Java Web Start Research Articles

Robust Cross-Validation of Linear Regression QSAR Models

A quantitative structure-activity relationship (QSAR) model is typically developed to predict the biochemical activity of untested compounds from the compounds' molecular structures. "The gold standard" of model validation is the blindfold prediction when the model's predictive power is assessed from how well the model predicts the activity values of compounds that were not considered in any way during the model development/calibration. However, during the development of a QSAR model, it is necessary to obtain some indication of the model's predictive power. This is often done by some form of cross-validation (CV). In this study, the concepts of the predictive power and fitting ability of a multiple linear regression (MLR) QSAR model were examined in the CV context allowing for the presence of outliers. Commonly used predictive power and fitting ability statistics were assessed via Monte Carlo cross-validation when applied to percent human intestinal absorption, blood-brain partition coefficient, and toxicity values of saxitoxin QSAR data sets, as well as three known benchmark data sets with known outlier contamination. It was found that (1) a robust version of MLR should always be preferred over the ordinary-least-squares MLR, regardless of the degree of outlier contamination and that (2) the model's predictive power should only be assessed via robust statistics. The Matlab and java source code used in this study is freely available from the QSAR-BENCH section of www.dmitrykonovalov.org for academic use. The Web site also contains the java-based QSAR-BENCH program, which could be run online via java's Web Start technology (supporting Windows, Mac OSX, Linux/Unix) to reproduce most of the reported results or apply the reported procedures to other data sets.

Integrating and annotating the interactome using the MiMI plugin for cytoscape

The MiMI molecular interaction repository integrates data from multiple sources, resolves interactions to standard gene names and symbols, links to annotation data from GO, MeSH and PubMed and normalizes the descriptions of interaction type. Here, we describe a Cytoscape plugin that retrieves interaction and annotation data from MiMI and links out to multiple data sources and tools. Community annotation of the interactome is supported. MiMI plugin v3.0.1 can be installed from within Cytoscape 2.6 using the Cytoscape plugin manager in 'Network and Attribute I/0' category. The plugin is also preloaded when Cytoscape is launched using Java WebStart at http://mimi.ncibi.org by querying a gene and clicking 'View in MiMI Plugin for Cytoscape' link.

I-SEGOPubmed: a web interface for semantic enabled browsing of PubMed using Gene Ontology

The rapid progress in bioinformatics and functional genomics lead to a vast amount of scientific literature. PubMed is one of the leading repositories and has approximately 20 million abstracts. Browsing such a huge repository to find relevant information as well as providing e-learning service requires new generation of interfaces. Methods such as GOPubmed are using keyword-based techniques. Keyword-based search methods often yield results that are not meaningful to the query. This problem can be partially addressed using a semantic enabled interface for browsing and information retrieval. A web interface called i-SEGOPubmed is being developed in CVPIA lab at the University of Memphis. i-SEGOPubmed enables semantically meaningful browsing of large volume of semi-structured data such as Pubmed using Gene Ontology. i-SEGOPubmed employs a client-server computing model. The SEGOPubmed engine [1] is used to process queries and web interface is using the Java Web Start, which uses Java Network Launching Protocol (JNLP) for downloading the application from the server to the client. Once the application is downloaded, Java Web Start initializes the application to check for the local resources. i-SEGOPubmed requires JRE (Java Runtime Environment) for its execution. It uses the Java Sockets to establish a data communication between the interface running on the client machine and the query processing done on the server machine. The server machine has a dedicated Server Socket listening to client requests. Once the server receives a request, it initializes a full duplex communication channel between the server and the client machine. Using this data channel, the interface sends the query to the server for further processing. Figure ​Figure11 shows the system architecture and the information flow of the proposed i-SEGOPubmed. Figure 1 Schematic diagram and information flow of the proposed i-SEGOPubmed.

I Resign! Resigning Jar Files with Initium.

