Object-oriented software tools for parallel PDE solvers

An object-oriented approach is taken to the problem of formulating portable, easy-to-modify PDE solvers for realistic problems in three space dimensions. The resulting software library, Cogito, contains tools for writing programs to be executed on MIMD computers with distributed memory. Difference methods on composite, structured grids are supported. Most of the Cogito classes have been implemented in Fortran 77, in such a way that the object-oriented design is visible. With respect to parallel performance, these tools yield code that is comparable to parallel solvers written in plain Fortran 77. The resulting programs are can be executed without modification on a large number of multicomputer platforms, and also on serial computers. The uppermost level of abstraction in Cogito concerns the problem of decoupling the numerical method from the PDE problem. The validity of these tools has been preliminarily demonstrated with a C++ implementation for one-dimensional problems.

An Integrated Software Application for the Ancient Coptic Language

Coptic language was an important period of the Egyptian language,coinciding with a period of social and cultural changes.Coptic is also associated with the Greek language,as its alphabet is used for the transcription of Coptic.Despite the fact that the Coptic element is strong in Greece,the theoretical background is rather weak.For this reason,it is considered necessary to create a software tool that aims to help in the translation of Coptic into Greek and at the same time to overcome various obstacles that the researcher may encounter while processing the various corpora or artifacts,such as processing issuer,diacritics etc.This tool consists of a database,a search engine and an interface.

Construction and Practices of the Course of Software Process&Tools Oriented Certified in Engineering Education

In recent years,it is the general trend to adopt the standards of international engineering education certification to construct curriculum.“Software Process and Tools”is one of the core courses of Harbin Institute of Technology’s software engineering undergraduate training program.Focusing on the construction work and practical exploration of the course in the process of reforming the software engineering professional curriculum system,and how to achieve the standards of engineering education certification,This paper makes a review and summary.This paper focuses on the status and the role of the course in the whole curriculum system,as well as project-driven teaching content design and practical teaching methods.And summarizes the experience and results of 3 rounds of teaching practice.

Application of the Agent in Agricultural Expert System Inspection Software

In reference to the status quo of research and the application of the agricultural expert system, this paper analyzes problems existing in the current development, and puts forward the idea of research and development for agriculturespecific software. The agent application is discussed, and an agent-based Agricultural Expert System Inspection Tool is constructed. In addition, this paper addresses the outlook in application, potential problems and the development trend of multi-agent-based inspection software for the agricultural expert system.

An Open CAM System for Dentistry on the Basis of China-made 5-axis Simultaneous Contouring CNC Machine Tool and Industrial CAM Software

China-made 5-axis simultaneous contouring CNC machine tool and domestically developed industrial computer-aided manufacture （CAM） technology were used for full crown fabrication and measurement of crown accuracy, with an attempt to establish an open CAM system for dental processing and to promote the introduction of domestic dental computer-aided design （CAD）/CAM system. Commercially available scanning equipment was used to make a basic digital tooth model after preparation of crown, and CAD software that comes with the scanning device was employed to design the crown by using domestic industrial CAM software to process the crown data in order to generate a solid model for machining purpose, and then China-made 5-axis simultaneous contouring CNC machine tool was used to complete machining of the whole crown and the internal accuracy of the crown internal was measured by using 3D-MicroCT. The results showed that China-made 5-axis simultaneous contouring CNC machine tool in combination with domestic industrial CAM technology can be used for crown making and the crown was well positioned in die. The internal accuracy was successfully measured by using 3D-MicroCT. It is concluded that an open CAM system for den-tistry on the basis of China-made 5-axis simultaneous contouring CNC machine tool and domestic industrial CAM software has been established, and development of the system will promote the introduction of domestically-produced dental CAD/CAM system.

“AniFair”:A GUI Based Software Tool for Multi-Criteria Decision Analysis--An Example of Assessing Animal Welfare

