Java Web Start Research Articles

Automated expert multiexponential biomodeling interactively over the Internet

DIMSUM, an acronym for DIMension of a SUM of exponentials, is a highly automated expert system for fitting multiexponential models of increasing dimension to time series data. Up to now, a researcher has needed an individual copy of DIMSUM on his or her own computer as well as support to learn how to use it. W3DIMSUM, a new implementation of DIMSUM, is web-based, new territory for interactive biomodeling, allowing interactive multiexponential model building and model discrimination over the Internet. The algorithms used are numerically intensive, so we have implemented a distributed system, with numerical processing done on our server. Only the user interface is run on the client machine, but users can load and save data and results on their machines, facilitated by our use of Java WebStart.

Java Web Start based software for automated quantitative nuclear analysis of prostate cancer and benign prostate hyperplasia

BackgroundAndrogen acts via androgen receptor (AR) and accurate measurement of the levels of AR protein expression is critical for prostate research. The expression of AR in paired specimens of benign prostate and prostate cancer from 20 African and 20 Caucasian Americans was compared to demonstrate an application of this system.MethodsA set of 200 immunopositive and 200 immunonegative nuclei were collected from the images using a macro developed in Image Pro Plus. Linear Discriminant and Logistic Regression analyses were performed on the data to generate classification coefficients. Classification coefficients render the automated image analysis software independent of the type of immunostaining or image acquisition system used. The image analysis software performs local segmentation and uses nuclear shape and size to detect prostatic epithelial nuclei. AR expression is described by (a) percentage of immunopositive nuclei; (b) percentage of immunopositive nuclear area; and (c) intensity of AR expression among immunopositive nuclei or areas.ResultsThe percent positive nuclei and percent nuclear area were similar by race in both benign prostate hyperplasia and prostate cancer. In prostate cancer epithelial nuclei, African Americans exhibited 38% higher levels of AR immunostaining than Caucasian Americans (two sided Student's t-tests; P < 0.05). Intensity of AR immunostaining was similar between races in benign prostate.ConclusionThe differences measured in the intensity of AR expression in prostate cancer were consistent with previous studies. Classification coefficients are required due to non-standardized immunostaining and image collection methods across medical institutions and research laboratories and helps customize the software for the specimen under study. The availability of a free, automated system creates new opportunities for testing, evaluation and use of this image analysis system by many research groups who study nuclear protein expression.

Java Web Start based software for automated quantitative nuclear analysis of prostate cancer and benign prostate hyperplasia

Java Web Start based software for automated quantitative nuclear analysis of prostate cancer and benign prostate hyperplasia

Chronos Age-Depth Plot: A Java application for stratigraphic data analysis

One of the most important steps in the analysis and correlation of stratigraphic data is establishing an age model or line of correlation (LOC) for an individual core hole or stratigraphic section. Chronos AgeDepth Plot (ADP) is a Java reimplementation of an earlier Macintosh program for plotting ages of stratigraphic events versus depth and interactively fitting an LOC to those data. ADP is delivered from the Chronos Web site via Java Web Start and runs locally on the user’s machine, allowing access to local data files as well as data from the Neptune database via a geographic-information-system interface. ADP allows the user to develop an LOC using a palette of tools for adding, moving, and deleting LOC control points. In addition, the user is able to zoom in to a more detailed view of different plot regions, toggle the display of different plot groups, and edit plot and axis titles and labels. Output options include saving the LOC control point data, the event data projected to the LOC, and the plot itself in portable-networkgraphics (PNG), Joint-Photographic-ExpertsGraphic (JPEG), or scalable-vector-graphics (SVG) format. The SVG output file is designed for convenient editing of various plot characteristics, with font and line characteristics for various plot elements and the palette of plotting symbols defined at the top of the file. In addition to being a useful application in its own right, ADP serves as a prototype for other clients interfacing with the Web services provided by the Chronos portal.

Synthetic Image Sequence Compression.

This paper describes a technique for compressing computer screen shots into a GIF animation file. The goal is to distribute the animations, to a variety of browsers, without requiring a plug-in or helper application. We seek to minimize the size of the image sequence, while maximizing the signal to noise ratio of the sequence. The GIF animation format has several constraints; images may have a maximum of 256 colors, and the images must all be of the same size. Further, to minimize overhead, we seek to make use of a single color lookup table for the entire animation. Several color quantization algorithms are compared, using SNR (Signal to Noise Ratio) as the metric of quality (as well as subjective appearance). We present the design of an interface, written in Java, and distributed freely using Java Web Start, that employs a well know neural network program and a color quantization algorithm to capture screen shots and save them to the GIF animation. GIF animations represent silent movies, as they have no sound to accompany them. However, they are still in wide use and have applications in entertainment and education. The techniques described are a part of the JSnap project, a joint project between the skunk works of DocJava, Inc. and Fairfield University.

SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation.

Transcriptional regulation is one of the most basic regulatory mechanisms in the cell. The accumulation of multiple metazoan genome sequences and the advent of high-throughput experimental techniques have motivated the development of a large number of bioinformatics methods for the detection of regulatory motifs. The regulatory process is extremely complex and individual computational algorithms typically have very limited success in genome-scale studies. Here, we argue the importance of integrating multiple computational algorithms and present an infrastructure that integrates eight web services covering key areas of transcriptional regulation. We have adopted the client-side integration technology and built a consistent input and output environment with a versatile visualization tool named SeqVISTA. The infrastructure will allow for easy integration of gene regulation analysis software that is scattered over the Internet. It will also enable bench biologists to perform an arsenal of analysis using cutting-edge methods in a familiar environment and bioinformatics researchers to focus on developing new algorithms without the need to invest substantial effort on complex pre- or post-processors. SeqVISTA is freely available to academic users and can be launched online at http://zlab.bu.edu/SeqVISTA/web.jnlp, provided that Java Web Start has been installed. In addition, a stand-alone version of the program can be downloaded and run locally. It can be obtained at http://zlab.bu.edu/SeqVISTA.

Development of Holonic Information Coordination Systems With Failure-Recovery Considerations

A holonic manufacturing system, designed to realize agile manufacturing, must (be able to) integrate the entire range of manufacturing activities from ordering, through design, modeling, production, to delivery. These activities are performed at many distributed sites. In order to effectively integrate these distributed sites, this work adopts distributed object and mobile object technologies, RosettaNet implementation framework, as well as holon and holarchy concepts derived from studying social organizations and living organisms to develop a holonic information coordination system (HICS). The generic holon is first developed by adopting the technologies of the distributed object-oriented approach with common object request broker architecture infrastructure, n-tier client/server architecture, a knowledge base, and data warehousing to achieve the properties of holon, error recovery, and security certification. The communication holon (CH) is then generated by inheriting the generic holon. Finally, CHs are employed to establish HICS. The CH exhibits basic holonic attributes, such as intelligence, autonomy, and cooperation. Furthermore, the CH can handle partner interface processes, and data exchange by various data formats following the standards of RosettaNet business messages. The failure recovery mechanism of the CH causes HICS to be more reliable than legacy systems. As such, HICS can meet the future requirements of supply-chain information integration of virtual enterprises. Note to Practitioners-An HICS that handles the information flow of the supply chain is proposed in this work. HICS is composed of many communication holons (CHs). Any company that would like to use HICS to exchange information for enterprise integration may possess a CH. The CH is implemented with the Java web-start technology. Therefore, any company can download a CH from the web server via a web browser. The company is, then, able to communicate with other members throughout the supply chain. Accordingly, CHs are scattered throughout the Internet/intranet and each CH can act as both an information supplier and an information consumer. Further, because the CH adopts the RoesettaNet implementation framework (RNIF), any company that has the capability of RNIF can also communicate with the members in the HICS framework via RosettaNet business messages.

Pelican: pedigree editor for linkage computer analysis.

Linkage analysis software requires an input text file that describes the structure of the pedigrees to be analysed. Manual creation of these files is tedious and error-prone, and a graphical input tool is desirable. This is currently only available in commercial packages that include much greater functionality. We have therefore developed Pelican, a lightweight graphical pedigree editor for rapid construction of linkage pedigree files and diagrams. The software runs on any Java-enabled machine (version 1.2 or higher). A Java Web Start launch, class files, a demonstration applet, source code and documentation are freely available at http://www.rfcgr.mrc.ac.uk/Software/PELICAN/

JDotter: a Java interface to multiple dotplots generated by dotter.

Java-Dotter (JDotter) is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client-server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly simplifies access to dotplot data in laboratories that deal with large numbers of genomes and have a multi-platform organization. Currently, JDotter is used via Java Web Start by the Poxvirus Bioinformatics Resource for examining dotplots of complete poxvirus genomes; http://athena.bioc.uvic.ca/pbr/jdotter/. The software is available for download from the same location. Installation instructions, the User's Manual, screenshots and examples are available at the JDotter home page http://athena.bioc.uvic.ca/pbr/jdotter/. The software and source code is free for non-commercial applications.

The Initium X.509 Certificate Wizard.

