Cross-platform Application Research Articles

A simple Qt based comparison program for ITK and VTK images.

This document describes a project that can compare many images simultaneously in a synchronized manner. Such an application can be used in any ITK/VTK image processing pipelines; the programmer can use it to quickly visualize and compare intermediate results of used filters within the pipeline.The goals of this project are two folds: (i) to be integrated in gdb pretty debuggers (for visual debugging of ITK pipelines), and, (ii) to provide a visual comparison widget for image-to-image plugins (ITK or VTK based filters). This project is part of the Gofigure2 development effort, an open-source, cross-platform application for visualizing, processing and analyzing of multidimensional microscopy data.

Consistency of predictive signature genes and classifiers generated using different microarray platforms

Microarray-based classifiers and associated signature genes generated from various platforms are abundantly reported in the literature; however, the utility of the classifiers and signature genes in cross-platform prediction applications remains largely uncertain. As part of the MicroArray Quality Control Phase II (MAQC-II) project, we show in this study 80–90% cross-platform prediction consistency using a large toxicogenomics data set by illustrating that: (1) the signature genes of a classifier generated from one platform can be directly applied to another platform to develop a predictive classifier; (2) a classifier developed using data generated from one platform can accurately predict samples that were profiled using a different platform. The results suggest the potential utility of using published signature genes in cross-platform applications and the possible adoption of the published classifiers for a variety of applications. The study reveals an opportunity for possible translation of biomarkers identified using microarrays to clinically validated non-array gene expression assays.

SOA-The Backbone of Modern Business

The present study examines about the key features of Service Oriented Architecture (SOA) and its utilization in modern business integration like various processes, employees, information, managers etc. Integration is the biggest challenge which is fulfilled by implementing of SOA in business. It provides more strength to business working as a backbone for various services and connecting the cross-platform application together.

Development and evaluation of QSPECT open-source software for the iterative reconstruction of SPECT images

In this study open-source software (QSPECT) suitable for the iterative reconstruction of single-photon emission computed tomography (SPECT) data is presented. QSPECT implements maximum likelihood expectation maximization and ordered subsets expectation maximization algorithms in a user-friendly graphical interface. The software functionality is described and validation results are presented. Maximum likelihood expectation maximization and ordered subsets expectation maximization algorithms are implemented in C++. The Qt toolkit, a standard C++ framework for developing high-performance cross-platform applications, has been used for the graphical user interface development. QSPECT is tested using original projection data from two clinical SPECT systems: (i) APEX SPX-6/6HR and (ii) Millennium MG. Phantom experiments were carried out to evaluate the quality of reconstructed images in terms of (i) spatial resolution, (ii) sensitivity to activity variations, and (iii) the presence of scatter media. A cardiac phantom was used to simulate a normal and abnormal scenario. Finally, clinical cardiac SPECT images were reconstructed. In all cases, QSPECT results were compared with the clinical systems reconstruction software that uses the standard filtered backprojection algorithm. The reconstructed images show that QSPECT, when compared with standard clinical reconstruction, provides images with higher contrast, reduced background, and better separation of small sources located in small distances. In addition, reconstruction with QSPECT provides more quantitative images, and reduces the background created by scatter media. Finally, the phantom and clinical cardiac images are reconstructed with similar quality. QSPECT is a freely distributed, open-source standalone application that provides real-time, high-quality SPECT images. The software can be further modified to improve reconstruction algorithms, and include more correction techniques, such as, scatter and attenuation correction.

ScripTree: scripting phylogenetic graphics

There is a large amount of tools for interactive display of phylogenetic trees. However, there is a shortage of tools for the automation of tree rendering. Scripting phylogenetic graphics would enable the saving of graphical analyses involving numerous and complex tree handling operations and would allow the automation of repetitive tasks. ScripTree is a tool intended to fill this gap. It is an interpreter to be used in batch mode. Phylogenetic graphics instructions, related to tree rendering as well as tree annotation, are stored in a text file and processed in a sequential way. ScripTree can be used online or downloaded at www.scriptree.org, under the GPL license. ScripTree, written in Tcl/Tk, is a cross-platform application available for Windows and Unix-like systems including OS X. It can be used either as a stand-alone package or included in a bioinformatic pipeline and linked to a HTTP server.

