Platform-independent Analysis Research Articles

Disorder-Robust Entanglement Transport.

We study the disorder-perturbed transport of two noninteracting entangled particles in the absence of backscattering. This situation is, for instance, realized along edges of topological insulators. We find profoundly different responses to disorder-induced dephasing for the center-of-mass and relative coordinates: While a mirror symmetry protects even highly delocalized relative states when resonant with the symmetry condition, delocalizations in the center of mass [e.g., two-particle (N=2) N00N states] remain fully sensitive to disorder. We demonstrate the relevance of these differences to the example of interferometric entanglement detection. Our platform-independent analysis is based on the treatment of disorder-averaged quantum systems with quantum master equations.

Systematic evaluation of the early access applied biosystems precision ID Globalfiler mixture ID and Globalfiler NGS STR panels for the ion S5 system

Systematic evaluation of the early access applied biosystems precision ID Globalfiler mixture ID and Globalfiler NGS STR panels for the ion S5 system

PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens

Large-scale genetic screens using CRISPR/Cas9 technology have emerged as a major tool for functional genomics. With its increased popularity, experimental biologists frequently acquire large sequencing datasets for which they often do not have an easy analysis option. While a few bioinformatic tools have been developed for this purpose, their utility is still hindered either due to limited functionality or the requirement of bioinformatic expertise. To make sequencing data analysis of CRISPR/Cas9 screens more accessible to a wide range of scientists, we developed a Platform-independent Analysis of Pooled Screens using Python (PinAPL-Py), which is operated as an intuitive web-service. PinAPL-Py implements state-of-the-art tools and statistical models, assembled in a comprehensive workflow covering sequence quality control, automated sgRNA sequence extraction, alignment, sgRNA enrichment/depletion analysis and gene ranking. The workflow is set up to use a variety of popular sgRNA libraries as well as custom libraries that can be easily uploaded. Various analysis options are offered, suitable to analyze a large variety of CRISPR/Cas9 screening experiments. Analysis output includes ranked lists of sgRNAs and genes, and publication-ready plots. PinAPL-Py helps to advance genome-wide screening efforts by combining comprehensive functionality with user-friendly implementation. PinAPL-Py is freely accessible at http://pinapl-py.ucsd.edu with instructions and test datasets.

Retraction Note: TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics.

Most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience. TREEFINDER is an easy-to-use integrative platform-independent analysis environment for molecular phylogenetics. In this paper the main features of TREEFINDER (version of April 2004) are described. TREEFINDER is written in ANSI C and Java and implements powerful statistical approaches for inferring gene tree and related analyzes. In addition, it provides a user-friendly graphical interface and a phylogenetic programming language. TREEFINDER is a versatile framework for analyzing phylogenetic data across different platforms that is suited both for exploratory as well as advanced studies.

Metamodels Evaluation of Web Engineering Methodologies to Develop Web Applications

The purpose of a metamodel in web engineering methodologies is for the platform independent analysis as well as the design of the content, navigation, and presentation issues of web applications. In the previous years, numbers of methodologies for the development of web applications were proposed, and most of them defined their notation for creating metamodels. The increasing expansion and complexity of web applications are a new challenge for web software developers. This paper presents a comparison study between metamodel of the three methodologies which are; UML-Based Web Engineering (UWE), Web Modeling Language (WebML) and Object Oriented Hypermedia (OOH). The aim is to show the capability of the methodologies to address the challenges in developing the web applications. The evaluation results presented in this paper help the designer in providing initial knowledge of the strengths and weaknesses of the three methodologies for developing web applications.

