canbek
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Ambient Computing or Ambient Intelligence (AmI) is emerging area in computer science aiming to create intelligently connected environments and Internet of Things. In this paper, we propose communication middleware architecture for AmI. This middleware architecture addresses problems of communication, networking, and abstraction of applications, although there are other aspects (e.g. HCI and Security) within general AmI framework. Within this middleware architecture, any application developer might address HCI and Security issues with extensibility features of this platform.
Keywords: AmI, ambient computing, middleware, distributedsystems, software-defined networking.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 16811372 Reductions of Control Flow Graphs
Authors: Robert Gold
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Control flow graphs are a well-known representation of the sequential control flow structure of programs with a multitude of applications. Not only single functions but also sets of functions or complete programs can be modeled by control flow graphs. In this case the size of the graphs can grow considerably and thus makes it difficult for software engineers to analyze the control flow. Graph reductions are helpful in this situation. In this paper we define reductions to subsets of nodes. Since executions of programs are represented by paths through the control flow graphs, paths should be preserved. Furthermore, the composition of reductions makes a stepwise analysis approach possible.
Keywords: Control flow graph, graph reduction.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 34851371 A Low Power High Frequency CMOS RF Four Quadrant Analog Mixer
Authors: M. Aleshams, A. Shahsavandi
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This paper describes a CMOS four-quadrant multiplier intended for use in the front-end receiver by utilizing the square-law characteristic of the MOS transistor in the saturation region. The circuit is based on 0.35 um CMOS technology simulated using HSPICE software. The mixer has a third-order inter the power consumption is 271uW from a single 1.2V power supply. One of the features of the proposed design is using two MOS transistors limitation to reduce the supply voltage, which leads to reduce the power consumption. This technique provides a GHz bandwidth response and low power consumption.Keywords: RF-Mixer, Multiplier, cut-off frequency, power consumption
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 20001370 Analysis of Plates with Varying Rigidities Using Finite Element Method
Authors: Karan Modi, Rajesh Kumar, Jyoti Katiyar, Shreya Thusoo
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This paper presents Finite Element Method (FEM) for analyzing the internal responses generated in thin rectangular plates with various edge conditions and rigidity conditions. Comparison has been made between the FEM (ANSYS software) results for displacement, stresses and moments generated with and without the consideration of hole in plate and different aspect ratios. In the end comparison for responses in plain and composite square plates has been studied.
Keywords: ANSYS, Finite Element Method, Plates, Static Analysis.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 29361369 The Application of Six Sigma to Integration of Computer Based Systems
Authors: Zenon Chaczko, Essam Rahali, Rizwan Tariq
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This paper introduces a process for the module level integration of computer based systems. It is based on the Six Sigma Process Improvement Model, where the goal of the process is to improve the overall quality of the system under development. We also present a conceptual framework that shows how this process can be implemented as an integration solution. Finally, we provide a partial implementation of key components in the conceptual framework.
Keywords: Software Quality, Six Sigma, System Integration, 3SI Process, 3SI Conceptual Framework.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 16591368 An Agent Oriented Architecture to Supply Multilanguage in EPR Systems
Authors: Hassan Haghighi, Seyedeh Zahra Hosseini, Seyedeh Elahe Jalambadani
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ERP systems are often supposed to be implemented and deployed in multi-national companies. On the other hand, an ERP developer may plan to market and sale its product in various countries. Therefore, an EPR system should have the ability to communicate with its users, who usually have different languages and cultures, in a suitable way. EPR support of Multilanguage capability is a solution to achieve this objective. In this paper, an agent oriented architecture including several independent but cooperative agents has been suggested that helps to implement Multilanguage EPR systems.Keywords: enterprise resource planning, Multilanguage, software architecture, agent oriented architecture, intelligence, learning, translation.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 16631367 SystemC Modeling of Adaptive Least Mean Square Filter
Authors: Kyu Han Kim, Soon Kyu Kwon, Heung Sun Yoon, Jong Tae Kim
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In this paper, we demonstrate the adaptive least-mean-square (LMS) filter modeling using SystemC. SystemC is a modeling language that allows designer to model both hardware and software component and makes it possible to design from high level system of abstraction to low level system of abstraction. We produced five adaptive least-mean-square filter models that are classed as five abstraction levels using SystemC proceeding from the abstract model to the more concrete model.Keywords: Adaptive Filter, Least-Mean-Square Algorithm, SystemC, Transversal Fir Filter.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 25251366 Capacitance Models of AlGaN/GaN High Electron Mobility Transistors
Authors: A. Douara, N. Kermas, B. Djellouli
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In this study, we report calculations of gate capacitance of AlGaN/GaN HEMTs with nextnano device simulation software. We have used a physical gate capacitance model for III-V FETs that incorporates quantum capacitance and centroid capacitance in the channel. These simulations explore various device structures with different values of barrier thickness and channel thickness. A detailed understanding of the impact of gate capacitance in HEMTs will allow us to determine their role in future 10 nm physical gate length node.