This paper describes the use of the Thawte’s “Web of Trust” X.509 certificates for signing and distributing executable Jar resources. A keytool wizard (called the Initium X.509 Certificate Wizard) was developed in order to help with the importation and management of certificates. A signed Jar file generally indicates that the signer authorizes the contents. Signing is accomplished using a certificate that has been issued by a Certificate Authority (CA). Several CA’s are available for this task; however, few of them are free, like the Thawte CA. Once a free certificate is obtained, Jar files may be distributed and named as verified from the signer. Trusted Jar files can be run outside of the “sandbox” and thus be given improved access to the target system. The impact of having a trusted Jar file is that Jar distribution systems (like Java Web Start, or Browser-based Applets) can run the program in the trusted manner. Therefore, such trusted programs can have access to the files, or be able to open connections to hosts other than the web host. The keytool wizard addresses a subproblem of the Initium project, a joint, on-going project between the Fairfield University and DocJava, Inc. Initium is a Latin word that means: “at the start”. 1 THE THAWTE WEB OF TRUST In order for Java Web Start to give unrestricted permission for a Java program to execute, it must use a “signed” Jar file. A signed Jar file is designed to prove that the originator is the author of the code. This does NOT prevent the author from writing harmful code. On the other hand, if you trust the author to write non-harmful code, you may feel safer about running the authors’ programs. THE INITIUM X.509 CERTIFICATE WIZARD 76 JOURNAL OF OBJECT TECHNOLOGY VOL. 3, NO. 10 In order to sign a Jar file, you need a digital certificate. Certificates are issued after a proper background check, by a Certification Authority (CA). This is not generally a free service. For example, Verisign asks for $200 or $400 per year, in order to issue a certificate. Applications that are signed by an untrusted signature (i.e., a signature that is not verified by a known CA) cause a dialog to be displayed saying: “It is highly recommended not to install and run this code”. The software that I write is typically given away. As a result, I am disinclined to pay $200-$400 per year. Therefore, a free (or at least very cheap) approach to obtaining a certificate appeals to my sense of thrift. The Thawte personal e-mail certificate can be used indefinitely, and at no cost. Thawte is a CA that can issue a digital certificate to an organization or an individual. It is the role of the CA to verify that the company ordering the certificate is a registered organization that controls its domain and that the person in the company, who ordered the certificate, is authorized to do so. Authentication helps to prevent spoofing. It is harder to substitute illegitimate programs for programs that come from established organizations when the programs must be properly signed. Con artists could make use of such untrusted programs to steal credit card numbers or create software that destroys or distorts data. Thus having an authentication procedure in place helps to establish trust and adds value to the Java programs that you distribute. From the point of view of grid computing, a grid operator will want some assurance that the program being submitted for execution is safe. At the very least, the program can be attributed to its signer before being deployed on the grid. In the event the grid application contained damaging code, the compute servers on the grid would become infected with the code faster than normally propagated computer contagions. Such a program places the entire grid as risk. 2 HOW DO I GET A CERTIFICATE? This section presents the steps that are needed in order to obtain a free personal e-mail certificate from Thawte. First you must visit https://www.thawte.com/email/index.html#, run by Thawte. You then click on “join” and fill out the application. Information needed includes, name, data of birth, and a “national identification number”. This can consist of a diver’s license number, social security number or passport number. You must also enter an e-mail address. Other information needed includes: your phone number, your mother’s maiden name, your father’s middle name, what is the make of your fridge, etc. Your free certificate will not show your name when you sign your jar files. Java Web Start, for example, will show your name as: “Thawte Freemail Member”. In order to obtain a certificate for signing your jar, you will have to wait for a confirmation e-mail from Thawte. This will contain the codes that you need in order to

Project Initium: Programmatic Deployment.

This paper describes the design and use of a Java Web Start framework called Initium. Initium generates a jar file that minimizes the number of included classes by performing a static class dependency analysis. It then prompts the programmer for security parameters that enable the programmatic signing of the jar file, for the purpose of authentication. Initium generates a local Java Network Launch Protocol file (JNLP file) for the purpose of testing, as well as a remote JNLP file, for deployment. Finally, Initium programmatically uploads both the JNLP and jar files to the web server, to complete the deployment cycle. The signing of a jar file enables web start clients to execute a Java application in a trusted and distributed manner. Trusted jar files can be executed outside of the “sandbox” and thus be given access to files, or be able to open connections to hosts other than the web host on the target system. Initium is a Latin word that means: “at the start”. It is part of an on-going project at both the DocJava Inc. skunk works and Fairfield University.

The design of Jemboss: a graphical user interface to EMBOSS.