Platform Independent Analysis of Probabilities on Multithreaded Programs

A concurrent program is intuitively associated with probability: the executions of the program can produce nondeterministic execution program paths due to the interleavings of threads, whereas some paths can always be executed more frequently than the others. An exploration of the probabilities on the execution paths is expected to provide engineers or compilers with support in helping, either at coding phase or at compile time, to optimize some hottest paths. However, it is not easy to take a static analysis of the probabilities on a concurrent program in that the scheduling of threads of a concurrent program usually depends on the operating system and hardware (e.g., processor) on which the program is executed, which may be vary from machine to machine. In this paper the authors propose a platform independent approach, called ProbPP, to analyzing probabilities on the execution paths of the multithreaded programs. The main idea of ProbPP is to calculate the probabilities on the basis of two kinds of probabilities: Primitive Dependent Probabilities (PDPs) representing the control dependent probabilities among the program statements and Thread Execution Probabilities (TEPs) representing the probabilities of threads being scheduled to execute. The authors have also conducted two preliminary experiments to evaluate the effectiveness and performance of ProbPP, and the experimental results show that ProbPP can provide engineers with acceptable accuracy.

Computational Complexity Analysis for a Class of Symmetric Cryptosystems Using Simple Arithmetic Operations and Memory Access Time

A secure cryptosystem could be very complicated, time consuming and hard to implement. Therefore, the complexity of the cryptosystem should be taken into account during design and implementation. In this work, the authors introduce a comprehensive and platform independent complexity analysis for a class of symmetric block cryptosystems, by which it will be easier to evaluate the performance of some used cryptosystems. Previous works lacked the comprehensiveness in their analysis, due to the fact that the memory access time was completely ignored, which greatly degrades the accuracy of the analysis and limits it to one data block only. In this paper the authors analytically compute the complexity for a class of symmetric cryptosystems in terms of the number of the clock cycles required and in terms of the required time for encryption/decryption, independently of the hardware or software used in the encryption/decryption process. Moreover, this is the first complexity analysis that considers the required time to access and retrieve information from memory, which makes the analysis more comprehensive and accurate than previous work as well as being general for any number of encryption data blocks. In addition, computer simulations are used to truly evaluate the accuracy of the analysis and to show how the analytical results match the simulation results.

Evaluation of high-resolution microarray platforms for genomic profiling of bone tumours

BackgroundSeveral high-density oligonucleotide microarray platforms are available for genome-wide single nucleotide polymorphism (SNP) detection and microarray-based comparative genomic hybridisation (array CGH), which may be used to detect copy number aberrations in human tumours. As part of the EuroBoNeT network of excellence for research on bone tumours (eurobonet.eu), we have evaluated four different commercial high-resolution microarray platforms in order to identify the most appropriate technology for mapping DNA copy number aberrations in such tumours.FindingsDNA from two different cytogenetically well-characterized bone sarcoma cell lines, representing a simple and a complex karyotype, respectively, was tested in duplicate on four high-resolution microarray platforms; Affymetrix Genome-Wide Human SNP Array 6.0, Agilent Human Genome CGH 244A, Illumina HumanExon510s-duo and Nimblegen HG18 CGH 385 k WG tiling v1.0. The data was analysed using the platform-specific analysis software, as well as a platform-independent analysis algorithm. DNA copy number was measured at six specific chromosomes or chromosomal regions, and compared with the expected ratio based on available cytogenetic information. All platforms performed well in terms of reproducibility and were able to delimit and score small amplifications and deletions at similar resolution, but Agilent microarrays showed better linearity and dynamic range. The platform-specific analysis software provided with each platform identified in general correct copy numbers, whereas using a platform-independent analysis algorithm, correct copy numbers were determined mainly for Agilent and Affymetrix microarrays.ConclusionsAll platforms performed reasonably well, but Agilent microarrays showed better dynamic range, and like Affymetrix microarrays performed well with the platform-independent analysis software, implying more robust data. Bone tumours like osteosarcomas are heterogeneous tumours with complex karyotypes that may be difficult to interpret, and it is of importance to be able to well separate the copy number levels and detect copy number changes in subpopulations. Taking all this into consideration, the Agilent and Affymetrix microarray platforms were found to be a better choice for mapping DNA copy numbers in bone tumours, the latter having the advantage of also providing heterozygosity information.

