Java-based Interface Research Articles

Dynamic switching of psychological test questions and design of scalable database: A study of web page data visualization and front-end interaction

As the need for efficient and user-friendly web applications in the field of psychological assessment continues to grow, traditional web development approaches are challenged to provide a dynamic and adaptive user experience. This study focuses on addressing these challenges through a comprehensive study that provides insight into the current state of psychological assessment web development, highlighting the shortcomings of traditional approaches, including the static limitations of Hyper Text Markup Language (HTML) and limited client-side scripting. The result is a user experience that lacks the responsiveness and flexibility that modern users expect. To tackle these problems, the intended solution suggested in this work combines a strong and scalable database design with a dynamic switching mechanism for psychological exam questions. Features-rich, aesthetically pleasing, and functioning client-server Web applications are created using technologies such as Servlets and Java Server Pages (JSP). The research contains practical case studies that demonstrate how Java-based user interface design can be successfully applied in real-world scenarios. The advantages of modularity, code reusability, and maintainability are demonstrated in these case studies. The study examines how selected technologies affect the performance, security, and accessibility of web UI, while also addressing load times, data integrity, and user inclusion issues. To summarize, this investigation underscores the crucial role of dynamic and scalable databases and Java-based technologies in enhancing the design of psychological assessment Web UIs.Developers can create web applications that exceed user expectations and provide superior user experience in the evolving digital landscape by using the proposed frameworks comprehensive toolkit.

NemoTrainer: Automated Conditioning for Stimulus-Directed Navigation and Decision Making in Free-Swimming Zebrafish.

Current methods for associative conditioning in animals involve human intervention that is labor intensive, stressful to animals, and introduces experimenter bias in the data. Here, we describe a simple apparatus and a flexible, microcontroller-based conditioning paradigm that minimizes human intervention. Our methodology exploits directed movement towards a target that depends on spatial working memory, including processing of sensory inputs, motivational drive, and attentional mechanisms. Within a stimulus-driven conditioning paradigm designed to train zebrafish, we present a localized pulse of light via LEDs and/or sounds via an underwater transducer. A webcam placed below a glass tank records fish-swimming behavior. For classical conditioning, animals simply associate a sound or light with an unconditioned stimulus, such as a small food reward presented at a fixed location, and swim towards that location to obtain a few grains of food dispensed automatically via a sensor-triggered, stepper motor. During operant conditioning, a fish must first approach a proximity sensor at a remote location and then swim to the reward location. For both types of conditioning, a timing-gated interrupt activates stepper motors via custom software embedded within a microcontroller (Arduino). "Ardulink", a Java facility, implements Arduino-computer communication protocols. In this way, a Java-based user interface running on a host computer can provide full experimental control. Alternatively, a similar level of control is achieved via an Arduino script communicating with an event-driven application controller running on the host computer. Either approach can enable precise, multi-day scheduling of training, including timing, location, and intensity of stimulus parameters; and the feeder. Learning can be tracked by monitoring turning, location, response times, and directional swimming of individual fish. This facilitates the comparison of performance within and across a cohort of animals. Our scheduling and control software and apparatus ("NemoTrainer") can be used to study multiple aspects of species-specific behaviors as well as the effects on them of various interventions.

An Integrated Agriculture, Atmosphere, and Hydrology Modeling System for Ecosystem Assessments.

