Java-based Application Research Articles

An easy-to-implement fuzzy expert package with applications using existing Java classes

In this study, we present a computer package to implement fuzzy expert systems using Java. The purpose of this study is to provide an easy-to-understand and easy-to-implement computer package for those people who want to develop their own customized Java-based fuzzy expert applications without using existing end-user fuzzy expert software. The code size of the proposed package is less than 300 code lines where some existing Java classes developed by Sun Microsystems, Inc., are utilized to handle necessary geometrical manipulations. We demonstrate the ideas of how we implement fuzzy expert systems with the existing Java classes by providing code fragments. To validate the proposed package, we first developed a console application to compare the results of using the proposed package with those of using an existing commercial fuzzy expert software package, Fuzzy Inference Development Environment (FIDE). The proposed package is well-modularized in software modules with high maintainability and customizability. To validate this, we developed three additional applications with the proposed package including a window-based application and two web-based applications: JSP Model 1 and JSP Model 2 (MVC design pattern). Through the developments of these applications, we find that it is extremely simple and straightforward to build customized fuzzy expert applications with the code fragments provided in this study, saving a lot of programming works. In additions, the proposed package has good extensibilities to establish piecewise linear membership functions and to approximate non-linear membership functions. Meanwhile, UML is also utilized to describe the structures and behaviors of the proposed package.

An adaptive user interface based on spatiotemporal structure learning

We developed a user interface prototype for the Android smartphone, which recommends a number of applications to best match the user's context. To consider the user's context of use, we utilized 5 prototypical variables; time, location, weather, emotion, and activities. The developed system derives the best three recommended applications based on the results of supervised machine learning from such data sets. To consider the history of past context information, in addition to the current one, we developed a novel and effective probabilistic learning and inference algorithm named "Spatiotemporal Structure Learning." By extending Naïve Bayesian Classifier, the spatiotemporal structure learning can create a probability model which represents relationship between time-series contextual variables. We implemented a prototype system which shows the current context and the inferred recommendation of applications. For the prototype system, we developed an Android widget application for the user interface and a Java-based server application which learns structure from training data and provides inference results in real time. To gather training data and evaluate the proposed system, we conducted a pilot study which showed 69 percent accuracy in predicting the user's application usage. The prototype demonstrated the feasibility of an adaptive user interface applied to a state of the art smartphone. We also believe that the suggested spatiotemporal structure learning can be applied to number of application areas including healthcare or energy problems.

SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation

BackgroundMultiple sequence alignment (MSA) plays a central role in nearly all bioinformatics and molecular evolutionary applications. MSA reconstruction is thus one of the most heavily scrutinized bioinformatics fields. Evaluating the quality of MSA reconstruction is often hindered by the lack of good reference MSAs. The use of sequence evolution simulation can provide such reference MSAs. Furthermore, none of the MSA viewing/editing programs currently available allows the user to make direct comparisons between two or more MSAs. Considering the importance of MSA quality in a wide range of research, it is desirable if MSA assessment can be performed more easily.ResultsWe have developed SuiteMSA, a java-based application that provides unique MSA viewers. Users can directly compare multiple MSAs and evaluate where the MSAs agree (are consistent) or disagree (are inconsistent). Several alignment statistics are provided to assist such comparisons. SuiteMSA also includes a graphical phylogeny editor/viewer as well as a graphical user interface for a sequence evolution simulator that can be used to construct reference MSAs.ConclusionsSuiteMSA provides researchers easy access to a sequence evolution simulator, reference alignments generated by the simulator, and a series of tools to evaluate the performance of the MSA reconstruction programs. It will help us improve the quality of MSAs, often the most important first steps of bioinformatics and other biological research.

