Cross-platform Tool Research Articles

Mobile Applications for Agricultural Online Portals – Cross-platform or Native Development

There exist several possible approaches to the development of mobile applications. The paper treats the options of native applications for mobile devices. It analyzes economic aspects of two approaches - native applications development with the help of tools for individual platforms (Windows Phone, Android, iOS) and native applications developed by cross-platform tools represented by the tool Xamarin. In the paper basic variables and a formula for costs calculation are defined. The conclusions show that the utilization of the cross-platform tool Xamarin can lead to significant costs reduction. However, further research is needed mainly in the area of both the complexity development by cross-platform tools and meeting the requirements on UI and UX.

Mobile Applications for Agricultural Online Portals – Cross-platform or Native Development

There exist several possible approaches to the development of mobile applications. The paper treats the options of native applications for mobile devices. It analyzes economic aspects of two approaches - native applications development with the help of tools for individual platforms (Windows Phone, Android, iOS) and native applications developed by cross-platform tools represented by the tool Xamarin. In the paper basic variables and a formula for costs calculation are defined. The conclusions show that the utilization of the cross-platform tool Xamarin can lead to significant costs reduction. However, further research is needed mainly in the area of both the complexity development by cross-platform tools and meeting the requirements on UI and UX.

Flash: building the interactive web

Adobe Flash began as a simple animation tool and grew into a multimedia platform that offered a generation of creators and innovators an astonishing range of opportunities to develop and distribute new kinds of digital content. For the better part of a decade, Flash was the de facto standard for dynamic online media, empowering amateur and professional developers to shape the future of the interactive Web. In this book, Anastasia Salter and John Murray trace the evolution of Flash into one of the engines of participatory culture. Salter and Murray investigate Flash as both a fundamental force that shaped perceptions of the web and a key technology that enabled innovative interactive experiences and new forms of gaming. They examine a series of works that exemplify Flash's role in shaping the experience and expectations of web multimedia. Topics include Flash as a platform for developing animation (and the Flashimation aesthetic); its capacities for scripting and interactive design; games and genres enabled by the reconstruction of the browser as a games portal; forms and genres of media art that use Flash; and Flash's stance on openness and standards--including its platform-defining battle over the ability to participate in Apple's own proprietary platforms. Flash's exit from the mobile environment in 2011 led some to declare that Flash was dead. But, as Salter and Murray show, not only does Flash live, but its role as a definitive cross-platform tool continues to influence web experience.

VEET: 3D Virtual Electrical Experimental Tool Supporting Multi-Modal User Interfaces and Platforms

This paper introduces a practical and cross-platform virtual electrical experimental tool (VEET) based on an off the shelf game engine called Unity3D which is powerful and flexible to develop Virtual and Augmented Reality (VR/AR) applications. Taking the electrical experiments of technological university as examples, the well designed virtual experimental system has the characteristics of lifelike three dimensional (3D) experimental environments, AR interactive interface on mobile devices, intelligent detecting mechanism and cross-platform. We described VEET’?s flexible design and demonstrate its use in teaching where 120 students from three classes conducted electrical experiments with it. The experiments in VEET were presented on desktop, mobile and web browser using low cost common devices (personal computer, android handheld device, Chrome browser). Evaluating the main performance parameters, the well practicability was confirmed.

A new tool for converting food frequency questionnaire data into nutrient and food group values: FETA research methods and availability

ObjectivesTo describe the research methods for the development of a new open source, cross-platform tool which processes data from the European Prospective Investigation into Cancer and Nutrition Norfolk Food Frequency...

RapidMic: Rapid Computation of the Maximal Information Coefficient

To discover relationships and associations rapidly in large-scale datasets, we propose a cross-platform tool for the rapid computation of the maximal information coefficient based on parallel computing methods. Through parallel processing, the provided tool can effectively analyze large-scale biological datasets with a markedly reduced computing time. The experimental results show that the proposed tool is notably fast, and is able to perform an all-pairs analysis of a large biological dataset using a normal computer. The source code and guidelines can be downloaded from https://github.com/HelloWorldCN/RapidMic.