This paper describes how to resign Jar files. Jar files (Java archives) are used by technologies (like Java Web Start) to deploy applications that are run with increased privileges. The Jar files are signed with certificates that generally expire after a year. The annual resigning of the files is therefore an event that occurs after the signer has forgotten how resigning is done. Manual resigning of Jar files is a tedious and error-prone task. All the more so when there are many of them. This article shows how to automate the task. Considering that I have over 250 Jar files that have to be resigned each year, a manual task is not an option. The methodology for resigning a Jar file cannot include signing the Jar file twice. Jar files that are signed twice create an error during verification. Unsigning a Jar file is not a straightforward task. Thus, our approach is to expand the Jar file, remove the expired certificate and then repack and resign the Jar file with the new certificate. We also show how to obtain a new certificate, from a free certificate provider. This paper addresses a sub-problem of the Initium project, a joint, on-going project between the Fairfield University and the DocJava, Inc. Initium is a Latin word that means: “at the start”.

SU-FF-T-328: Open Source, ImageJ Based, Web Accessible Tool for Treatment Plan Evaluation

Purpose: To develop a cross platform, open source, web accessible, Java based treatment plan visualization and evaluation software using the ImageJ toolkit. Method and Materials: The application can be launched from any web browser with Java Web Start. The treatment plan and structures may be imported in PinnacleTM or in DICOM format. For Pinnacle format, the patients and plans may be selected from the clinical database. This system supports the standard viewing of isodose lines, regions of interest and dose volume histograms generated in real time. To assist in plan evaluation, the software can automatically compare the DVHs to planning guidelines to ensure both target coverage and normal tissue tolerances. The constraints can be volumetric or absolute. Conclusion: We have written an open source software tool that allows one to review a treatment plan remotely from any web browser. To facilitate research, dose volumes can be imported in binary format and dose volumes and DVHs can be exported as binary or ASCII. Future plans include a fast dose calculation engine for both photon and proton treatments and better support of batch processing through macros. Conflict of Interest: SRA with Philips Medical Systems.

The Saverbeans Screensaver and Initium RJS System Integration: Part 5 By.

This paper describes the integration of our Java-based screensaver framework with our Initium Remote Job Submission (IRJS) grid computing middleware. Initium RJS is a Java Web Start (JAWS) based grid-computing technology. This is part 5 of a 5 part series. In parts 1, 2, and 3, we described screensavers for MS Windows, Xwindows, and the Macintosh. Part 4, describe automatic deployment of the screensavers into the MS Windows and XWindows systems. This paper introduces the use of our grid system. We provide an example that shows how to take a von Neumann style program, break it up, and deploy it to our grid system.

BioNetBuilder: automatic integration of biological networks

BioNetBuilder is an open-source client-server Cytoscape plugin that offers a user-friendly interface to create biological networks integrated from several databases. Users can create networks for approximately 1500 organisms, including common model organisms and human. Currently supported databases include: DIP, BIND, Prolinks, KEGG, HPRD, The BioGrid and GO, among others. The BioNetBuilder plugin client is available as a Java Webstart, providing a platform-independent network interface to these public databases. http://err.bio.nyu.edu/cytoscape/bionetbuilder/

Developments in CORG: a gene-centric comparative genomics resource

The CORG resource (Comparative Regulatory Genomics, ) provides extensive cross-species comparisons of promoter regions in particular and whole gene loci in general. Pairwise as well as multiple alignments of 10 vertebrate species form the key component of CORG. We implemented a rapid alignment approach based on weight matrix motif anchors to ensure efficient computation and biologically informative alignments. All CORG workbench components have been enhanced towards more flexibility and interactivity. Reference sequence based data presentation and analysis was put into the well-known and modular Generic Genome Browser framework. Herein, various plugins facilitate online data analysis and integration with static conservation data. Main emphasis was put on the design of a new JAVA WebStart application for comparative data display. Flexible data import and export options for standard formats complete the provided services.

ET viewer: an application for predicting and visualizing functional sites in protein structures

The Evolutionary Trace Viewer (ETV) provides a one-stop environment in which to run, visualize and interpret Evolutionary Trace (ET) predictions of functional sites in protein structures. ETV is implemented using Java to run across different operating systems using Java Web Start technology. The ETV is available for download from our website at http://mammoth.bcm.tmc.edu/traceview/index.html. This webpage also links to sample trace results and a user manual that describes ET Viewer functions in detail.