A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method

BackgroundThe Molecular Interaction Map (MIM) notation offers a standard set of symbols and rules on their usage for the depiction of cellular signaling network diagrams. Such diagrams are essential for disseminating biological information in a concise manner. A lack of software tools for the notation restricts wider usage of the notation. Development of software is facilitated by a more detailed specification regarding software requirements than has previously existed for the MIM notation.ResultsA formal implementation of the MIM notation was developed based on a core set of previously defined glyphs. This implementation provides a detailed specification of the properties of the elements of the MIM notation. Building upon this specification, a machine-readable format is provided as a standardized mechanism for the storage and exchange of MIM diagrams. This new format is accompanied by a Java-based application programming interface to help software developers to integrate MIM support into software projects. A validation mechanism is also provided to determine whether MIM datasets are in accordance with syntax rules provided by the new specification.ConclusionsThe work presented here provides key foundational components to promote software development for the MIM notation. These components will speed up the development of interoperable tools supporting the MIM notation and will aid in the translation of data stored in MIM diagrams to other standardized formats. Several projects utilizing this implementation of the notation are outlined herein. The MIM specification is available as an additional file to this publication. Source code, libraries, documentation, and examples are available at http://discover.nci.nih.gov/mim.

PRIDEViewer: A novel user-friendly interface to visualize PRIDE XML files

Current standardization initiatives have greatly contributed to share the information derived by proteomics experiments. One of these initiatives is the XML-based repository PRIDE (PRoteomics IDEntification database), although an XML-based document does not appear to present a user-friendly view at the first glance. PRIDEViewer is a novel Java-based application that presents the information available in a PRIDE XML file in a user-friendly manner, facilitating the interaction among end users as well as the understanding and evaluation of the compiled information. PRIDEViewer is freely available at: http://proteo.cnb.csic.es/prideviewer/.

Preventing SQL Injection through Automatic Query Sanitization with ASSIST

Web applications are becoming an essential part of our everyday lives. Many of our activities are dependent on the functionality and security of these applications. As the scale of these applications grows, injection vulnerabilities such as SQL injection are major security challenges for developers today. This paper presents the technique of automatic query sanitization to automatically remove SQL injection vulnerabilities in code. In our technique, a combination of static analysis and program transformation are used to automatically instrument web applications with sanitization code. We have implemented this technique in a tool named ASSIST (Automatic and Static SQL Injection Sanitization Tool) for protecting Java-based web applications. Our experimental evaluation showed that our technique is effective against SQL injection vulnerabilities and has a low overhead.

Product Architecture and Quality: A Study of Open-Source Software Development

We examine how the architecture of products relates to their quality. Using an architectural representation that accounts for both the hierarchical and dependency relationships between modules and components, we define a new construct, system cyclicality. System cyclicality recognizes component loops, which are akin to design iterations — a concept typically associated with models of product development processes rather than the products themselves. System cyclicality captures the fraction of mutually interdependent components in a system. Through a multilevel analysis of several open-source, Java-based applications developed by the Apache Software Foundation, we study the relationship between system cyclicality and the generation of bugs. At the system level, we examine 122 releases representing 19 applications and find that system cyclicality is positively associated with the number of bugs in a system. At the component level, we examine 28,395 components and find that components involved in loops are likely to be affected by a larger number of bugs. We find that, in order to identify the set of product components involved in cyclical dependencies that are detrimental to product quality, it is imperative to remove from consideration the architectural decisions by which components are assigned into modules: it is necessary to focus only on the patterns of dependencies among product components without considering how components are grouped together into modules. Our results suggest that new product development managers are likely to benefit from proactively examining the architecture of the system they develop and monitoring its cyclicality as one of their strategies to reduce defects.

No-Heap remote objects for distributed real-time Java

This article presents an approach to providing real-time support for Java's Remote Method Invocation (RMI) and its integration with the RTSJ memory model in order to leave out garbage collection. A new construct for remote objects, called No-heap Remote object ( NhRo ), is introduced. The use of a NhRo guarantees that memory required to perform a remote invocation (at the server side) does not use heap memory. Thus, the aim is to avoid garbage collection in the remote invocation process, improving predictability and memory isolation of distributed Java-based real-time applications. The article presents the bare model and the main programming patterns that are associated with the NhRo model. Sun RMI implementation has been modified to integrate the NhRo model in both static and dynamic environments.