Micro-Analyzer: Automatic preprocessing of Affymetrix microarray data

A current trend in genomics is the investigation of the cell mechanism using different technologies, in order to explain the relationship among genes, molecular processes and diseases. For instance, the combined use of gene-expression arrays and genomic arrays has been demonstrated as an effective instrument in clinical practice. Consequently, in a single experiment different kind of microarrays may be used, resulting in the production of different types of binary data (images and textual raw data). The analysis of microarray data requires an initial preprocessing phase, that makes raw data suitable for use on existing analysis platforms, such as the TIGR M4 (TM4) Suite. An additional challenge to be faced by emerging data analysis platforms is the ability to treat in a combined way those different microarray formats coupled with clinical data. In fact, resulting integrated data may include both numerical and symbolic data (e.g. gene expression and SNPs regarding molecular data), as well as temporal data (e.g. the response to a drug, time to progression and survival rate), regarding clinical data.Raw data preprocessing is a crucial step in analysis but is often performed in a manual and error prone way using different software tools. Thus novel, platform independent, and possibly open source tools enabling the semi-automatic preprocessing and annotation of different microarray data are needed.The paper presents Micro-Analyzer (Microarray Analyzer), a cross-platform tool for the automatic normalization, summarization and annotation of Affymetrix gene expression and SNP binary data. It represents the evolution of the μ-CS tool, extending the preprocessing to SNP arrays that were not allowed in μ-CS. The Micro-Analyzer is provided as a Java standalone tool and enables users to read, preprocess and analyse binary microarray data (gene expression and SNPs) by invoking TM4 platform. It avoids: (i) the manual invocation of external tools (e.g. the Affymetrix Power Tools), (ii) the manual loading of preprocessing libraries, and (iii) the management of intermediate files, such as results and metadata.Micro-Analyzer users can directly manage Affymetrix binary data without worrying about locating and invoking the proper preprocessing tools and chip-specific libraries. Moreover, users of the Micro-Analyzer tool can load the preprocessed data directly into the well-known TM4 platform, extending in such a way also the TM4 capabilities. Consequently, Micro Analyzer offers the following advantages: (i) it reduces possible errors in the preprocessing and further analysis phases, e.g. due to the incorrect choice of parameters or due to the use of old libraries, (ii) it enables the combined and centralized pre-processing of different arrays, (iii) it may enhance the quality of further analysis by storing the workflow, i.e. information about the preprocessing steps, and (iv) finally Micro-Analzyer is freely available as a standalone application at the project web site http://sourceforge.net/projects/microanalyzer/.

AUREA: an open-source software system for accurate and user-friendly identification of relative expression molecular signatures

BackgroundPublic databases such as the NCBI Gene Expression Omnibus contain extensive and exponentially increasing amounts of high-throughput data that can be applied to molecular phenotype characterization. Collectively, these data can be analyzed for such purposes as disease diagnosis or phenotype classification. One family of algorithms that has proven useful for disease classification is based on relative expression analysis and includes the Top-Scoring Pair (TSP), k-Top-Scoring Pairs (k-TSP), Top-Scoring Triplet (TST) and Differential Rank Conservation (DIRAC) algorithms. These relative expression analysis algorithms hold significant advantages for identifying interpretable molecular signatures for disease classification, and have been implemented previously on a variety of computational platforms with varying degrees of usability. To increase the user-base and maximize the utility of these methods, we developed the program AUREA (Adaptive Unified Relative Expression Analyzer)—a cross-platform tool that has a consistent application programming interface (API), an easy-to-use graphical user interface (GUI), fast running times and automated parameter discovery.ResultsHerein, we describe AUREA, an efficient, cohesive, and user-friendly open-source software system that comprises a suite of methods for relative expression analysis. AUREA incorporates existing methods, while extending their capabilities and bringing uniformity to their interfaces. We demonstrate that combining these algorithms and adaptively tuning parameters on the training sets makes these algorithms more consistent in their performance and demonstrate the effectiveness of our adaptive parameter tuner by comparing accuracy across diverse datasets.ConclusionsWe have integrated several relative expression analysis algorithms and provided a unified interface for their implementation while making data acquisition, parameter fixing, data merging, and results analysis ‘point-and-click’ simple. The unified interface and the adaptive parameter tuning of AUREA provide an effective framework in which to investigate the massive amounts of publically available data by both ‘in silico’ and ‘bench’ scientists. AUREA can be found at http://price.systemsbiology.net/AUREA/.

Intelligent Tracking Assistance System Based on GPS and GSM

In recent years, GPS (Global Positioning System) developed rapidly, and widely used in car navigation, logistics, monitoring and other fields. However, intelligent tracking assistance for the old is relatively backward in the application. With GSM (Global System for Mobile Communications) and the QT cross-platform development tool, we design an intelligent tracking and assistance system. The system consists of the user and the terminals. The user can track the old, while the terminal can send alarm messages to the user when the old press the alarm button. We design and implement the display, alarm, help and query functions. Also, the system has good portability and scalability.