Exploration of biological network centralities with CentiBiN.

BackgroundThe elucidation of whole-cell regulatory, metabolic, interaction and other biological networks generates the need for a meaningful ranking of network elements. Centrality analysis ranks network elements according to their importance within the network structure and different centrality measures focus on different importance concepts. Central elements of biological networks have been found to be, for example, essential for viability.ResultsCentiBiN (Centralities in Biological Networks) is a tool for the computation and exploration of centralities in biological networks such as protein-protein interaction networks. It computes 17 different centralities for directed or undirected networks, ranging from local measures, that is, measures that only consider the direct neighbourhood of a network element, to global measures. CentiBiN supports the exploration of the centrality distribution by visualising central elements within the network and provides several layout mechanisms for the automatic generation of graphical representations of a network. It supports different input formats, especially for biological networks, and the export of the computed centralities to other tools.ConclusionCentiBiN helps systems biology researchers to identify crucial elements of biological networks. CentiBiN including a user guide and example data sets is available free of charge at . CentiBiN is available in two different versions: a Java Web Start application and an installable Windows application.

The Gaggle: An open-source software system for integrating bioinformatics software and data sources

BackgroundSystems biologists work with many kinds of data, from many different sources, using a variety of software tools. Each of these tools typically excels at one type of analysis, such as of microarrays, of metabolic networks and of predicted protein structure. A crucial challenge is to combine the capabilities of these (and other forthcoming) data resources and tools to create a data exploration and analysis environment that does justice to the variety and complexity of systems biology data sets. A solution to this problem should recognize that data types, formats and software in this high throughput age of biology are constantly changing.ResultsIn this paper we describe the Gaggle -a simple, open-source Java software environment that helps to solve the problem of software and database integration. Guided by the classic software engineering strategy of separation of concerns and a policy of semantic flexibility, it integrates existing popular programs and web resources into a user-friendly, easily-extended environment.We demonstrate that four simple data types (names, matrices, networks, and associative arrays) are sufficient to bring together diverse databases and software. We highlight some capabilities of the Gaggle with an exploration of Helicobacter pylori pathogenesis genes, in which we identify a putative ricin-like protein -a discovery made possible by simultaneous data exploration using a wide range of publicly available data and a variety of popular bioinformatics software tools.ConclusionWe have integrated diverse databases (for example, KEGG, BioCyc, String) and software (Cytoscape, DataMatrixViewer, R statistical environment, and TIGR Microarray Expression Viewer). Through this loose coupling of diverse software and databases the Gaggle enables simultaneous exploration of experimental data (mRNA and protein abundance, protein-protein and protein-DNA interactions), functional associations (operon, chromosomal proximity, phylogenetic pattern), metabolic pathways (KEGG) and Pubmed abstracts (STRING web resource), creating an exploratory environment useful to 'web browser and spreadsheet biologists', to statistically savvy computational biologists, and those in between. The Gaggle uses Java RMI and Java Web Start technologies and can be found at .

VANTED: a system for advanced data analysis and visualization in the context of biological networks.

BackgroundRecent advances with high-throughput methods in life-science research have increased the need for automatized data analysis and visual exploration techniques. Sophisticated bioinformatics tools are essential to deduct biologically meaningful interpretations from the large amount of experimental data, and help to understand biological processes.ResultsWe present VANTED, a tool for the visualization and analysis of networks with related experimental data. Data from large-scale biochemical experiments is uploaded into the software via a Microsoft Excel-based form. Then it can be mapped on a network that is either drawn with the tool itself, downloaded from the KEGG Pathway database, or imported using standard network exchange formats. Transcript, enzyme, and metabolite data can be presented in the context of their underlying networks, e. g. metabolic pathways or classification hierarchies. Visualization and navigation methods support the visual exploration of the data-enriched networks. Statistical methods allow analysis and comparison of multiple data sets such as different developmental stages or genetically different lines. Correlation networks can be automatically generated from the data and substances can be clustered according to similar behavior over time. As examples, metabolite profiling and enzyme activity data sets have been visualized in different metabolic maps, correlation networks have been generated and similar time patterns detected. Some relationships between different metabolites were discovered which are in close accordance with the literature.ConclusionVANTED greatly helps researchers in the analysis and interpretation of biochemical data, and thus is a useful tool for modern biological research. VANTED as a Java Web Start Application including a user guide and example data sets is available free of charge at .