Osteoarthritis Index delivered by mobile phone (m-WOMAC) is valid, reliable, and responsive

Objectives To evaluate the validity, reliability, responsiveness, and mode preference of electronic data capture (EDC) using the Western Ontario and McMaster (WOMAC) numerical rating scale (NRS) 3.1 Osteoarthritis (OA) Index on Motorola V3 mobile phones. Study Design and Setting Patients with OA undergoing hip or knee joint replacement were assessed preoperatively and 3–4 months postoperatively, completing the WOMAC Index in paper (p-WOMAC) and electronic (m-WOMAC) format in random order. Results Data were successfully and securely transmitted from patients in Australia to a server in the United States. Pearson correlations between the summated total index scores (TISs) for the p-WOMAC and m-WOMAC pre- and postsurgery were 0.98 and 0.99 ( P < 0.0001). There were no clinically important or statistically significant between-method differences in the adjusted total summated scores, pre- and postsurgery (adjusted mean differences = 4.44, P = 0.474 and 1.73, P = 0.781, respectively). Internal consistency estimates of m-WOMAC reliability were 0.87–0.98. The m-WOMAC detected clinically important, statistically significant ( P < 0.0001) improvements in pain, stiffness, function, and TIS. No statistically significant differences in mode preference were detected. Conclusions There was close agreement and no significant differences between m-WOMAC and p-WOMAC scores. This study confirms the validity, reliability, and responsiveness of the Exco InTouch-engineered, Java-based m-WOMAC Index application. EDC with the m-WOMAC Index provides unique opportunities for using quantitative measurement in clinical research and practice.

Robin: An Intuitive Wizard Application for R-Based Expression Microarray Quality Assessment and Analysis

The wide application of high-throughput transcriptomics using microarrays has generated a plethora of technical platforms, data repositories, and sophisticated statistical analysis methods, leaving the individual scientist with the problem of choosing the appropriate approach to address a biological question. Several software applications that provide a rich environment for microarray analysis and data storage are available (e.g. GeneSpring, EMMA2), but these are mostly commercial or require an advanced informatics infrastructure. There is a need for a noncommercial, easy-to-use graphical application that aids the lab researcher to find the proper method to analyze microarray data, without this requiring expert understanding of the complex underlying statistics, or programming skills. We have developed Robin, a Java-based graphical wizard application that harnesses the advanced statistical analysis functions of the R/BioConductor project. Robin implements streamlined workflows that guide the user through all steps of two-color, single-color, or Affymetrix microarray analysis. It provides functions for thorough quality assessment of the data and automatically generates warnings to notify the user of potential outliers, low-quality chips, or low statistical power. The results are generated in a standard format that allows ready use with both specialized analysis tools like MapMan and PageMan and generic spreadsheet applications. To further improve user friendliness, Robin includes both integrated help and comprehensive external documentation. To demonstrate the statistical power and ease of use of the workflows in Robin, we present a case study in which we apply Robin to analyze a two-color microarray experiment comparing gene expression in tomato (Solanum lycopersicum) leaves, flowers, and roots.

An Assessment of Design Patterns' Influence on a Java-based E-Commerce Application

Design patterns, acting as recurring solutions to common problems, offer significant benefits such as avoiding unnecessary complexity, and promoting code reuse, maintainability and extensibility. This paper describes how four not technology-specific or language-specific design patterns (Front Controller, Model View Controller, Transfer Object and Service to Worker) can be applied to one typical e-commerce application developed using Java EE platform. The first goal is to evaluate the improvement of design properties after the implementation of each design pattern using software metrics. Another goal is to assess the influence of design patterns on the maintainability of the e-commerce application under study by examining the evolution of software metrics when performing certain extensions. The results indicate that the application of patterns positively influences design properties such as coupling, complexity and messaging implying a possible improvement in high-level quality attributes such as flexibility, extensibility and reusability.