Multi-criteria decision analysis deals with decision problems in which multiple criteria need to be considered. The criteria might be measured on different scales so that comparability is difficult. One approach to help the user to organize the problem and to reflect on his or her assessment on the decision is Measuring Attractiveness by a Categorical Based Evaluation TecHnique (MACBETH). Here the user needs to provide qualitative judgment about differences of attractiveness regarding pairs of options. MACBETH was implemented in the M-MACBETH software using the additive aggregation model. The present article introduces the software tool “AniFair” which combines the MACBETH approach with the Choquet integral as an aggregation function, because the Choquet integral enables the modeling of interaction between criteria. With the Choquet integral, the user can define constraints on the relative importance of criteria (Shapley value) and the interaction between criteria. In contrast to M-MACBETH, with every instance of “AniFair” the user is made available at least two aggregation level. “AniFair” provides Graphical User Interfaces for the entering of information. The software tool is introduced via an example from the Welfare Quality Assessment protocol for pigs. With this, “AniFair” is applied to real data that were collected from thirteen farms in Northern Germany by an animal welfare expert. The “AniFair” results enabled a division of the farms into five groups of comparable performance concerning the welfare principle “Good feeding”. Hereby, the results differed in how much the interaction between criteria contributed to the Choquet integral values. The shares varied from 5% to 55%. With this, the vulnerability of aggregation results towards relative importance of and interaction between criteria was stressed, as changes in the ranking due to the definition of constraints could be shown. All results were exported to human readable txt or csv files for further analyses, and advice could be given to the farmers on how to improve their welfare situation.

Computer Aided Software Engineering(CASE)for CAD Systems Production

In the paper the basic elements of CAD systems from software point of view are dis- cussed.The creation and next the modification of CAD systems needs specialized software tools.In the paper the idea computer Aided Software Engineering(CASE)for CAD systems production and practi- cal software realization of such a software tool is considered.The main element of this tool is special program provided for convenient storage and modification of CAD source program.In the paper the simple examples are presented and discussed.

SET-MRTS:An Empirical Experiment Tool for Real-Time Scheduling and Synchronization

In the real-time scheduling theory,schedulability and synchronization analyses are used to evaluate scheduling algorithms and real-time locking protocols,respectively,and the empirical synthesis experiment is one of the major methods to compare the performance of such analyses.However,since many sophisticated techniques have been adopted to improve the analytical accuracy,the implementation of such analyses and experiments is often time-consuming.This paper proposes a schedulability experiment toolkit for multiprocessor real-time systems(SET-MRTS),which provides a framework with infrastructures to implement the schedulability and synchronization analyses and the deployment of empirical synthesis experiments.Besides,with well-designed peripheral components for the input and output,experiments can be conducted easily and flexibly on SET-MRTS.This demonstration further proves the effectiveness of SET-MRTS in both functionality and availability.

Radio Optical Network Simulation Tool (RONST)

This paper presents a radio optical network simulation tool(RONST)for modeling optical-wireless systems.For a typical optical and electrical chain environment,performance should be optimized concurrently before system implementation.As a result,simulating such systems turns out to be a multidisciplinary problem.The governing equations are incompatible with co-simulation in the traditional environments of existing software(SW)packages.The ultra-wideband(UWB)technology is an ideal candidate for providing high-speed short-range access for wireless services.The limited wireless reach of this technology is a significant limitation.A feasible solution to the problem of extending UWB signals is to transmit these signals to endusers via optical fibers.This concept implies the need for the establishment of a dependable environment for studying such systems.Therefore,the essential novelty of the proposed SW is that it provides designers,engineers,and researchers with a dependable simulation framework that can accurately and efficiently predict and/or optimize the behavior of such systems in a single optical-electronic simulation package.Furthermore,it is supported by a strong mathematical foundation with integrated algorithms to achieve broad flexibility and low computational cost.To validate the proposed tool,RONST was deployed on an ultra-wideband over fiber(UWBoF)system.The bit error rate(BER)has been calculated over a UWBoF system,and there is good agreement between the experimental and simulated results.

A GIS Approach Using Morphometric Data Analysis for the Identification of Subsurface Recent Tectonic Activity. Case Study in Quaternary Outcrops—North West of Tunisia

The combination of structural and lithological data with morphometric indicators in a GIS environment constitutes a methodological approach with high added value to identify neotectonic deformations, in particular in the Quaternary outcrops where faults are generally masked by thick recent sediments. This approach, based on the crossing of multisource data, is used in this work to understand the mechanisms that generate landscape forms in the Quaternary outcrop of Oued Lahmar, which belongs to the northwest of Tunisia. In fact, the databases of various morphometric indicators, extracted from the hydrographic network, have been generated using remote sensing data and open sources applications. This database has been enriched by lithological and tectonic data extracted from the regional geological map, to understand the results of the morphometric analysis. The results obtained provide valuable information on the identification of subsurface activity in Oued Lahmar and large vicinity areas with heterogeneous geomorphic and structural characteristics. Indeed, this study revealed the existence of an E-W subsurface tectonic control covered by the Quaternary sedimentary series not indicated on the geological map of the region. This tectonic direction, which follows most of the magmatic outcrop edge in the region, may allow the intrusion of magma and the rejuvenation of ancient deep faults.

