Java-based Tool Research Articles

Use of XML and Java for collaborative petroleum reservoir modeling on the Internet

The GEMINI (Geo-Engineering Modeling through INternet Informatics) is a public-domain, web-based freeware that is made up of an integrated suite of 14 Java-based software tools to accomplish on-line, real-time geologic and engineering reservoir modeling. GEMINI facilitates distant collaborations for small company and academic clients, negotiating analyses of both single and multiple wells. The system operates on a single server and an enterprise database. External data sets must be uploaded into this database. Feedback from GEMINI users provided the impetus to develop Stand Alone Web Start Applications of GEMINI modules that reside in and operate from the user's PC. In this version, the GEMINI modules run as applets, which may reside in local user PCs, on the server, or Java Web Start. In this enhanced version, XML-based data handling procedures are used to access data from remote and local databases and save results for later access and analyses. The XML data handling process also integrates different stand-alone GEMINI modules enabling the user(s) to access multiple databases. It provides flexibility to the user to customize analytical approach, database location, and level of collaboration. An example integrated field-study using GEMINI modules and Stand Alone Web Start Applications is provided to demonstrate the versatile applicability of this freeware for cost-effective reservoir modeling.

The learning of control concepts using interactive tools

This paper discusses the creation of interactive computer simulations that implement virtual laboratories in the field of Control Engineering education. Easy Java Simulations (Ejs, http://fem.um.es/Ejs/), a Java-based tool that helps create interactive dynamic simulations, is introduced. This tool can be used on its own, generating stand-alone Java applications or applets, or in conjunction with Matlab/Simulink, using them as the internal engine that describes and solves the model. We describe in this paper this particular feature in detail, and provide some examples that show the advantages that this tool offers to the world-wide engineering education community. Ejs is a freeware, open source, tool aimed for educators with low profile in programming but deep knowledge on certain technical and scientific fields. The tool allows to develop complete, interactive simulations in three steps: describing the mathematical model (optionally using Matlab/Simulink), building the user interface using off-the-shelf graphical elements, and connecting certain properties of these elements to the variables of the model. This last step is the key point to transform a classical simulation into a full interactive application. © 2005 Wiley Periodicals, Inc. Comput Appl Eng Educ 13: 84–98, 2005; Published online in Wiley InterScience (www.interscience.wiley.com); DOI 10.1002/cae.20033

CR-EST: a resource for crop ESTs.

The crop expressed sequence tag database, CR-EST (http://pgrc.ipk-gatersleben.de/cr-est/), is a publicly available online resource providing access to sequence, classification, clustering and annotation data of crop EST projects. CR-EST currently holds more than 200 000 sequences derived from 41 cDNA libraries of four species: barley, wheat, pea and potato. The barley section comprises approximately one-third of all publicly available ESTs. CR-EST deploys an automatic EST preparation pipeline that includes the identification of chimeric clones in order to transparently display the data quality. Sequences are clustered in species-specific projects to currently generate a non-redundant set of ∼22 600 consensus sequences and ∼17 200 singletons, which form the basis of the provided set of unigenes. A web application allows the user to compute BLAST alignments of query sequences against the CR-EST database, query data from Gene Ontology and metabolic pathway annotations and query sequence similarities from stored BLAST results. CR-EST also features interactive JAVA-based tools, allowing the visualization of open reading frames and the explorative analysis of Gene Ontology mappings applied to ESTs.

PartiGeneDB--collating partial genomes

Owing to the high costs involved, only 28 eukaryotic genomes have been fully sequenced to date. On the other hand, an increasing number of projects have been initiated to generate survey sequence data for a large number of other eukaryotic organisms. For the most part, these data are poorly organized and difficult to analyse. Here, we present PartiGeneDB (http://www.partigenedb.org), a publicly available database resource, which collates and processes these sequence datasets on a species-specific basis to form non-redundant sets of gene objects—which we term partial genomes. Users may query the database to identify particular genes of interest either on the basis of sequence similarity or via the use of simple text searches for specific patterns of BLAST annotation. Alternatively, users can examine entire partial genome datasets on the basis of relative expression of gene objects or by the use of an interactive Java-based tool (SimiTri), which displays sequence similarity relationships for a large number of sequence objects in a single graphic. PartiGeneDB facilitates regular incremental updates of new sequence datasets associated with both new and exisitng species. PartiGeneDB currently contains the assembled partial genomes derived from 1.83 million sequences associated with 247 different eukaryotes.

Ligand.Info Small-Molecule Meta-Database

Ligand.Info is a compilation of various publicly available databases of small molecules. The total size of the Meta-Database is over 1 million entries. The compound records contain calculated three-dimensional coordinates and sometimes information about biological activity. Some molecules have information about FDA drug approving status or about anti-HIV activity. Meta-Database can be downloaded from the http://Ligand.Info web page. The database can also be screened using a Java-based tool. The tool can interactively cluster sets of molecules on the user side and automatically download similar molecules from the server. The application requires the Java Runtime Environment 1.4 or higher, which can be automatically downloaded from Sun Microsystems or Apple Computer and installed during the first use of Ligand.Info on desktop systems, which support Java (Ms Windows, Mac OS, Solaris, and Linux). The Ligand.Info Meta-Database can be used for virtual high-throughput screening of new potential drugs. Presented examples showed that using a known antiviral drug as query the system was able to find others antiviral drugs and inhibitors.