Examples of Hamiltonian Stationary Lagrangian Tori in $$\mathbb{C}P^2$$

In this paper we will give a new family of Hamiltonian stationary Lagrangian tori in the complex projective plane \(\mathbb{C}P^2\) with S1-symmetry. We also provide a Java Web Start application to visualize such kind of tori through suitable projections.

PathSys: integrating molecular interaction graphs for systems biology.

BackgroundThe goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately.ResultsHere we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae) and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping.ConclusionResults from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at .

The Initium RJS ScreenSaver: Part 2, UNIX.

This paper describes a Java-based screensaver technology for the Initium Remote Job Submission (RJS) system running on UNIX XWindows. Initium RJS is a Java Web Start (JAWS) technology that enables Java-based grid computing. The Initium RJS system uses screensavers to enable CPU scavenging. A screensaver is a program that activates during a period of user-computer quiescence. Detection of this quiet time enables the use of otherwise wasted CPU cycles. When the period of user-computer quiescence ceases, the screensaver terminates any currently running compute jobs, releasing the computer back for general use. Such a program constitutes a first step toward utilizing otherwise idle compute resources in a grid computing system. We are motivated to study screen-savers because they represent a minimally invasive technology for volunteering CPU services. Typically, computers are used between 40 and 60 hours out of a 168-hour week. This represents approximately 35% utilization. Our theory is that a screen-saver based cycle scavenging will improve this number dramatically. We are motivated to provide a Java-based environment in order to capitalize on Java’s inherent heterogeneity. This makes a larger universe of grid-compute servers available, without requiring changes to the computational program. This paper is part 2 of a 5 part series on Java-based screensavers. Part 1 addressed the creation of screensavers on MS Windows platform systems. Parts 2 and 3 address the Linux and Macintosh-based screensavers. Part 4 addresses the automatic deployment and installation of the screensavers. Part 5 speaks to the problem of screensaver integration with the Initium RJS system. Initium RJS is a joint project between DocJava, Inc. and Fairfield University. The goal of the Initium RJS system is to improve the accessibility of grid computing to Java developers. THE INITIUM RJS SCREENSAVER: PART 2, UNIX 8 JOURNAL OF OBJECT TECHNOLOGY VOL. 5, NO. 6

Remote Job Submission Security.