Intelligent System Design for Stator Windings Faults Diagnosis:Suitable for Maintenance Work

The short circuit is a severe fault that occurs in the stator windings. Therefore, it is very important to diagnose this type of failure in its beginning before it causes unscheduled stop and the machine loss. In this context, the Support Vector Machine (SVM) is a tool of considerable importance for standard classification. From some training data, it can diagnose whether or not there is a short circuit beginning, and which is important for predictive maintenance. This work proposes a technique for early detection of a short circuit between the turns aiming at its implementation in a real plant. The paper shows simulation and experimental results, and validates the proposed technique.

A Computational Solution of Natural Convection Flow in a Rotating Fluid with Radiative Heat Transfer

An analysis of the hydromagnetic free convective flow past a vertical infinite porous plate in a rotating fluid is carried out. The temperatures involved are assumed to be very large so that the radiative heat transfer is significant, which renders the problem very non-linear even on the assumption of a differential approximation for the radiative flux. The temperature and velocity fields are computed using a generic software tool based on the Nakamura finite difference scheme. The genericity of the software tool is in the sense that it is a common solution to the category of time dependent laminar fluid flows expressed in one spatial coordinate. The input equations, together with other relevant parameters, are transformed into postfix code which will be farther interpreted in the computation process. The influence of the various parameters entering into the problem is shown graphically followed by a discussion of results.

Reliability Assessment Tool Based on Deep Learning and Data Preprocessing for OSS

Recently, many open source software (OSS) developed by various OSS projects. Also, the reliability assessment methods of OSS have been proposed by several researchers. Many methods for software reliability assessment have been proposed by software reliability growth models. Moreover, our research group has been proposed the method of reliability assessment for the OSS. Many OSS use bug tracking system (BTS) to manage software faults after it released. It keeps a detailed record of the environment in terms of the faults. There are several methods of reliability assessment based on deep learning for OSS fault data in the past. On the other hand, the data registered in BTS differences depending on OSS projects. Also, some projects have the specific collection data. The BTS has the specific collection data for each project. We focus on the recorded data. Moreover, we investigate the difference between the general data and the specific one for the estimation of OSS reliability. As a result, we show that the reliability estimation results by using specific data are better than the method using general data. Then, we show the characteristics between the specified data and general one in this paper. We also develop the GUI-based software to perform these reliability analyses so that even those who are not familiar with deep learning implementations can perform reliability analyses of OSS.

A Generic Computational Solution of a Natural Convection Flow past an Infinite Vertical Porous Plate

A simulation was carried out on an unsteady flow of a viscous, incompressible and electrically conducting fluid past an infinite vertical porous plate. A generic computer program using the Galerkin finite element method is employed to solve the coupled non-linear differential equations for velocity and temperature fields. The diffusion equation, the energy equation, the momentum equations and other relevant parameters are transformed into interpretable postfix codes. Numerical calculations are carried out on the flow fields both in the presence of cooling and heating of the plate by free convection currents. The effects of the dimensionless parameters, namely, the Prandtl number, the Eckert number, the modified Grashof number, the Schmidt number and the time on the temperature and velocity distributions are discussed.

A Novel Gaussian Extrapolation Approach for 2D Gel Electrophoresis Saturated Protein Spots

Analysis of images obtained from two-dimensional gel electrophoresis （2D-GE） is a topic of utmost importance in bioinformatics research, since commercial and academic software available currently has proven to be neither completely effective nor fully automatic, often requiring manual revision and refinement of computer generated matches. In this work, we present an effective technique for the detection and the reconstruction of over-saturated protein spots. Firstly, the algorithm reveals overexposed areas, where spots may be truncated, and plateau regions caused by smeared and overlapping spots. Next, it reconstructs the correct distribution of pixel values in these overexposed areas and plateau regions, using a two-dimensional least-squares fitting based on a generalized Gaussian distribution. Pixel correction in saturated and smeared spots allows more accurate quantification, providing more reliable image analysis results. The method is validated for processing.highly exposed 2D-GE images, comparing reconstructed spots with the corresponding non-saturated image, demonstrating that the algorithm enables correct spot quantification.

Web Resources for Metagenomics Studies

The development of next-generation sequencing （NGS） platforms spawned an enormous volume of data. This explosion in data has unearthed new scalability challenges for existing bioinformatics tools. The analysis of metagenomic sequences using bioinformatics pipelines is complicated by the substantial complexity of these data. In this article, we review several commonly-used online tools for metagenomies data analysis with respect to their quality and detail of analysis using simulated metagenolnies data. There are at least a dozen such software tools presently available in the public domain. Among them, MGRAST, IMG/M, and METAVIR are the most well-known tools according to the number of citations by peer-reviewed scientific media up to mid-2015. Here, we describe 12 online tools with respect to their web link, annotation pipelines, clustering methods, online user support, and availability of data storage. We have also done the rating for each tool to screen more potential and preferential tools and evaluated five best tools using synthetie metagenome. The article comprehensively deals with the contemporary problems and the prospects of metagenomies from a bioinformatics viewpoint.

