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runtime monitoring for next generation java ME platform

COMPUTERS & SECURITY 2010年第1期29卷 74-87页

作者： Costa, Gabriele Martinelli, Fabio Mori, Paolo Schaefer, Christian Walter, Thomas DOCOMO Euro Labs D-80687 Munich Germany CNR Inst Informat & Telemat I-56100 Pisa Italy

Many modern mobile devices, such as mobile phones or Personal digital assistants (PDAs), are able to run java applications, such as games, Internet browsers, chat tools and so on. These applications perform some operations on the mobile device, that are critical from the security point of view, such as connecting to the Internet, sending and receiving SMS messages, connecting to other devices through the Bluetooth interface, browsing the user's contact list, and so on. Hence, an adequate security support is required to protect the device from malicious applications. This paper proposes an enhanced security support for next generation java Micro Edition platform. This support performs a runtime monitoring of the operations performed by the java applications, and enforces a security policy that defines which operations applications are allowed to perform. Two possible design approaches for the security support are presented and compared. (C) 2009 Elsevier Ltd. All rights reserved.

关键词： java java runtime environment runtime monitoring Security policy Program in-lining Performance

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JCoDA: a tool for detecting evolutionary selection

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BMC BIOINFORMATICS 2010年第1期11卷 1-9页

作者： Steinway, Steven N. Dannenfelser, Ruth Laucius, Christopher D. Hayes, James E. Nayak, Sudhir Coll New Jersey Dept Biol Ewing NJ 08628 USA Weill Cornell Grad Sch Med Sci New York NY 10065 USA

Background: The incorporation of annotated sequence information from multiple related species in commonly used databases (Ensembl, Flybase, Saccharomyces Genome Database, Wormbase, etc.) has increased dramatically over the last few years. This influx of information has provided a considerable amount of raw material for evaluation of evolutionary relationships. To aid in the process, we have developed JCoDA (java Codon Delimited Alignment) as a simple-to-use visualization tool for the detection of site specific and regional positive/negative evolutionary selection amongst homologous coding sequences. Results: JCoDA accepts user-inputted unaligned or pre-aligned coding sequences, performs a codon-delimited alignment using ClustalW, and determines the dN/dS calculations using PAML (Phylogenetic Analysis Using Maximum Likelihood, yn00 and codeml) in order to identify regions and sites under evolutionary selection. The JCoDA package includes a graphical interface for Phylip (Phylogeny Inference Package) to generate phylogenetic trees, manages formatting of all required file types, and streamlines passage of information between underlying programs. The raw data are output to user configurable graphs with sliding window options for straightforward visualization of pairwise or gene family comparisons. Additionally, codon-delimited alignments are output in a variety of common formats and all dN/dS calculations can be output in comma-separated value (CSV) format for downstream analysis. To illustrate the types of analyses that are facilitated by JCoDA, we have taken advantage of the well studied sex determination pathway in nematodes as well as the extensive sequence information available to identify genes under positive selection, examples of regional positive selection, and differences in selection based on the role of genes in the sex determination pathway. Conclusions: JCoDA is a configurable, open source, user-friendly visualization tool for performing evolutionary analy

关键词： Evolutionary Selection Slide Window Analysis Phylogeny Inference Package java runtime environment Pairwise Calculation

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Have java's Security Issues Gotten out of Hand?

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COMPUTER 2012年第12期45卷 18-21页

作者： Garber, Lee

In the past year, security experts have found many vulnerabilities, some critical, in java. This represents a serious trend because java is so widely used.

关键词： Security Of Data java Security Experts java Security Issues Exploit Toolkit Security java java runtime environment Browsers java Virtual Machine

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JSME: a free molecule editor in javaScript

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JOURNAL OF CHEMINFORMATICS 2013年第1期5卷 1-6页

作者： Bienfait, Bruno Ertl, Peter Mol Networks GmbH D-91052 Erlangen Germany Novartis Inst BioMed Res CH-4056 Basel Switzerland