FusionViewer: An Open Source Toolkit for Viewing Multimodality Images

FusionViewer is an open source and platform independent viewer that has been specifically designed for PET/CT image display. The combination of PET and CT images offers complementary functional and anatomical information. The application (FusionViewer) facilitates efficient visualization and analysis of PET/CT studies via different viewing modes (linked cursor display, alpha-blend mode, checkerboard mode and split window mode). FusionViewer is implemented in Java and uses the Java OpenGL (JOGL) library and the Insight Segmentation and Registration Toolkit (ITK) library, which make it both a fast and cross-platform application. Its intuitive graphical user interface makes it easy to be used by physicians, radiologists, and research scientists. Several analysis and display tools are already available (navigator, zoom, pan, screen snapshot, ROI, and line measure tool; alpha-blending, checkerboard display, and split window display). Along with PET/CT, several other modalities where co-registered images are often visualized simultaneously have benefited from the use of this software.

A framework for efficient and rapid development of cross-platform audio applications

In this article, we present CLAM, a C++ software framework, that offers a complete development and research platform for the audio and music domain. It offers an abstract model for audio systems and includes a repository of processing algorithms and data types as well as all the necessary tools for audio and control input/output. The framework offers tools that enable the exploitation of all these features to easily build cross-platform applications or rapid prototypes for media processing algorithms and systems. Furthermore, included ready-to-use applications can be used for tasks such as audio analysis/synthesis, plug-in development, feature extraction or metadata annotation. CLAM represents a step forward over other similar existing environments in the multimedia domain. Nevertheless, it also shares models and constructs with many of those. These commonalities are expressed in the form of a metamodel for multimedia processing systems and a design pattern language.

Parallel Performance Modeling using a Genetic Programming-based Error Correction Procedure

Performance models of high performance computing (HPC) applications are important for several reasons. First, they provide insight to designers of HPC systems on the role of subsystems such as the processor or the network in determining application performance. Second, they allow HPC centers more accurately to target procurements to resource requirements. Third, they can be used to identify application performance bottlenecks and to provide insights about scalability issues. The suitability of a performance model, however, for a particular performance investigation is a function of both the accuracy and the cost of the model. A semi-empirical model previously published by the authors for an astrophysics application was shown to be inaccurate when predicting communication cost for large numbers of processors. It is hypothesized that this deficiency is due to the inability of the model adequately to capture communication contention (threshold effects) as well as other unmodeled components such as noise and I/O contention. In this paper we present a new approach to capture these unknown features to improve the predictive capabilities of the model. This approach uses a systematic model error-correction procedure that uses evolutionary algorithms to find an error correction term to augment the eXisting model. Four variations of this procedure were investigated and all were shown to produce better results than the original model. Successful cross-platform application of this approach showed that it adequately captures machine dependent characteristics. This approach was then successfully demonstrated for a second application, further showing its versatility.

CLAM: A Framework for Audio and Music Application Development

The CLAM (C++ Library for Audio and Music) development framework offers a complete R&D platform for the audio and music domain. Winner of the 2006 ACM Open Source Multimedia Software Competition, CLAM originated in an effort to organize a repository of audio-processing algorithms. Today it includes an abstract model for audio systems, a repository of processing algorithms and data types, and several tools and stand-alone applications. Developers can exploit all these features to build cross-platform applications or rapid prototypes for testing signal- and media-processing algorithms and systems

A Web-Based Java Framework for Cross-Platform Mobile GIS and Remote Sensing Applications

A cross-platform Web-based Java development framework for Mobile Geographic Information Systems (Mobile GIS) and remote sensing (RS) applications is introduced for the notebook computer, Pocket PC, and mobile phone platforms. Using these platforms, Java software technology is examined for its crossplatform utility in the development of various Mobile GIS and map/image display functions. The three case studies developed with Java 2 Standard Edition (J2SE), Java 2 Micro Edition (J2ME), and Mobile Information Device Profile (MIDP) are examined within the context of mobile GIS. Significant challenges in developing cross-platform Mobile GIS applications are also discussed. These obstacles include heterogeneous operating systems, different wireless communications protocols, lowbandwidth network connections, and the general lack of usability.