Jemboss is a graphical user interface (GUI) for the European Molecular Biology Open Software Suite (EMBOSS). It is being developed at the MRC UK HGMP-RC as part of the EMBOSS project. This paper explains the technical aspects of the Jemboss client-server design. The client-server model optionally allows that a Jemboss user have an account on the remote server. The Jemboss client is written in Java and is downloaded automatically to a user's workstation via Java Web Start using the HTML protocol. The client then communicates with the remote server using SOAP (Simple Object Access Protocol). A Tomcat server listens on the remote machine and communicates the SOAP requests to a Jemboss server, again written in Java. This Java server interprets the client requests and executes them through Java Native Interface (JNI) code written in the C language. Another C program having setuid privilege, jembossctl, is called by the JNI code to perform the client requests under the user's account on the server. The commands include execution of EMBOSS applications, file management and project management tasks. Jemboss allows the use of JSSE for encryption of communication between the client and server. The GUI parses the EMBOSS Ajax Command Definition language for form generation and maximum input flexibility. Jemboss interacts directly with the EMBOSS libraries to allow dynamic generation of application default settings. This interface is part of the EMBOSS distribution and has attracted much interest. It has been set up at many other sites globally as well as being used at the HGMP-RC for registered users. The software, EMBOSS and Jemboss, is freely available to academics and commercial users under the GPL licence. It can be downloaded from the EMBOSS ftp server: http://www.uk.embnet.org/Software/EMBOSS/, ftp://ftp.uk.embnet.org/pub/EMBOSS/. Registered HGMP-RC users can access an installed server from: http://www.uk.embnet.org/Software/EMBOSS/Jemboss/

Project management system for structural and functional proteomics: Sesame.

A computing infrastructure (Sesame) has been designed to manage and link individual steps in complex projects. Sesame is being developed to support a large-scale structural proteomics pilot project. When complete, the system is expected to manage all steps from target selection to data-bank deposition and report writing. We report here on the design criteria of the Sesame system and on results demonstrating successful achievement of the basic goals of its architecture. The Sesame software package, which follows the client/server paradigm, consists of a framework, which supports secure interactions among the three tiers of the system (the client, server, and database tiers), and application modules that carry out specific tasks. The framework utilizes industry standards. The client tier is written in Java2 and can be accessed anywhere through the Internet. All the development on the server tier is also carried out in Java2 so as to accommodate a wide variety of computer platforms. The database tier employs a commercial database management system. Each Sesame application module consists of a simple user interface in the client tier, corresponding objects in the server tier, and relevant data stored in the centralized database. For security, access to stored data is controlled by access privileges. The system facilitates both local and remote collaborations. Because users interact with the system using Java Web Start or through a web browser, access is limited only by the availability of an Internet connection. We describe several Sesame modules that have been developed to the point where they are being utilized routinely to support steps involved in structural and functional proteomics. This software is available to parties interested in using it and assisting to guide its further development.

Web-based distribution of geo-scientific models

Scientific model developers have learned that the time required for the science and research phases of software development is relatively short when compared with the time needed to develop GUIs, writing documentation, developing support programs (e.g. pre-processors, visualization tools, and reports), debugging source code, and modifying the software for various computer operating systems. Another component of model development that requires a great deal of time and effort is the distribution and maintenance of model software. Consider the example of the US Geological Survey’s (USGS) Modular Modeling System (MMS). MMS allows a user to build a hydrologic model by selecting a set of modules that simulate a number of hydrologic processes. MMS is currently being used on various computer systems (e.g. Windows, Solaris, Linux, HP-UX, and AIX). Because each of these operating systems is slightly different, several versions of the software have been developed and maintained. When updates occur, they need to be added and tested for each version of the model. This process is time consuming. MMS is distributed via the internet from a web page. Users download MMS from the web page and then go through the task of installing the model on their system and then running it. Because so many different computer systems are used, the developers spend a considerable amount of time dealing with software bugs and trying to update various versions of the software. Each time the software is loaded onto a new system there are new problems to deal with, none of which have to do with the physics of the model; all are related to differences in computer operating systems. These problems are time consuming and take scientists away from further development of the physics included in the models. To overcome these problems, a method is needed whereby model developers can distribute an executable version of a model that will operate on all computer systems. The advent of the Internet and Java programming language makes this type of model distribution possible. This method of model distribution allows the delivery of (1) executable programs; (2) model documentation and (3) a robust GUI for model operation, all in a single Java archive file. Additionally, there is the issue of security related to the distribution of a model from the internet. For a model to be useful to a user, the user must be able to both input their own data files to a model and write output to his/her own computer. Sitraka Software (2001) proposes several guidelines for choosing an effective deployment strategy. Based on the anticipated end user and the nature of the application, Java Web Start (JWS) provides a way to address the security issues. JWS is a platform independent way to launch a wide variety of Java applications from a computer desktop or a web browser. The following sections describe the procedures necessary to implement and distribute a model with this method.