Measures of Physical Activity Using Cell Phones: Validation Using Criterion Methods

Background Physical activity is associated with reduced risks of many chronic diseases. Data collected on physical activity in large epidemiological studies is often based on paper questionnaires. The validity of these questionnaires is debated, and more effective methods are needed.Objective This study evaluates repeated measures of physical activity level (PAL) and the feasibility of using a Java-based questionnaire downloaded onto cell phones for collection of such data. The data obtained were compared with reference estimates based on the doubly labeled water method and indirect calorimetry (PALref).Method Using a Java-based cell phone application, 22 women reported their physical activity based on two short questions answered daily over a 14-day period (PALcell). Results were compared with reference data obtained from the doubly labeled water method and indirect calorimetry (PALref). Results were also compared against physical activity levels assessed by two regular paper questionnaires completed by women at the end of the 14-day period (PALquest1 and PALquest2). PALcell, PALquest1, and PALquest2 were compared with PALref using the Bland and Altman procedure.Results The mean difference between PALcell and PALref was small (0.014) with narrow limits of agreement (2SD = 0.30). Compared with PALref, the mean difference was also small for PALquest1 and PALquest2 (0.004 and 0.07, respectively); however, the limits of agreement were wider (PALquest1, 2SD = 0.50 and PALquest2, 2SD = 0.90). The test for trend was statistically significant for PALquest1 (slope of regression line = 0.79, P = .04) as well as for PALquest2 (slope of regression line = 1.58, P < .001) when compared with PALref.Conclusion A Java-based physical activity questionnaire administered daily using cell phones produced PAL estimates that agreed well with PAL reference values. Furthermore, the limits of agreement between PAL obtained using cell phones, and reference values were narrower than for corresponding estimates obtained using paper questionnaires. Java-based questionnaires downloaded onto cell phones may be a feasible and cost-effective method of data collection for large-scale prospective studies of physical activity.

Thermoluminescence digital color images and their evaluation using a Java-based application

Luminescence dating involves the observation of naturally accumulated radiation damage, caused by radioisotopes such as U and Th, in the form of the glow stimulated by heating or exposure to light.The emission color of luminescence varies among samples. A thermoluminescence color image (TLCI) can be recorded using a digital camera after irradiation with gamma rays, which results in significant radiation damage, thereby enhancing the luminescence. A new application was developed to handle RGB (red-green-blue) information for each pixel. The application enables the automatic plotting of pixel data on a CIE (Commission Internationale de l’Eclairoge) chromaticity diagram and counting of the number of pixels within a color zone, as defined by dividing the color space into five color zones. The application helps to handle many digital TLCIs in a short time and is useful for statistical color analyses.

Wisdom of crowds versus wisdom of linguists – measuring the semantic relatedness of words

AbstractIn this article, we present a comprehensive study aimed at computing semantic relatedness of word pairs. We analyze the performance of a large number of semantic relatedness measures proposed in the literature with respect to different experimental conditions, such as (i) the datasets employed, (ii) the language (English or German), (iii) the underlying knowledge source, and (iv) the evaluation task (computing scores of semantic relatedness, ranking word pairs, solving word choice problems). To our knowledge, this study is the first to systematically analyze semantic relatedness on a large number of datasets with different properties, while emphasizing the role of the knowledge source compiled either by the ‘wisdom of linguists’ (i.e., classical wordnets) or by the ‘wisdom of crowds’ (i.e., collaboratively constructed knowledge sources like Wikipedia).The article discusses benefits and drawbacks of different approaches to evaluating semantic relatedness. We show that results should be interpreted carefully to evaluate particular aspects of semantic relatedness. For the first time, we employ a vector based measure of semantic relatedness, relying on a concept space built from documents, to the first paragraph of Wikipedia articles, to English WordNet glosses, and to GermaNet based pseudo glosses. Contrary to previous research (Strube and Ponzetto 2006; Gabrilovich and Markovitch 2007; Zesch et al. 2007), we find that ‘wisdom of crowds’ based resources are not superior to ‘wisdom of linguists’ based resources. We also find that using the first paragraph of a Wikipedia article as opposed to the whole article leads to better precision, but decreases recall. Finally, we present two systems that were developed to aid the experiments presented herein and are freely available1 for research purposes: (i) DEXTRACT, a software to semi-automatically construct corpus-driven semantic relatedness datasets, and (ii) JWPL, a Java-based high-performance Wikipedia Application Programming Interface (API) for building natural language processing (NLP) applications.