We present a regional-scale integrated modeling system (IMS) that includes Environmental Policy Integrated Climate (EPIC), Weather Research and Forecast (WRF), Community Multiscale Air Quality (CMAQ), and Soil and Water Assessment Tool (SWAT) models. The centerpiece of the IMS is the Fertilizer Emission Scenario Tool for CMAQ (FEST-C), which includes a Java-based interface and EPIC adapted to regional applications along with built-in database and tools. The SWAT integration capability is a key enhanced feature in the current release of FEST-C v1.4. For integrated modeling demonstration and evaluation, FEST-C EPIC is simulated over three individual years with WRF/CMAQ weather and N deposition. Simulated yearly changes in water and N budgets along with yields for two major crops (corn grain and soybean) match those inferred from intuitive physical reasoning and survey data given different-year weather conditions. Yearlong air quality simulations with an improved bidirectional ammonia flux modeling approach directly using EPIC-simulated soil properties including NH3 content helps reduce biases of simulated gas-phase NH3 and NH4+ wet deposition over the growing season. Integrated hydrology and water quality simulations applied to the Mississippi River Basin show that estimated monthly streamflow and dissolved N near the outlet to the Gulf of Mexico display similar seasonal patterns as observed. Limitations and issues in different parts of the integrated multimedia simulations are identified and discussed to target areas for future improvements.Plain Language SummaryComputer modeling tools with land-water-air processes are important for understanding nutrient cycling and its negative impacts on air and water quality. We have developed an integrated modeling system that includes agriculture, atmosphere, and hydrology components. The centerpiece of the system is a computer system that includes an agricultural ecosystem model and tools used to connect different modeling components. The agricultural system can conduct simulations for 42 types of grassland and cropland with the influence of site, soil, and management information along with weather and nitrogen deposition from the atmosphere component. An air quality computer model then uses information from the agricultural model, such as how much ammonia is in the soil, to predict how much ammonia gets in the air. Then, the watershed hydrology and water quality model uses the information from the agricultural and atmospheric models to understand the influence of agriculture and atmosphere on water quality. The paper demonstrates and evaluates the integrated modeling system on issues mainly related to N cycling. The system performs reasonably well in comparison with survey and observation data given the configured modeling constraints. The paper also identifies and discusses the advantages and limitations in each part of the system for future applications and improvements.

An Interface to Model 3D Hydrological Process of a Soak-Away Rain Garden

To mitigate the adverse impact of urbanization around the world, several best management practices, in other words green infrastructures, have been used in a way that protect the natural hydrology of the catchment and are more beneficial to the environment. Soak-away rain garden, shallow, landscaped depressions commonly located in parking lots or within small pockets in residential areas, is one of those best management practices or green infrastructures. However, though in the past few decades the mathematical modeling work and the science of computer simulation have enhanced the understanding of hydrological processes, there is still a lack of modeling studies that focus on understanding the three-dimensional (3D) hydrological processes, such as the 3D ex-filtration process of a soak-away rain garden in a sufficient level of details. Thus, this paper develops a 3D mathematical model to represent the hydrological processes of a soak-away rain garden using COMSOL Multiphysics Java API, a Java-based interface of COMSOL Multiphysics. The developed model is demonstrated with a design hyetograph of 3-month average rainfall intensities of Singapore.

A genetic algorithm based optimization framework to visualize, evaluate, and modify 3D space configurations in Desktop VR

This paper presents the design and implementation of a Desktop VR (Virtual Reality) framework for generating and evaluating Pareto-optimal alternate 3D spatial configurations using GA (genetic algorithms). The 3-tier framework involves the generation of the Pareto-optimal plans using GA which are subsequently visualized first using a Java-based 2D Interface and finally in the form of a 3D VR scene. The search spaces (function domains) are extremely large in today’s multifaceted interior design situations, and the optimization procedure involves conflicting objective functions, and limitations in the form of constraint functions. The interior space allocation problem is formulated and implemented as the “optimal configuration of artifacts”. When using GAs, a group of Pareto-optimal solutions (Pareto set) are available for the planners and decision-makers, wherefrom one solution ought to be picked. Therefore, this study applies a tool to not only visually evaluate the plans, but also to interact with those plans to develop them further if needed. Besides enabling the optimal spatial configuration of the scene elements, this framework also facilitates evaluation and interaction via the 3D VR worlds. The framework aids the proactive exploration, analysis, and finalization of design aspects such as color, size, lighting, etc. of the various elements prior to the actual construction. The results demonstrate the robust performance of the GA and the final 3D VR environment with dynamic interactive capabilities. This final interface facilitates “GA-Compliant” transformations and scene modifications thereby facilitating the exploration and examination of alternative scene configurations.