Behind BANANA: Design and Implementation of a Tool for Nesting Analysis of Mobile Ambients

We present a survey of the work on control-flow analysis carried on by the Venice Team during the Mefisto project. We study security issues, in particular information leakage detection, in the context of the Mobile Ambient calculus. We describe BANANA, a Java-based tool for ambient nesting analysis, by focussing on analysis accuracy and algorithmic optimizations.

Nesting analysis of mobile ambients

A new algorithm is introduced for analyzing possible nestings in mobile ambient calculus. It improves both time and space complexities of the technique proposed by Nielson and Seidl. The improvements are achieved by enhancing the data structure representations, and by reducing the computation to the control flow analysis constraints that are effectively necessary to get to the least solution. These theoretical results are also supported by experimental tests run on a Java-based tool that implements a suite of algorithms for nesting analysis of mobile ambients.

Multitracer: a Java-based tool for anatomic delineation of grayscale volumetric images

A Java-based tool for delineating anatomic boundaries in 8- and 16- bit grayscale volumetric images is described. Modern features implemented by the tool include the ability to simultaneously view the current cursor position and the previously delineated boundaries on three orthogonal planes, the ability to magnify images during delineation using high-quality interpolation, the ability to encode and save boundaries with subvoxel resolution, and the ability to utilize coregistered images interchangeably during delineation. Additional features facilitate use of the tool in a multiuser, multiplatform environment and provide support for the documentation of anatomic delineation protocols. In addition to providing direct estimates of structure volumes, areas, and lengths, the tool allows contoured boundaries to be exported for more sophisticated analyses. The tool also provides support for manual editing of image volumes to remove confounding structures and for manual correction of image volumes that have been inaccurately edited. In addition to its research utility, the tool also has potential value in education, allowing students to interact with volumetric data and structural boundaries in three dimensions.

Java multimedia telecollaboration

Using Java-based tools in multimedia collaborative environments accessed over the Internet can increase an application's client base. Most operating systems support Java, and its compile once-run everywhere architecture is easy to maintain and update. The Java-based tools presented here let users share Internet resources, including resources originally designed for single use.

EnteriX 2003: visualization tools for genome alignments of Enterobacteriaceae

We describe EnteriX, a suite of three web-based visualization tools for graphically portraying alignment information from comparisons among several fixed and user-supplied sequences from related enterobacterial species, anchored on a reference genome (http://bio.cse.psu.edu/). The first visualization, Enteric, displays stacked pairwise alignments between a reference genome and each of the related bacteria, represented schematically as PIPs (Percent Identity Plots). Encoded in the views are large-scale genomic rearrangement events and functional landmarks. The second visualization, Menteric, computes and displays 1 Kb views of nucleotide-level multiple alignments of the sequences, together with annotations of genes, regulatory sites and conserved regions. The third, a Java-based tool named Maj, displays alignment information in two formats, corresponding roughly to the Enteric and Menteric views, and adds zoom-in capabilities. The uses of such tools are diverse, from examining the multiple sequence alignment to infer conserved sites with potential regulatory roles, to scrutinizing the commonalities and differences between the genomes for pathogenicity or phylogenetic studies. The EnteriX suite currently includes >15 enterobacterial genomes, generates views centered on four different anchor genomes and provides support for including user sequences in the alignments.

Java editor for biological pathways.

A visual Java-based tool for drawing and annotating biological pathways was developed. This tool integrates the possibilities of charting elements with different attributes (size, color, labels), drawing connections between elements in distinct characteristics (color, structure, width, arrows), as well as adding links to molecular biology databases, promoter sequences, information on the function of the genes or gene products, and references. It is easy to use and system independent. The result of the editing process is a PNG (portable network graphics) file for the images and XML (extended markup language) file for the appropriate links.

A Web-based Database System for Providing Technical Information on ATM Networking Platforms

This paper presents a Web-based database hosting technical information about pioneering ATM networking platforms, associated research activities engaging these platforms, and related important trials conducted in the framework of these research activities. The paper outlines the organisation and structure of the information content in the database and discusses methods of access through the WWW interface. Besides the “static” information offered by the database, other Java-based tools provide for the on-line monitoring of the status of the ATM platforms and for manipulating data arising from technological trials on these platforms. The integration of these tools with the database, under a common WWW interface is discussed.