Background: A molecule editor, i.e. a program facilitating graphical input and interactive editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. Today, when a web browser has become the universal scientific user interface, a tool to edit molecules directly within the web browser is essential. One of the most popular tools for molecular structure input on the web is the JME applet. Since its release nearly 15 years ago, however the web environment has changed and java applets are facing increasing implementation hurdles due to their maintenance and support requirements, as well as security issues. This prompted us to update the JME editor and port it to a modern Internet programming language - javaScript. Summary: The actual molecule editing java code of the JME editor was translated into javaScript with help of the Google Web Toolkit compiler and a custom library that emulates a subset of the GUI features of the java runtime environment. In this process, the editor was enhanced by additional functionalities including a substituent menu, copy/paste, drag and drop and undo/redo capabilities and an integrated help. In addition to desktop computers, the editor supports molecule editing on touch devices, including iPhone, iPad and Android phones and tablets. In analogy to JME the new editor is named JSME. This new molecule editor is compact, easy to use and easy to incorporate into web pages. Conclusions: A free molecule editor written in javaScript was developed and is released under the terms of permissive BSD license. The editor is compatible with JME, has practically the same user interface as well as the web application programming interface. The JSME editor is available for download from the project web page http://***/jsme/

关键词： java Code Scalar Vector Graphic java runtime environment Rich Internet Application Input Tool

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Using MATLAB software with Tomcat server and java platform for remote image analysis in pathology

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DIAGNOSTIC PATHOLOGY 2011年第1-Sup期6卷 S18-S18页

作者： Markiewicz, Tomasz Warsaw Univ Technol Inst Theory Elect Engn Measurement & Informat Sys PL-00662 Warsaw Poland Mil Inst Med Dept Pathol PL-04141 Warsaw Poland

Background: The Matlab software is a one of the most advanced development tool for application in engineering practice. From our point of view the most important is the image processing toolbox, offering many built-in functions, including mathematical morphology, and implementation of a many artificial neural networks as AI. It is very popular platform for creation of the specialized program for image analysis, also in pathology. Based on the latest version of Matlab Builder java toolbox, it is possible to create the software, serving as a remote system for image analysis in pathology via internet communication. The internet platform can be realized based on java Servlet Pages with Tomcat server as servlet container. Methods: In presented software implementation we propose remote image analysis realized by Matlab algorithms. These algorithms can be compiled to executable jar file with the help of Matlab Builder java toolbox. The Matlab function must be declared with the set of input data, output structure with numerical results and Matlab web figure. Any function prepared in that manner can be used as a java function in java Servlet Pages (JSP). The graphical user interface providing the input data and displaying the results (also in graphical form) must be implemented in JSP. Additionally the data storage to database can be implemented within algorithm written in Matlab with the help of Matlab Database Toolbox directly with the image processing. The complete JSP page can be run by Tomcat server. Results: The proposed tool for remote image analysis was tested on the Computerized Analysis of Medical Images (CAMI) software developed by author. The user provides image and case information (diagnosis, staining, image parameter etc.). When analysis is initialized, input data with image are sent to servlet on Tomcat. When analysis is done, client obtains the graphical results as an image with marked recognized cells and also the quantitative output. Additionally, the resu

关键词： Remote User User Session Image Processing Toolbox Internet Platform java runtime environment

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JRed: Program Customization and Bloatware Mitigation Based on Static Analysis 40

JRed: Program Customization and Bloatware Mitigation Based o...

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40th Annual IEEE Computer Software and Applications Conference Symposium (COMPSAC) / Symposium on Software Engineering Technology and Applications (SETA)

作者： Jiang, Yufei Wu, Dinghao Liu, Peng Penn State Univ University Pk PA 16802 USA

ISBN: (纸本)9781467388450

Modern software engineering practice increasingly brings redundant code into software products, which has caused a phenomenon called bloatware, leading to software system maintenance, performance and reliability issues as well as security problems. With the rapid advances of smart devices and a more connected world, it is never more important to trim bloatware to improve the leanness, agility, reliability, performance, and security of the interconnected software and network systems. Previous methods have limited scopes and are usually not fully automated. In this paper, we propose a new static-analysis-enabled approach to trimming unused code from both java applications and java runtime environment (JRE) automatically. We have built a tool called JRed on top of the Soot framework. We have conducted a fairly comprehensive evaluation of JRed based on a set of criteria: code size, code complexity, memory footprint, execution and garbage collection time, and security. Our experimental results show that, java application size can be reduced by 44.5% on average and the JRE code can be reduced by more than 82.5% on average. The code complexity is significantly reduced according to a set of well-known metrics. Furthermore, we report that by trimming redundant code, 48.6% of the known security vulnerabilities in the java runtime environment JRE 6 update 45 has been removed.