Prototype of a secure wireless patient monitoring system for the medical community

Many medical applications set new demands on sensor network designs. They often involve highly variable data rates, multiple receivers and security. Most existing sensor network designs do not adequately support these requirements, focusing instead on aggregating small amounts of data from nodes without security. In this paper, we present a software design for medical sensor networks. This framework provides a set of protocols and services specifically tailored for this application domain. It includes a secure communications model, an interface for periodic collection of sensor data, a dynamic sensor discovery protocol and protocols that monitor and save up to 70% of the energy of a node. The framework is built in TinyOS and a JAVA based user interface is provided to debug the framework and display the measured data. An extensive evaluation of the framework of a 6-node sensor test-bed is presented, measuring scalability and robustness as the number of sensors and the per node data rate are varied. The results show that the proposed framework is a scalable, robust, reliable and secure solution for medical applications.

VisualRepbase: an interface for the study of occurrences of transposable element families.

BackgroundRepbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Repbase already has software for entering new sequence families and for comparing the user's sequence with the database of consensus sequences.ResultsWe describe the software named VisualRepbase and the associated database, which allow for displaying and analyzing all occurrences of transposable element families present in an annotated genome. VisualRepbase is a Java-based interface which can download selected occurrences of transposable elements, show the distribution of given families on the chromosome, and present the localization of these occurrences with regard to gene annotations and other families of transposable elements in Repbase. In addition, it has several features for saving the graphical representation of occurrences, saving all sequences in FASTA format, and searching and saving all annotated genes that are surrounded by these occurrences.ConclusionVisualRepbase is available as a downloadable version. It can be found at .

RECOVIR: An application package to automatically identify some single stranded RNA viruses using capsid protein residues that uniquely distinguish among these viruses

BackgroundMost single stranded RNA (ssRNA) viruses mutate rapidly to generate large number of strains having highly divergent capsid sequences. Accurate strain recognition in uncharacterized target capsid sequences is essential for epidemiology, diagnostics, and vaccine development. Strain recognition based on similarity scores between target sequences and sequences of homology matched reference strains is often time consuming and ambiguous. This is especially true if only partial target sequences are available or if different ssRNA virus families are jointly analyzed. In such cases, knowledge of residues that uniquely distinguish among known reference strains is critical for rapid and unambiguous strain identification. Conventional sequence comparisons are unable to identify such capsid residues due to high sequence divergence among the ssRNA virus reference strains. Consequently, automated general methods to reliably identify strains using strain distinguishing residues are not currently available.ResultsWe present here RECOVIR ("recognize viruses"), a software tool to automatically detect strains of caliciviruses and picornaviruses by comparing their capsid residues with built-in databases of residues that uniquely distinguish among known reference strains of these viruses. The databases were created by constructing partitioned phylogenetic trees of complete capsid sequences of these viruses. Strains were correctly identified for more than 300 complete and partial target sequences by comparing the database residues with the aligned residues of these sequences. It required about 5 seconds of real time to process each sequence. A Java-based user interface coupled with Perl-coded computational modules ensures high portability of the software. RECOVIR currently runs on Windows XP and Linux platforms. The software generalizes a manual method briefly outlined earlier for human caliciviruses.ConclusionThis study shows implementation of an automated method to identify virus strains using databases of capsid residues. The method is implemented to detect strains of caliciviruses and picornaviruses, two of the most highly divergent ssRNA virus families, and therefore, especially difficult to identify using a uniform method. It is feasible to incorporate the approach into classification schemes of caliciviruses and picornaviruses and to extend the approach to recognize and classify other ssRNA virus families.

Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor

BackgroundRepbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Updating and maintenance of the database requires specialized tools, which we have created and made available for use with Repbase, and which may be useful as a template for other curated databases.ResultsWe describe the software tools RepbaseSubmitter and Censor, which are designed to facilitate updating and screening the content of Repbase. RepbaseSubmitter is a java-based interface for formatting and annotating Repbase entries. It eliminates many common formatting errors, and automates actions such as calculation of sequence lengths and composition, thus facilitating curation of Repbase sequences. In addition, it has several features for predicting protein coding regions in sequences; searching and including Pubmed references in Repbase entries; and searching the NCBI taxonomy database for correct inclusion of species information and taxonomic position. Censor is a tool to rapidly identify repetitive elements by comparison to known repeats. It uses WU-BLAST for speed and sensitivity, and can conduct DNA-DNA, DNA-protein, or translated DNA-translated DNA searches of genomic sequence. Defragmented output includes a map of repeats present in the query sequence, with the options to report masked query sequence(s), repeat sequences found in the query, and alignments.ConclusionCensor and RepbaseSubmitter are available as both web-based services and downloadable versions. They can be found at (RepbaseSubmitter) and (Censor).

Development of distributed bioinformatics applications with GMP

AbstractWe present the design and use of gMP as a tool for developing distributed bioinformatics applications. gMP is a purely Java‐based interface that adds MPI‐like message‐passing and collective communication to the genomics Research Network Architecture (gRNA). The gRNA is a highly programmable, modular environment specifically designed to invigorate the development of genome‐centric tools for life science research. We demonstrate the development of a distributed application to detect regulatory elements using correlation with gene expression data. Its implementation with gMP leads to significant runtime savings on our distributed gRNA system. Copyright © 2004 John Wiley & Sons, Ltd.

Force-reflecting teleoperation over the internet: the JBIT project

An ever-growing number of Internet-connected devices are now accessible to a multitude of users. Being an ubiquitous communication means, the Internet could enable any user to reach and command any device connected to the network. This paper reports the successful application of real-time closed-loop control over the Internet in the Java-Based Interface for Telerobotics (JBIT) system, in which the Internet users can access and command a two-degrees-of-freedom robot in real time, receiving both visual and force feedback. When closed-loop control of a remote system comes into play, careful evaluation of the performance and limits of the communication system in use is mandatory. The reported analysis shows that the main Internet limits are unknown available throughput, variable delay, and loss of some data packets, in particular when the network is congested. Once the limits of the communication system are known, it is shown that it is possible to use the Internet for the remote closed-loop control of a slave robot, provided that suitable strategies to guarantee operability and safety of the controlled system are implemented. Such strategies are concerned with on-line identification of the connection characteristics, adaptation of the data rate to the available throughput, recovery of the missing packet, and handling of the variable delay. Moreover, visual feedback dataflow shares the same Internet connection with the real-time control data. To prevent congestion, new tools for adaptive dataflow management have been developed. Finally, an improved coordinating force control scheme, aimed at enhancing the transparency of the teleoperator, is presented.

Evaluating Tandem Language Learning in the MOO: Discourse Repair Strategies in a Bilingual Internet Project

Over the past years, the Internet has developed communication tools as well as information resources. Text-based tools have been established as valuable modular environments for education. One of them, the MOO virtual environment, has maintained its appeal, not least through initiatives such as the CALLMOO project, which developed an educational database with a Java-based interface and undertook systematic research on educational uses of MOOs (Aarseth & Jopp, 1998). In this paper, we will give a short overview of the concepts of learners autonomy and tandem learning. We will then look at repair strategies as represented in two types of data, questionnaires and transcripts, from a bilateral tandem MOO project between Information and Communication Technology (ICT) students from Trinity College Dublin and the Fachhochschule Rhein-Sieg near St. Augustin, Germany. By triangulating the data, we will show how repair strategies, in particular translation and paraphrase are distributed, and how learners’ intentions of their use (as evidenced by the questionnaire) and their actual realisations (in transcripts) work towards regulating native speaker/non-native speaker discourse, thereby supporting students in becoming more autonomous.