Web Accessibility: Practical Advice for the Library and Information Professional

Web Accessibility: Practical Advice for the Library and Information Professional

Autonomous seafloor recorders and autodetection buoys to monitor whale activity for long-term and near-real-time applications.

Biologists and engineers from Cornell have installed arrays of autonomous seafloor recorders in multiple ocean habitats. These systems are designed to continuously monitor for the occurrence of endangered whales, particularly right whales; provide critical data on whale seasonal occurrence, distribution and relative numbers; and evaluate potential noise impacts from manmade activities and commercial shipping. Recent studies have been conducted in Massachusetts Bay around commercial LNG ports, the Arctic Ocean at seismic study locations, and in New York waters extending to the shelf edge. In combination with Cornell-developed MATLAB- and JAVA-based software applications, these seafloor recorders have been utilized to evaluate seasonal whale presence, calculate levels of commercial shipping and construction noise, and locate and track the movements and behaviors of individual whales under different acoustic conditions. Cornell and ocean engineers from the Woods Hole Oceanographic Institution have installed an operational network of autodetection buoys off New England to provide near-real-time data on right whale presence to transiting LNG vessels, government agencies, and public entities. When combined, the seafloor and autodetection buoy systems provide a powerful mechanism for understanding whale behavioral ecology and describing their acoustic habitats, while mitigating the risks from ship strike and noise exposure.

Neues Konzept einer computergestützten Dokumentation von Netzhautbefunden bei Frühgeborenenretinopathie

Pathological findings and clinical course of retinopathy of prematurity (ROP) are often documented with hand drawings. The use of software-based standardised symbols for ROP staging leads to improved documentation quality. We developed graphical symbols for all ROP stages as well as plus disease. All of the symbols were integrated into a java-based application as a particular ROP category of a complete symbol library for retinal changes. The symbols can be placed on a schematic retina with a mouse click. Using anchors each symbol can be individually adapted to the specific finding (size, position, shape). The use of standardised symbols in a software package allows the computer-aided manufacturing of graphically high-quality documentation in affordable time. The distinct assignment of all symbols to the ROP stages prevents misinterpretation and sketchy, illegible hand drawings. The digital documentation of pathological changes of ROP provides an easy, economic and standardised method to record retinal findings.

A toolkit for efficient numerical applications in Java

Java is widely recognized as a good object-oriented programming language. However, it is often considered as too slow for numerically intensive applications. This paper presents a software toolkit that brings the computational efficiency of numerical Fortran libraries to Java. The toolkit is organized in two layers. In the first layer, Java wrappers provide access to numerical libraries like BLAS, LAPACK or NAG. The second layer comprises vector and matrix classes as well as classes for common linear algebra tasks. Numerical experiments show that this strategy can substantially improve the performance of Java-based numerical applications.

Display and analysis of historical and instrumental seismological data pertaining to India and adjoining regions, using the Java-based software application—‘Kampan 2006’

The seismological records of past events provide insight into the seismic activities in an area. They help in preparing long-term plans to manage earthquake disasters. We present a system to display and analyse historical seismological data using the Java-based software application Kampan 2006. This interactive multi-purpose tool can display and analyse seismological data with a simple click of the mouse. The design and development of Kampan 2006 strictly followed the concepts of software engineering. We used the programming capabilities of Java to the fullest extent in developing Kampan 2006.

An accelerator design for speedup of Java execution in consumer mobile devices

In today’s consumer electronics market, Java has become one of the most important programming languages for the rapid development of mobile applications – spanning from home appliances/controllers, mobile and communication devices, to network-centric applets. However, the demand for high-performance low-power Java-based consumer mobile applications puts forward new challenges to the system design and implementation. This paper analyzes the energy consumption, execution efficiency, and speed issues of Java applications in a typical consumer mobile device environment. By adopting a hardware-assisted approach, we introduce a Java accelerator with a companion Java virtual machine. The accelerator is designed in an asynchronous style, and can be integrated with most existing processors and operating systems. The core architecture, design philosophy, and implementation considerations are presented in detail in this paper.