关键词： Bloatware java runtime environment Program Customization Software Analysis Static Analysis

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InGeno - an integrated genome and ortholog viewer for improved genome to genome comparisons

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BMC BIOINFORMATICS 2006年第1期7卷 461-461页

作者： Liang, Chunguang Dandekar, Thomas Univ Wurzburg Bioctr Dept Bioinformat D-97074 Wurzburg Germany European Mol Biol Lab D-69012 Heidelberg Germany

Background: Systematic genome comparisons are an important tool to reveal gene functions, pathogenic features, metabolic pathways and genome evolution in the era of post-genomics. Furthermore, such comparisons provide important clues for vaccines and drug development. Existing genome comparison software often lacks accurate information on orthologs, the function of similar genes identified and genome-wide reports and lists on specific functions. All these features and further analyses are provided here in the context of a modular software tool "inGeno" written in java with Biojava subroutines. Results: InGeno provides a user-friendly interactive visualization platform for sequence comparisons (comprehensive reciprocal protein-protein comparisons) between complete genome sequences and all associated annotations and features. The comparison data can be acquired from several different sequence analysis programs in flexible formats. Automatic dot-plot analysis includes output reduction, filtering, ortholog testing and linear regression, followed by smart clustering (local collinear blocks;LCBs) to reveal similar genome regions. Further, the system provides genome alignment and visualization editor, collinear relationships and strain-specific islands. Specific annotations and functions are parsed, recognized, clustered, logically concatenated and visualized and summarized in reports. Conclusion: As shown in this study, inGeno can be applied to study and compare in particular prokaryotic genomes against each other (gram positive and negative as well as close and more distantly related species) and has been proven to be sensitive and accurate. This modular software is user-friendly and easily accommodates new routines to meet specific user-defined requirements.

关键词： Hemolytic Uremic Syndrome Annotation File Strain MG1655 Genome Viewer java runtime environment

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Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development

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BMC BIOINFORMATICS 2010年第1期11卷 478-478页

作者： Terrat, Sebastien Peyretaillade, Eric Goncalves, Olivier Dugat-Bony, Eric Gravelat, Fabrice Mone, Anne Biderre-Petit, Corinne Boucher, Delphine Troquet, Julien Peyret, Pierre Univ Clermont Ferrand 2 Univ Auvergne Lab Microorganismes Genome & Environm F-63000 Clermont Ferrand France CNRS Lab Microorganismes Genome & Environm F-63173 Aubiere France Univ Clermont Ferrand 2 Univ Blaise Pascal Lab Microorganismes Genome & Environm F-63000 Clermont Ferrand France Biopole Clermont Limagne Biobasic Environm F-63360 St Beauzire France

Background: Microorganisms display vast diversity, and each one has its own set of genes, cell components and metabolic reactions. To assess their huge unexploited metabolic potential in different ecosystems, we need high throughput tools, such as functional microarrays, that allow the simultaneous analysis of thousands of genes. However, most classical functional microarrays use specific probes that monitor only known sequences, and so fail to cover the full microbial gene diversity present in complex environments. We have thus developed an algorithm, implemented in the user-friendly program Metabolic Design, to design efficient explorative probes. Results: First we have validated our approach by studying eight enzymes involved in the degradation of polycyclic aromatic hydrocarbons from the model strain Sphingomonas paucimobilis sp. EPA505 using a designed microarray of 8,048 probes. As expected, microarray assays identified the targeted set of genes induced during biodegradation kinetics experiments with various pollutants. We have then confirmed the identity of these new genes by sequencing, and corroborated the quantitative discrimination of our microarray by quantitative real-time PCR. Finally, we have assessed metabolic capacities of microbial communities in soil contaminated with aromatic hydrocarbons. Results show that our probe design (sensitivity and explorative quality) can be used to study a complex environment efficiently. Conclusions: We successfully use our microarray to detect gene expression encoding enzymes involved in polycyclic aromatic hydrocarbon degradation for the model strain. In addition, DNA microarray experiments performed on soil polluted by organic pollutants without prior sequence assumptions demonstrate high specificity and sensitivity for gene detection. Metabolic Design is thus a powerful, efficient tool that can be used to design explorative probes and monitor metabolic pathways in complex environments, and it may also be used to s

关键词： Polycyclic Aromatic Hydrocarbon Probe Design Roche NimbleGen java runtime environment TrEMBL Database