A web-based simulation system for transport and retention of dissolved contaminants in soil

The movement of contaminants through the soil matrix is primarily a liquid phase process in which the chemical partitions between sorbed and dissolved phases. These phenomena have been modeled extensively and several computer models were developed. The use of those computer programs requires installation of the software in the users machine. Usually, post-processing of the numerical output provided by the software is required. In this paper, a web-based simulation environment for retention and transport of dissolved organic and inorganic compounds in soils is presented. The system was developed using Java and is based on the Multi-reaction Transport Model of heavy metals in soil. The mathematical and numerical formulation of the model is briefly sketched. The core computing components of the simulation environment were written in C or fortran for their computational efficiency. The emerging Java Native Interface (JNI) technique and the Swing interface were used to design a user-friendly simulator. Java security problems (due to the use of applets calling native libraries) are discussed and a solution to avoid security restrictions is provided. The simulation system provides interactive user control and real time visualization through standard web browsers. The Java-based simulation code was used to analyze a hypothetical soil contamination problem. The almost instantaneous visualization of results provided by the Java-based interface resulted in efficient and easy analyses. Although a performance comparison was not in mind, the evaluation of the same scenario using the original fortran code took three times as much total time (program run, evaluation of results and post-processing) as that using the Java simulation system.

Support for collaborative design reasoning in shared virtual spaces

This paper discusses collaborative design, emphasizing the elaboration and transformations of a problem space, and the role that unstructured verbal communication and graphic communication can play in these processes. An asynchronous collaborative system, called the Immersive Discussion Tool (IDT), is introduced as a means for supporting productive design exchanges. IDT allows collaborators to reason about 3-D models over the Internet using view-dependent and view-independent diagrammatic marks, dynamic simulations, geometric design surrogates and text annotations. IDT relies on VRML to view the models, with an extensive Java-based interface driving the interactive behavior, including the construction and playback of graphical annotations, the management of threaded discussions, and the management of file input/output. The development and initial implementation of IDT has revealed the difficulty of constructing complex marks in a virtual 3-D space. Possible strategies for dealing with these problems are suggested.

An Astronomical Data Archive System with a Java-Based User Interface

Abstract We have developed a data archive system for the optical telescopes of Okayama Astrophysical Observatory and Kiso Observatory. The archive system has a Java-based user interface and is accessible through the World Wide Web. Using this interface, users are able to search and preview observational data and also to refer to an environmental database of meteorological data and night-sky images. Most of the user interface, including an image previewer and environmental data viewers, has been developed as Java applets. The previewer has many functions, such as plotting a profile of a spectral image with its wavelength scale. The environmental viewers are useful to know the weather condition during an observation and to evaluate the quality of observational data. The applets have good performance running on client platforms, realizing interoperability of the system, and reducing network traffic. This system is also a prototype of the data-archive system of Subaru Telescope.

Multicriteria DSS with Historical Database for Attenuator Selection

A computerized information system has been developed for the management of field data on vehicle impacts with crash attenuators. The system has been developed for an intranet platform with a Java-based interface. A central Oracle database contains a variety of data describing site conditions, maintenance history, and accident characteristics. Several standard reports can be generated, summarizing attenuator usage, life-cycle costs, and accident outcomes under a variety of site or crash conditions. In addition, a multicriteria decision support system uses historical data to rank attenuators based on their past performance under specific site conditions. This application supports the design and selection of attenuators for new locations; it can also be used to analyze current placement recommendations for common scenarios. Use of the system will allow highway safety personnel to better understand the performance and applicability of various types of crash attenuators. Further, the research extends the concept of a decision hierarchy by: (1) using deterministic and heuristic importance functions to vary the weights to reflect changes in site conditions; and (2) using a possibilistic matching algorithm to include historical data that partially matches the user-input site characteristics in the performance evaluations.

Moo in your face: researching, designing, and programming a user-friendly interface

Promoters of multi-user, object-oriented domains (MOOs) in composition point to the capability for student collaboration and conversation throughout the writing process as a valuable feature; detractors, however, draw attention to the difficulty for students to negotiate the somewhat arcane, text-based MOO interface, which affords no easy, intuitive way for students to learn how to exist in that virtual world, and often results in confusing conversations. The learning curve of a MOO and its confusing interface blockade effective use. Current research on Web-browser interface design provides several principles for developing a user-friendly Telnet interface that creates a sense of presence for the user. An IBM/PC-compatible interface, Pueblo from Chaco Communications, Inc., allows developers to modify the interface to provide a sense of presence for the user. In addition, access to the sites for non-IBM users was developed. For Web browsers, a Java-based interface and a WOO interface allow students to access and function in the MOO more quickly than a purely text-based client did. Work in programming a variety of interfaces has led to a more intuitive environment for students and instructors who use MOOs.