This paper presents the middleware needed to deploy jobs to non-geographically colocated clusters with decentralized look-up severs. We have named our framework the Initium Remote Job Submission (RJS) system. Initium generates a jar file that is signed by a trusted certificate authority CA [Lyon]. The jar is run by a Computation Server (CS), (a remote computer running the Initium Computer Server Software). A Web Server (WS) has a Java Network Launch Protocol (JNLP) file that makes reference to a signed jar file on a web server. The signed jar file contains a job for the computation server. This jar file is called the computation jar. The computation jar is executed on the CS and the answer is sent back to the server using RMI over SSL (RMI/SSL). A look-up server (LUS) is used to register computation servers as they come on line. When a computation server is started, it registers with a LUS. The LUS then updates its list of computation servers, in the cluster. Look-up servers can be started using Java Web Start. They can be contacted with multicast protocols. 1 THE DISTRIBUTED COMPUTING SECURITY PROBLEM We seek to create a framework that exploits idle CPU’s on the network. We are subject to the constraint that our code must be downloaded over the Internet (that is, a normally insecure channel). Further that the configuration should be automatic. In addition, the code should be verified as originating from a trusted source. Finally, computed answers should be returned over a secure link to a Web Server (WS). The web server is able to hold “jobs” for deployment, and hold computed answers. 1.1 Approach Our approach for authentication and encryption is to use Java Secure Socket Extension (JSSE) to implement a Java technology version of Secure Socked Layer (SSL) protocols. This is integrated into the Java 2 SDK, Standard Edition v 1.4 [Sun 2004]. Our goal is to securely download a list of jobs to the LUS, and securely upload the answer jar to the WS. All LUS – CS commutation is on the LAN behind the firewall. Most grid systems use SSL for authentication, but by default do not establish encrypted communication in a secure manner [Globus 2]. Our approach requires that we encrypt all WS-LUS communication via a session key. In order to establish the session key, WS and LUS must agree on shared key, without sending any secret data in the clear. To do this, REMOTE JOB SUBMISSION SECURITY 14 JOURNAL OF OBJECT TECHNOLOGY VOL. 5 NO. 1 we use the RSA key exchange algorithm as a standard method for SSL key exchange. In RSA key exchange, the WS encrypts a number of random bytes with the LUS's public RSA key and they both use this shared secret to create the session keys. In order to guarantee the integrity of the messages, we use the Message-Digest 5 (MD5) algorithm. The MD5 algorithm is intended for digital signature applications, where a large file must be compressed in a secure manner before being encrypted with a private (secret) key under a public-key cryptosystem such as RSA [Rivest]. The CS receives a URL to a jnlp file and downloads the Java Web Start “job” in order to compute it. The owner of the CS must accept the job owner certificate. Once the certificate is trusted, all jobs signed by it will be executed automatically. RSA algorithms ensure secure communication and MD5 message digest ensures that no one has altered the data in transit. An alternative approach to security might use the Kerberos network authentication protocol [Kerberos] or SSH protocol [OpenSSH]. However, such tools are vulnerable, as the attackers can gain access to user's password as it is being typed [Basney]. 1.2 Motivation Industrial computers are typically idle 14 or more hours per workday. If we assume that they are also idle on the weekend then they are idle 118 hours out of every 168 hours during the week (i.e., 70% of the time). We are motivated to address security issues in grid computing because an insecure network could be exploited by an advisory in order to gain access to data, destroy data, and steal logins or services (email, CPU cycles). Users will not agree to donate their CPU time without an assurance of security. A grid-based virus can spread faster than a normal virus, since it uses push technology to deploy itself and runs on-demand. Grids need to be protected not only because they are high-value assets representing lots of hardware and software, but also because they often serve a strategic function that's central to success [Myer].

The Initium RJS Screensaver: Part 4, Automatic Deployment.

The Intium RJS System makes use of screensavers to perform CPU scavenging for grid computing. This article shows how to automate the installation of the IRJS screensaver. The manual installation of the IRJS screensaver, presented in parts 1 and 2 of this series, has been automated to ease installation. A Java Web Start application has been created to complete the installation of the screensaver for Windows and Unix/Linux platform. This application performs an operating system identification and proceeds to download, install, and configure the screensaver files. The installation of the screensaver is a function of the OS, due to differences in screensavers support. Our three previous papers showed how to create screensavers in Java for Windows, Linux and Mac operating systems.

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research

We present here Blast2GO (B2G), a research tool designed with the main purpose of enabling Gene Ontology (GO) based data mining on sequence data for which no GO annotation is yet available. B2G joints in one application GO annotation based on similarity searches with statistical analysis and highlighted visualization on directed acyclic graphs. This tool offers a suitable platform for functional genomics research in non-model species. B2G is an intuitive and interactive desktop application that allows monitoring and comprehension of the whole annotation and analysis process. Blast2GO is freely available via Java Web Start at http://www.blast2go.de. http://www.blast2go.de -> Evaluation.

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.

MAVisto: a tool for the exploration of network motifs

MAVisto is a tool for the exploration of motifs in biological networks. It provides a flexible motif search algorithm and different views for the analysis and visualization of network motifs. These views help to explore interesting motifs: the frequency of motif occurrences can be compared with randomized networks, a list of motifs along with information about structure and number of occurrences depending on the reuse of network elements shows potentially interesting motifs, a motif fingerprint reveals the overall distribution of motifs of a given size and the distribution of a particular motif in the network can be visualized using an advanced layout algorithm. MAVisto is platform independent and available free of charge as a Java webstart application at http://mavisto.ipk-gatersleben.de/ schwoebb@ipk-gatersleben.de Can be found at http://mavisto.ipk-gatersleben.de/