Keywords: AlGaN/GaN, centroid capacitance, gate capacitance, HEMT, quantum capacitance.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 18871365 Using Technology with a New Model of Management Development by Simulation of Neural Network and its Application on Intelligent Schools
Authors: Ahmad Ghayoumi, Mehdi Ghayoumi
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Intelligent schools are those which use IT devices and technologies as media software, hardware and networks to improve learning process. On the other hand management improvement is best described as the process from which managers learn and improve their skills not only to benefit themselves but also their employing organizations Here, we present a model Management improvement System that has been applied on some schools and have made strict improvement.Keywords: Intelligent school, Management development system, Learning station, Teaching station
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 10861364 Signature Recognition Using Conjugate Gradient Neural Networks
Authors: Jamal Fathi Abu Hasna
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There are two common methodologies to verify signatures: the functional approach and the parametric approach. This paper presents a new approach for dynamic handwritten signature verification (HSV) using the Neural Network with verification by the Conjugate Gradient Neural Network (NN). It is yet another avenue in the approach to HSV that is found to produce excellent results when compared with other methods of dynamic. Experimental results show the system is insensitive to the order of base-classifiers and gets a high verification ratio.Keywords: Signature Verification, MATLAB Software, Conjugate Gradient, Segmentation, Skilled Forgery, and Genuine.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 16301363 Developing of Intelligent Schools with a New Model of Strategic Management System
Authors: Ahmad Ghayoumi, Mehdi Ghayoumi
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Intelligent schools are those which use IT devices and technologies as media software, hardware and networks to improve learning process. On the other hand Strategic management is a field that deals with the major intended and emergent initiatives taken by general managers on behalf of owners, involving utilization of resources, to enhance the performance of firms in their external environments. Here, we present a model Strategic Management System that has been applied on some schools and have made strict improvement.Keywords: Intelligent school, Strategic management system, Learning station, Teaching station
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 13881362 Network Based High Performance Computing
Authors: Karanjeet Singh Kahlon, Gurvinder Singh, Arjan Singh
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In the past few years there is a change in the view of high performance applications and parallel computing. Initially such applications were targeted towards dedicated parallel machines. Recently trend is changing towards building meta-applications composed of several modules that exploit heterogeneous platforms and employ hybrid forms of parallelism. The aim of this paper is to propose a model of virtual parallel computing. Virtual parallel computing system provides a flexible object oriented software framework that makes it easy for programmers to write various parallel applications.
Keywords: Applet, Efficiency, Java, LAN
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 18971361 Description and Analysis of Embedded Firewall Techniques
Authors: Ahmed Abou Elfarag, A. Baith M., Hassan H. Alkhishali
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With the turn of this century, many researchers started showing interest in Embedded Firewall (EF) implementations. These are not the usual firewalls that are used as checkpoints at network gateways. They are, rather, applied near those hosts that need protection. Hence by using them, individual or grouped network components can be protected from the inside as well as from external attacks. This paper presents a study of EF-s, looking at their architecture and problems. A comparative study assesses how practical each kind is. It particularly focuses on the architecture, weak points, and portability of each kind. A look at their use by different categories of users is also presented.Keywords: Embedded Firewall (EF), Network Interface Card (NIC), Virtual Machine Software (VMware), Virtual Firewall (VF).