Creating entertainment applications for cellular phones

Cellular phones offer a whole range of interesting and exciting possibilities for entertainment systems coupled with a very resource-constrained environment. In this article we consider the possibilities currently achievable through the example of a networked sports service. Applications that keep users up-to-date with sports results and playing fantasy team games, based on the results of actual events, are well established on the Internet; they attract millions of subscribers world-wide. As yet, the sports results services on cellular phones, even within countries that offer 3G services, are by and large SMS or WAP-based, and there are no dedicated fantasy team game services for cellular phones. In this article we present a novel application using GPRS that not only keeps users up-to-date, wherever they are, with the events of the English Premier Football League, but also provides the opportunity of playing a real-time fantasy football game as these events transpire. As we are seeing moves by cellular phone manufacturers to adopt standardized operating systems, we compare application development in Symbian, Brew, and J2ME. Although J2ME is not an operating system, it has, up until recently, been the only means of cross-platform application development for cellular phonesThis application not only takes advantage of the "nature" of the cellular network, rather than porting existing services off the Internet, but radically improves currently available services in terms of cost and efficiency. It also highlights the fact that resource constraints on a cellular phone are not a bar to creating compelling content. This technique could be applied to a whole range of sports from Formula 1 to baseball.

VitaPad: visualization tools for the analysis of pathway data

Packages that support the creation of pathway diagrams are limited by their inability to be readily extended to new classes of pathway-related data. VitaPad is a cross-platform application that enables users to create and modify biological pathway diagrams and incorporate microarray data with them. It improves on existing software in the following areas: (i) It can create diagrams dynamically through graph layout algorithms. (ii) It is open-source and uses an open XML format to store data, allowing for easy extension or integration with other tools. (iii) It features a cutting-edge user interface with intuitive controls, high-resolution graphics and fully customizable appearance. http://bioinformatics.med.yale.edu matthew.holford@yale.edu; hongyu.zhao@yale.edu.

Cross platform comparison of multigene predictors of response to neoadjuvant paclitaxel/FAC chemotherapy in breast cancer generated by cDNA arrays and Affymetrix GeneChips

503 Background: Transcriptional profiling is under study as a clinical research tool to classify cancer into clinically relevant sub-groups. Comparison of results across multiple laboratories and platforms is critical for the future development of a useful diagnostic test. Methods: In this study, we compared muligene predictors developed on 2 distinct profiling platforms Affymetrix GeneChip and Millennium cDNA arrays using pre-treatment fine needle aspirates of 33 breast cancer patients. RNA was hybridized from the same samples to both arrays. We independently identified gene expression signatures associated with pathologic complete response (pCR) to neoadjuvant paclitaxel followed by 5-FU, doxorubicin, cyclophosphamide chemotherapy on each platfrom and examined their predictive value on the other platform. Results: Only 30 % of all measurements of corresponding genes on both platforms showed Person correlation coefficient of ≥ 0.7, 54 % of cDNA clones matched with ≥ 1 probe sets on the Affy chip and there was large variation in probe set to probe set correlation with the matching cDNA result. The top response discriminating gene lists consisted of 182 genes for Affy p≤0.006 and 45 for cDNA, p≤ 0.002, with only 17 gene overlap. The top genes performed well in intra-platform supervised hierarchical clustering each correctly separating 91% of cases. However cross-platform application resulted in substantially lower clustering accuracy of 45% (Affy to cDNA) and 79% (cDNA to Affy). When only the 17 overlapping genes were used for clustering 67% (Affy) and 64% (cDNA) of cases were correctly clustered. Similar results were obtained when linear discriminant analysis and Generic Algorithm were used for outcome prediction. Conclusion: Distinct predictive marker sets can be identified from the same samples using different gene expression profiling platforms. Predictors perform well on one platform but cross-platform comparisons are less informative. Misclassification rates may be slightly improved with careful gene selection of probes with high correlation coefficients. No significant financial relationships to disclose.