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GeneViTo: Visualizing gene-product functional and structural features in genomic datasets

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BMC BIOINFORMATICS 2003年第1期4卷 53-53页

作者： Vernikos, GS Gkogkas, CG Promponas, VJ Hamodrakas, SJ Univ Athens Fac Biol Dept Cell Biol & Biophys Athens 15701 Greece

Background: The availability of increasing amounts of sequence data from completely sequenced genomes boosts the development of new computational methods for automated genome annotation and comparative genomics. Therefore, there is a need for tools that facilitate the visualization of raw data and results produced by bioinformatics analysis, providing new means for interactive genome exploration. Visual inspection can be used as a basis to assess the quality of various analysis algorithms and to aid in-depth genomic studies. Results: GeneViTo is a java-based computer application that serves as a workbench for genome-wide analysis through visual interaction. The application deals with various experimental information concerning both DNA and protein sequences (derived from public sequence databases or proprietary data sources) and meta-data obtained by various prediction algorithms, classification schemes or user-defined features. Interaction with a Graphical User Interface (GUI) allows easy extraction of genomic and proteomic data referring to the sequence itself, sequence features, or general structural and functional features. Emphasis is laid on the potential comparison between annotation and prediction data in order to offer a supplement to the provided information, especially in cases of "poor" annotation, or an evaluation of available predictions. Moreover, desired information can be output in high quality JPEG image files for further elaboration and scientific use. A compilation of properly formatted GeneViTo input data for demonstration is available to interested readers for two completely sequenced prokaryotes, Chlamydia trachomatis and Methanococcus jannaschii. Conclusions: GeneViTo offers an inspectional view of genomic functional elements, concerning data stemming both from database annotation and analysis tools for an overall analysis of existing genomes. The application is compatible with Linux or Windows ME-2000-XP operating systems, provided that the

关键词： Transmembrane Segment Genomic Element java Programming Language java runtime environment Graphic Panel

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LabKey Server NAb: A tool for analyzing, visualizing and sharing results from neutralizing antibody assays

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BMC IMMUNOLOGY 2011年第1期12卷 33-33页

作者： Piehler, Britt Nelson, Elizabeth K. Eckels, Josh Ramsay, Sarah Lum, Karl Wood, Blake Greene, Kelli M. Gao, Hongmei Seaman, Michael S. Montefiori, David C. Igra, Mark LabKey Software Seattle WA 98102 USA Fred Hutchinson Canc Res Ctr Stat Ctr HIV AIDS Res & Prevent SCHARP Seattle WA 98109 USA Duke Univ Med Ctr Dept Surg Durham NC 27710 USA Harvard Univ Sch Med Beth Israel Deaconess Med Ctr Div Viral Pathogenesis Boston MA 02115 USA

Background: Multiple types of assays allow sensitive detection of virus-specific neutralizing antibodies. For example, the extent of antibody neutralization of HIV-1, SIV and SHIV can be measured in the TZM-bl cell line through the degree of luciferase reporter gene expression after infection. In the past, neutralization curves and titers for this standard assay have been calculated using an Excel macro. Updating all instances of such a macro with new techniques can be unwieldy and introduce non-uniformity across multi-lab teams. Using Excel also poses challenges in centrally storing, sharing and associating raw data files and results. Results: We present LabKey Server's NAb tool for organizing, analyzing and securely sharing data, files and results for neutralizing antibody (NAb) assays, including the luciferase-based TZM-bl NAb assay. The customizable tool supports high-throughput experiments and includes a graphical plate template designer, allowing researchers to quickly adapt calculations to new plate layouts. The tool calculates the percent neutralization for each serum dilution based on luminescence measurements, fits a range of neutralization curves to titration results and uses these curves to estimate the neutralizing antibody titers for benchmark dilutions. Results, curve visualizations and raw data files are stored in a database and shared through a secure, web-based interface. NAb results can be integrated with other data sources based on sample identifiers. It is simple to make results public after publication by updating folder security settings. Conclusions: Standardized tools for analyzing, archiving and sharing assay results can improve the reproducibility, comparability and reliability of results obtained across many labs. LabKey Server and its NAb tool are freely available as open source software at http://*** under the Apache 2.0 license. Many members of the HIV research community can also access the LabKey Server NAb tool without ins

关键词： Neutralization Curve Neutralize Antibody Titer Excel Macro java runtime environment Neutralize Antibody Assay

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