Enterprise-scale image distribution with a Web PACS.

The integration of images with existing and new health care information systems poses a number of challenges in a multi-facility network: image distribution to clinicians; making DICOM image headers consistent across information systems; and integration of teleradiology into PACS. A novel, Web-based enterprise PACS architecture introduced at Massachusetts General Hospital provides a solution. Four AMICAS Web/Intranet Image Servers were installed as the default DICOM destination of 10 digital modalities. A fifth AMICAS receives teleradiology studies via the Internet. Each AMICAS includes: a Java-based interface to the IDXrad radiology information system (RIS), a DICOM autorouter to tape-library archives and to the Agfa PACS, a wavelet image compressor/decompressor that preserves compatibility with DICOM workstations, a Web server to distribute images throughout the enterprise, and an extensible interface which permits links between other HIS and AMICAS. Using wavelet compression and Internet standards as its native formats, AMICAS creates a bridge to the DICOM networks of remote imaging centers via the Internet. This teleradiology capability is integrated into the DICOM network and the PACS thereby eliminating the need for special teleradiology workstations. AMICAS has been installed at MGH since March of 1997. During that time, it has been a reliable component of the evolving digital image distribution system. As a result, the recently renovated neurosurgical ICU will be filmless and use only AMICAS workstations for mission-critical patient care.

A smart itsy bitsy spider for the Web

As part of the ongoing Illinois Digital Library Initiative project, this research proposes an intelligent agent approach to Web searching. In this experiment, we developed two Web personal spiders based on best first search and genetic algorithm techniques, respectively. These personal spiders can dynamically take a user's selected starting homepages and search for the most closely related homepages in the Web, based on the links and keyword indexing. A graphical, dynamic, Java-based interface was developed and is available for Web access. A system architecture for implementing such an agent-based spider is presented, followed by detailed discussions of benchmark testing and user evaluation results. In benchmark testing, although the genetic algorithm spider did not outperform the best first search spider, we found both results to be comparable and complementary. In user evaluation, the genetic algorithm spider obtained significantly higher recall value than that of the best first search spider. However, their precision values were not statistically different. The mutation process introduced in genetic algorithm allows users to find other potential relevant homepages that cannot be explored via a conventional local search process. In addition, we found the Java-based interface to be a necessary component for design of a truly interactive and dynamic Web agent. © 1998 John Wiley & Sons, Inc.

An intelligent personal spider (agent) for dynamic Internet/Intranet searching

As Internet services based on the World-Wide Web become more popular, information overload has become a pressing research problem. Difficulties with search on Internet will worsen as the amount of on-line information increases. A scalable approach to Internet search is critical to the success of Internet services and other current and future National Information Infrastructure (NII) applications. As part of the ongoing Illinois Digital Library Initiative project, this research proposes an intelligent personal spider (agent) approach to Internet searching. The approach, which is grounded on automatic textual analysis and general-purpose search algorithms, is expected to be an improvement over the current static and inefficient Internet searches. In this experiment, we implemented Internet personal spiders based on best first search and genetic algorithm techniques. These personal spiders can dynamically take a user's selected starting homepages and search for the most closely related homepages in the web, based on the links and keyword indexing. A plain, static CGI/HTML-based interface was developed earlier, followed by a recent enhancement of a graphical, dynamic Java-based interface. Preliminary evaluation results and two working prototypes (available for Web access) are presented. Although the examples and evaluations presented are mainly based on Internet applications, the applicability of the proposed techniques to the potentially more rewarding Intranet applications should be obvious. In particular, we believe the proposed agent design can be used to locate organization-wide information, to gather new, time-critical organizational information, and to support team-building and communication in Intranets.