Java-based tools for accurate bandwidth measurement of Digital Subscriber Line networks1

This paper presents the design and implementation of Java-based tools for accurate bandwidth measurement for xDSL (Digital Subscriber Line) networks, including the ADSL (Asymmetric DSL) case with different upstream and downstream bandwidths. First, a

Java for On-line Distributed Monitoring of Heterogeneous Systems and Services

The control and management of Web-based service quality require the extension of the Internet infrastructure with monitoring functions to ascertain dynamically the state of networked resources. We describe the design and implementation of the Monitoring Application Programming Interface (MAPI), a Java-based tool for the on-line monitoring of Internet heterogeneous resources, which provides monitoring indicators at different levels of abstraction. At the application level, it instruments the Java Virtual Machine (JVM) to notify several different types of events triggered during the execution of Java applications, e.g. object allocation and method calls. At the kernel level, MAPI inspects system-specific information generally hidden by the JVM, e.g. CPU usage and incoming network packets, by integrating with Simple Network Management Protocol agents and platform-dependent monitoring modules. MAPI is the core part of a portable tool for distributed monitoring, control and management in the Internet environment. The tool is implemented in terms of mobile agents that move close to the monitored resources to enforce distributed management policies autonomously, with a significant reduction in both reaction time and traffic overhead.

A general-purpose Java tool for action dispatching and supervision in nuclear fusion experiments

In nuclear fusion experiments, the plasma discharge requires a preparation sequence followed by a data acquisition phase. During these phases, the control and data acquisition system is required to carry out a sequence of operations for set up of the various devices, data readout, and on-line computation. An action dispatcher tool must comply with several requirements such as the support for a distributed and heterogeneous environment, a comprehensive user interface for the supervision of the whole sequence, and the need for web-based support. The paper describes the architecture of a general-purpose Java-based tool for action dispatching. The use of the platform-independent Java framework, combined with the generic approach in the architecture definition, satisfies the above requirements. The Java framework has been chosen for the implementation because of its platform-independence, network, and multithreading support. The architecture of the tool has been kept quite generic, thus making the tool adaptable to a variety of operating environments with minimal changes in the application code.

Aktuelle Entwicklungsumgebungen für mobile Agenten und Multiagentensysteme

In the last few vicars the research in mobile agents, and multi agent systems has begun to leave the theoretical research arena and has turned towards developing practical applications and development tools. Agent-based systems are able to work autonomously on given tasks and to adapt themselves to a dynamic environment and changing tasks. For the development of distributed systems the programming language Java has proven suitable. This paper introduces into some of Java-based development tools for the design of intelligent and mobile agents and multi agent systems. In particular, the analysis of architecture of systems, the support of communication and cooperation, and consisting security architectures are considered.

A Java-based tool for reasoning about models of computation through simulating finite automata and Turing machines

Interactive visualization tools for models of computation provide a more compelling means of exploration and feedback than traditional paper and pencil methods in theory of computation courses. The Java Computability Toolkit (JCT) is introduced here as a new teaching aide and as an exploratory student's supplement to a course on theory of computation. JCT consists of two Java multiple-window, web-accessible, graphical environments, allowing the construction and simulation of finite automata and Turing machines. This paper discusses JCT's use, design, and applications in teaching.

Managing complex documents over the WWW: a case study for XML

The use of the World Wide Web as a communication medium for knowledge engineers and software designers is limited by the lack of tools for writing, sharing, and verifying documents written with design notations. For instance, the Z language has a rich set of mathematical characters, and requires graphic-rich boxes and schemas for structuring a specification document. It is difficult to integrate Z specifications and text on WWW pages written with HTML, and traditional tools are not suited for the task. On the other hand, a newly proposed standard for markup languages, namely XML, allows one to define any set of markup elements; hence, it is suitable for describing any kind of notation. Unfortunately, the proposed standard for rendering XML documents, namely XSL, provides for text-only (although sophisticated) rendering of XML documents, and thus it cannot be used for more complex notations. We present a Java-based tool for applying any notation to elements of XML documents. These XML documents can thus be shown on current-generation WWW browsers with Java capabilities. A complete package for displaying Z specifications has been implemented and integrated with standard text parts. Being a complete rendering engine, text parts and Z specifications can be freely intermixed, and all the standard features of XML (including HTML links and form elements) are available outside and inside Z specifications. Furthermore, the extensibility of our engine allows any additional notations to be supported and integrated with the ones we describe.

Using Java and JavaScript in the Virtual Programming Laboratory: a Web-based parallel programming environment

The Virtual Programming Laboratory (VPL) is a Web-based virtual programming environment built based on a client–server architecture. The system can be accessed on any platform (Unix, PC or Mac) using a standard Java-enabled browser. Software delivery over the Web imposes a novel set of constraints on design. We outline the tradeoffs in this design space, motivate the choices necessary to deliver an application, and detail the lessons learned in the process. We discuss the role of Java and other Web technologies in the realization of the design. VPL facilitates the development and execution of parallel programs. The initial prototype supports high-level parallel programming based on Fortran 90 and High Performance Fortran (HPF), as well as explicit low-level programming with the MPI message-passing interface. Supplementary Java-based platform-independent tools for data and performance visualization are an integral part of the VPL. Pablo SDDF trace files generated by the Pablo performance instrumentation system are used for post-mortem performance visualization. © 1997 John Wiley & Sons, Ltd.