AnalyzeNNLS: Magnetic resonance multiexponential decay image analysis

Exponential decays are fundamental to magnetic resonance imaging, yet adequately sampling and analyzing multiexponential decays is rarely attempted. The advantage of multiexponential analysis is the quantification of sub-voxel structure caused by water compartmentalization, with application as a non-invasive imaging biomarker for myelin. We have developed AnalyzeNNLS, software designed specifically for multiexponential decay image analysis that has a user-friendly graphical user interface and can analyze data from many MR manufacturers. AnalyzeNNLS is a simple, platform independent analysis tool that was created using the extensive mathematical and visualization libraries in Matlab, and released as open source code allowing scientists to evaluate, scrutinize, improve, and expand.

Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0

BackgroundThe growing whole genome sequence databases necessitate the development of user-friendly software tools to mine these data. Web-based tools are particularly useful to wet-bench biologists as they enable platform-independent analysis of sequence data, without having to perform complex programming tasks and software compiling.FindingsGeneOrder4.0 is a web-based "on-the-fly" synteny and gene order analysis tool for comparative bacterial genomics (ca. 8 Mb). It enables the visualization of synteny by plotting protein similarity scores between two genomes and it also provides visual annotation of "hypothetical" proteins from older archived genomes based on more recent annotations.ConclusionsThe web-based software tool GeneOrder4.0 is a user-friendly application that has been updated to allow the rapid analysis of synteny and gene order in large bacterial genomes. It is developed with the wet-bench researcher in mind.

Quantitative analysis of packet-processing applications regarding architectural guidelines for network-processing-engine development

This paper presents a simulation-based profile-driven quantitative analysis of packet-processing applications. In this domain, demands for increasing the performance and the ongoing development of network protocols both call for flexible and performance-optimized engines. Based on the achieved profiling results, we introduce platform-independent analysis that locates the performance bottlenecks and architectural challenges of a packet-processing engine. Finally based on these results, we extract helpful architectural guidelines for design of a flexible and high-performance embedded processor that is optimized for packet-processing operations in high-performance and cost-sensitive network embedded applications.

TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

BackgroundMost analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience.ResultsTREEFINDER is an easy-to-use integrative platform-independent analysis environment for molecular phylogenetics. In this paper the main features of TREEFINDER (version of April 2004) are described. TREEFINDER is written in ANSI C and Java and implements powerful statistical approaches for inferring gene tree and related analyzes. In addition, it provides a user-friendly graphical interface and a phylogenetic programming language.ConclusionsTREEFINDER is a versatile framework for analyzing phylogenetic data across different platforms that is suited both for exploratory as well as advanced studies.

Platform independent dynamic Java virtual machine analysis: the Java Grande Forum benchmark suite

AbstractIn this paper we present a platform independent analysis of the dynamic profiles of Java programs when executing on the Java Virtual Machine. The Java programs selected are taken from the Java Grande Forum benchmark suite and five different Java‐to‐bytecode compilers are analysed. The results presented describe the dynamic instruction usage frequencies, as well as the sizes of the local variable, parameter and operand stacks during execution on the JVM.These results, presenting a picture of the actual (rather than presumed) behaviour of the JVM, have implications both for the coverage aspects of the Java Grande benchmark suites, for the performance of the Java‐to‐bytecode compilers and for the design of the JVM. Copyright © 2003 John Wiley & Sons, Ltd.

An internet based surface texture information system

This paper presents an internet based surface texture analysis and information system, which applies Java and internet technology to engineering metrology. The system includes most of the standardized and advanced analysis tools and a database for surface texture. The most distinct feature of this system is that it can run on the internet, which enables platform independent and remote data and analysis of surface texture.

A practical method for specification and analysis of exception handling-a Java/JVM case study

We provide a rigorous framework for language and platform independent design and analysis of exception handling mechanisms in modern programming languages and their implementations. To illustrate the practicality of the method we develop it for the exception handling mechanism of Java and show that its implementation on the Java Virtual Machine (JVM) Is correct. For this purpose we define precise abstract models for exception handling in Java and in the JVM and define a compilation scheme of Java to JVM code which allows us to prove that, in corresponding runs, Java and the JVM throw the same exceptions and with equivalent effect. Thus, the compilation scheme can, with reasonable confidence, be used as a standard reference for Java exception handling compilation.