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 17061360 Sensitivity Analysis of Real-Time Systems
Authors: Benjamin Gorry, Andrew Ireland, Peter King
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Verification of real-time software systems can be expensive in terms of time and resources. Testing is the main method of proving correctness but has been shown to be a long and time consuming process. Everyday engineers are usually unwilling to adopt formal approaches to correctness because of the overhead associated with developing their knowledge of such techniques. Performance modelling techniques allow systems to be evaluated with respect to timing constraints. This paper describes PARTES, a framework which guides the extraction of performance models from programs written in an annotated subset of C.Keywords: Performance Modelling, Real-time, SensitivityAnalysis.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 15001359 A New Approach to Feedback Shift Registers
Authors: Myat Su Mon Win
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The pseudorandom number generators based on linear feedback shift registers (LFSRs), are very quick, easy and secure in the implementation of hardware and software. Thus they are very popular and widely used. But LFSRs lead to fairly easy cryptanalysis due to their completely linearity properties. In this paper, we propose a stochastic generator, which is called Random Feedback Shift Register (RFSR), using stochastic transformation (Random block) with one-way and non-linearity properties.Keywords: Linear Feedback Shift Register, Non Linearity, R_Block, Random Feedback Shift Register
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 18001358 The Open Knowledge Kernel
Authors: Adrian Perreau de Pinninck, David Dupplaw, Spyros Kotoulas, Ronny Siebes
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Web services are pieces of software that can be invoked via a standardized protocol. They can be combined via formalized taskflow languages. The Open Knowledge system is a fully distributed system using P2P technology, that allows users to publish the setaskflows, and programmers to register their web services or publish implementations of them, for the roles described in these workflows.Besides this, the system offers the functionality to select a peer that could coordinate such an interaction model and inform web services when it is their 'turn'. In this paper we describe the architecture and implementation of the Open Knowledge Kernel which provides the core functionality of the Open Knowledge system.
Keywords: Architecture, P2P, Web Services, Semantic Web
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 13911357 Stochastic Simulation of Reaction-Diffusion Systems
Authors: Paola Lecca, Lorenzo Dematte
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Reactiondiffusion systems are mathematical models that describe how the concentration of one or more substances distributed in space changes under the influence of local chemical reactions in which the substances are converted into each other, and diffusion which causes the substances to spread out in space. The classical representation of a reaction-diffusion system is given by semi-linear parabolic partial differential equations, whose general form is ÔêétX(x, t) = DΔX(x, t), where X(x, t) is the state vector, D is the matrix of the diffusion coefficients and Δ is the Laplace operator. If the solute move in an homogeneous system in thermal equilibrium, the diffusion coefficients are constants that do not depend on the local concentration of solvent and of solutes and on local temperature of the medium. In this paper a new stochastic reaction-diffusion model in which the diffusion coefficients are function of the local concentration, viscosity and frictional forces of solvent and solute is presented. Such a model provides a more realistic description of the molecular kinetics in non-homogenoeus and highly structured media as the intra- and inter-cellular spaces. The movement of a molecule A from a region i to a region j of the space is described as a first order reaction Ai k- → Aj , where the rate constant k depends on the diffusion coefficient. Representing the diffusional motion as a chemical reaction allows to assimilate a reaction-diffusion system to a pure reaction system and to simulate it with Gillespie-inspired stochastic simulation algorithms. The stochastic time evolution of the system is given by the occurrence of diffusion events and chemical reaction events. At each time step an event (reaction or diffusion) is selected from a probability distribution of waiting times determined by the specific speed of reaction and diffusion events. Redi is the software tool, developed to implement the model of reaction-diffusion kinetics and dynamics. It is a free software, that can be downloaded from http://www.cosbi.eu. To demonstrate the validity of the new reaction-diffusion model, the simulation results of the chaperone-assisted protein folding in cytoplasm obtained with Redi are reported. This case study is redrawing the attention of the scientific community due to current interests on protein aggregation as a potential cause for neurodegenerative diseases.
Keywords: Reaction-diffusion systems, Fick's law, stochastic simulation algorithm.
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