Cross-platform network applications with mono

Cross-platform network applications with mono

An Authoring Technology for Multidevice Web Applications

The rapid proliferation of mobile computing devices has increased the complexity and cost of cross-platform application development. Multidevice authoring technology (MDAT) lets developers build a generic application common to multiple devices and customize it for specific devices. We developed MDAT an end-to-end development methodology and toolset, to reduce the complexity of creating interactive, form-based Web applications that execute on heterogeneous devices. Web application refers to conventional, servlet-based Web applications as well as portlet applications. A portlet is a Web application component that a Web portal server aggregates with other portlets.

Lga972: a cross-platform application for optimizing LD studies using a genetic algorithm.

lga972 is a user-friendly cross-platform application with a graphical interface for determining the design features of two-stage genetic linkage disequilibrium studies that minimize the genotyping burden.

GenomeMixer: a complex genetic cross simulator.

GenomeMixer is a cross-platform application that simulates meiotic recombination events for large and complex multigenerational genetic crosses among sexually reproducing diploid species and outputs simulated progeny to several standard mapping programs. Documentation, C++ source, and binaries for Mac OS X and x86 Linux are freely available at http://www.nervenet.org/genome_mixer/. GenomeMixer can be compiled on any system with support for the Trolltech Qt toolkit, including Windows.

ATOMS: crystallography for the X-ray absorption spectroscopist.

ATOMS is a user application providing crystallographic functionality useful to x-ray absorption spectroscopists. ATOMS is also a set of reusable, object-oriented software modules written in the Perl programming language providing crystallographic functionality and access to databases of absorption coefficients and anomalous scattering factors. The main use of the ATOMS program is to generate input data for the ab initio, multiple scattering, x-ray absorption spectroscopy code FEFF. However the code offers many additional features, including useful calculations involving absorption coefficients and simulations of Diffraction Anomalous Fine-Structure (DAFS) spectra. Command line, graphical, and web-based interfaces to the code are offered as part of the standard distribution. As Perl runs on a wide variety of common computer platforms, ATOMS itself is a cross platform application. All text presented to the user can be internationalized - support for four languages is currently included in the package. Development of ATOMS is active - a FEFF interface, structure visualization, and additional crystallographic calculations are among the future developments.

Integrating Web-based e-commerce applications with business application systems

The World Wide Web has become an environment for distributed applications of all kinds. The originally intended use of the Web as distributed system for knowledge-interchange seems to disappear, compared to the increasing number of electronic commerce Web applications. Organizations offer products and services in the Web, and use the Web as a means to integrate their (heterogeneous) business application systems. Offering Web-based products requires combining services of different application systems, which were built on the coarse-grained Web implementation model. Reusing the respective fine-grained services and application systems respectively integrating these cross-platform application systems increases quality and reduces costs of the new product. However, communication between (legacy) business application systems has to be ensured on an abstract level to realize this scenario. The Web as a global point of sale seems to be very promising but obviously suffers from its heritage – the coarse-grained implementation model. We introduce a generic integration layer that uses an object-oriented approach as well as the WebComposition Markup Language to facilitate the reuse of code and design, and show how inter-application communication can be provided by means of an additional basic integration layer.

Enterprise computing: the Java factor

The ubiquitous availability of Web browsers on multiple platforms and user familiarity with browser technology provide numerous advantages: a uniform interface; support for multimedia and user interaction and collaboration; a simple communication protocol that has been implemented in all major hardware and software platforms; and support by almost all vendors who package Web engines within their products. Such factors have expedited the implementation of network centric computing as a productive infrastructure for corporate environments. The addition of Java, with its ability to build cross platform application logic into a browser, gives network centric computing the potential to better meet enterprise computing needs. Because it lets users interact with the application on the client rather than the server, Java enables better utilization of both the server and the client's computational capability. Java can also provide sessions state information (for client side session control and resource management) in an otherwise stateless Web world. Besides naturally decentralizing application execution, Java makes it possible to decentralize application deployment. In large enterprises, organization wide applications such as personnel timekeeping or document routing can benefit from Java implementations. One immediate impact is a noticeable reduction of the server load during peak hours. Finally, Java enabled browsers can provide greater functionality than HTML.