Prediction of diabetes and hypertension using multi-layer perceptron neural networks

Background:Diabetes and hypertension are two of the commonest diseases in the world.As they unfavorably affect people of different age groups,they have become a cause of concern and must be predicted and diagnosed well in advance.Objective:This research aims to determine the effectiveness of artificial neural networks(ANNs)in predicting diabetes and blood pressure diseases and to point out the factors which have a high impact on these diseases.Sample:This work used two online datasets which consist of data collected from 768 individuals.We applied neural network algorithms to predict if the individuals have those two diseases based on some factors.Diabetes prediction is based on five factors:age,weight,fat-ratio,glucose,and insulin,while blood pressure prediction is based on six factors:age,weight,fat-ratio,blood pressure,alcohol,and smoking.Method:A model based on the Multi-Layer Perceptron Neural Network(MLP)was implemented.The inputs of the network were the factors for each disease,while the output was the prediction of the disease’s occurrence.The model performance was compared with other classifiers such as Support Vector Machine(SVM)and K-Nearest Neighbors(KNN).We used performance metrics measures to assess the accuracy and performance of MLP.Also,a tool was implemented to help diagnose the diseases and to understand the results.Result:The model predicted the two diseases with correct classification rate(CCR)of 77.6%for diabetes and 68.7%for hypertension.The results indicate that MLP correctly predicts the probability of being diseased or not,and the performance can be significantly increased compared with both SVM and KNN.This shows MLPs effectiveness in early disease prediction.

Bioinformatics Research on Chronic Superficial Gastritis of Pi-deficiency Syndrome by Gene Arrays

Objective： To determine the bioinformatical characteristics of differential gene expression in patients with chronic superficial gastritis （CSG） with the Pi-deficiency syndrome （PDS） and those of the non- Pi-deficiency syndrome （non-PDS）, i.e. patients of CSG with Pi （脾）-Wei （胃） dampnese-heat syndrome and healthy persons. Methods： With the BRB-Array Tools software package, original data collection and bioinformatic analysis of gene arrays were conducted in 6 CSG patients of PDS （CSG-PDS）, 6 CSG patients of non-PDS （CSG-nPDS）, and 6 healthy volunteers （Normal）. Results： Compared with non-PDS, the gene expressions in PDS with regards to protein synthesis, energy metabolism, immune reaction and ionic transport tended to be down-regulated, while those concerning secretion, cytoskeleton and ubiquitinization were up-regulated dominantly. Conclusions： The two kinds of samples, CSG-PDS/Normal and CSG-PDS/CSG-nPDS, have their respective gene expression profiles with different characteristics. Gene expression profile has certain referential significance in syndrome classification.

An Object-Oriented Model of User Interface Generation Tool

This paper mainly introduces a model of the Object-Oriented User Interface Gen-eration Tool (OOUIGT) and describes the procedure of the implementation. The oOUIGT (FasTool) has been implemented on SGI workstation. This enables the UI designing not to be a lower level programming procedure, but to be a higher level description procedure which is formal,convenient, comprehensive and fast.

Untargeted LC–MS Data Preprocessing in Metabolomics

Liquid chromatography–mass spectrometry(LC–MS)has enabled the detection of thousands of metabolite features from a single biological sample that produces large and complex datasets.One of the key issues in LC–MS-based metabolomics is comprehensive and accurate analysis of enormous amount of data.Many free data preprocessing tools,such as XCMS,MZmine,MAVEN,and MetaboAnalyst,as well as commercial software,have been developed to facilitate data processing.However,researchers are challenged by the inevitable and unconquerable yields of numerous false-positive peaks,and human errors while manually removing such false peaks.Even with continuous improvements of data processing tools,there can still be many mistakes generated during data preprocessing.In addition,many data preprocessing software exist,and every tool has its own advantages and disadvantages.Thereby,a researcher needs to judge what kind of software or tools to choose that most suit their vendor proprietary formats and goal of downstream analysis.Here,we provided a brief introduction of the general steps of raw MS data processing,and properties of automated data processing tools.Then,characteristics of mainly free data preprocessing software were summarized for researchers’consideration in conducting metabolomics study.