Micro-Analyzer: a tool for automatic pre-processing of multiple Affymetrix arrays

Motivations. A current trend in genomics is the investigation of cell mechanism using different technologies in order to explain the relationship among genes, molecular processes and diseases on a different scale. For instance, the combined use of expression arrays and SNP arrays has been demonstrated as an effective instrument in clinical practices [1,3,4]. Consequently, in a single experiment different kind of microarrays may be used, resulting in the production of different types of binary data (images and raw data). The analysis of microarray data requires an initial preprocessing phase of raw data that makes them suitable for use on existing platforms, such as the TIGR M4 Suite. An additional challenge to be faced by emerging data analysis platforms is the ability to treat in a combined way such different microarray data coupled with clinical data. In fact resulting integrated data may include both numerical and symbolic data (e.g. gene expression and SNPs regarding molecular data), as well as temporal data (e.g. the response to a drug, time to progression, survival rate, etc., regarding clinical data). Raw data preprocessing is a crucial step in analysis but is often performed in a manual and error prone way using different software tools. Thus novel, platform independent, and possibly open source tools enabling the semi-automatic preprocessing and annotation of different microarray data are needed. Methods. The paper presents Micro-Analyzer (Microarray Cel file Summarizer), a cross-platform tool for the automatic normalization, summarization and annotation of Affymetrix expression and SNP data binary data. It represents the evolution of the μ-CS tool, extending the preprocessing to SNP arrays that were not allowed in μ-CS [2]. Using the tools made available by Affymetrix (e.g. apt-summarize and apt-genotype), the user needs to download from the Affymetrix web site the right preprocessing and annotation libraries, then needs to manually invoke such tools to obtain preprocessed data and then has to import them into an external data analysis tools, e.g. TMEV. This approach presents numerous drawbacks, among those the need to manually perform all these tasks and the possibility to use the wrong or older libraries, obtaining wrong results, finally, data must be manually imported into analysis tools. To reduce such drawbacks we propose Micro-Analyzer. Micro-Analyzer is based on a client-server architecture. The Micro-Analyzer client is provided as a Java standalone tool and enables users to read, preprocess and analyse binary microarray data (gene expression and SNPs). It avoids: (i) the manual invocation of external tools (e.g. the Affymetrix Power Tools), (ii) the manual loading of preprocessing libraries, and (iii) the management of intermediate files. The Micro-Analyzer server automatically updates the references to the summarization and annotation libraries, hiding to the user the location of libraries and automatizing the process of updating such libraries when new versions of the microarray are released. By using Micro-Analyzer the user may preprocess both data using a single tool, retaining the advantage of storing in a single way both preprocessing results and metadata. Results. Micro-Analyzer users can directly manage Affymetrix binary data without worrying about locating and invoking the proper preprocessing tools and chip-specific libraries. Moreover, users of the Micro-Analyzer tool can load the preprocessed data directly into the well-known TM4 platform, extending in such a way even the TM4 capabilities. Consequently, Micro Analyzer offers the following advantages: (i) it reduces possible errors in the preprocessing and further analysis phases, e.g. due to the incorrect choice of parameters or due to the use of old libraries, (ii) it enables the centralized pre-processing of different arrays, (iii) it may enhance the quality of further analysis by storing the information about the preprocessing steps. Availability http://sourceforge.net/projects/microanalyzer/

μ-CS: An extension of the TM4 platform to manage Affymetrix binary data

BackgroundA main goal in understanding cell mechanisms is to explain the relationship among genes and related molecular processes through the combined use of technological platforms and bioinformatics analysis. High throughput platforms, such as microarrays, enable the investigation of the whole genome in a single experiment. There exist different kind of microarray platforms, that produce different types of binary data (images and raw data). Moreover, also considering a single vendor, different chips are available. The analysis of microarray data requires an initial preprocessing phase (i.e. normalization and summarization) of raw data that makes them suitable for use on existing platforms, such as the TIGR M4 Suite. Nevertheless, the annotations of data with additional information such as gene function, is needed to perform more powerful analysis. Raw data preprocessing and annotation is often performed in a manual and error prone way. Moreover, many available preprocessing tools do not support annotation. Thus novel, platform independent, and possibly open source tools enabling the semi-automatic preprocessing and annotation of microarray data are needed.ResultsThe paper presents μ-CS (Microarray Cel file Summarizer), a cross-platform tool for the automatic normalization, summarization and annotation of Affymetrix binary data. μ-CS is based on a client-server architecture. The μ-CS client is provided both as a plug-in of the TIGR M4 platform and as a Java standalone tool and enables users to read, preprocess and analyse binary microarray data, avoiding the manual invocation of external tools (e.g. the Affymetrix Power Tools), the manual loading of preprocessing libraries, and the management of intermediate files. The μ-CS server automatically updates the references to the summarization and annotation libraries that are provided to the μ-CS client before the preprocessing. The μ-CS server is based on the web services technology and can be easily extended to support more microarray vendors (e.g. Illumina).ConclusionsThus μ-CS users can directly manage binary data without worrying about locating and invoking the proper preprocessing tools and chip-specific libraries. Moreover, users of the μ-CS plugin for TM4 can manage Affymetrix binary files without using external tools, such as APT (Affymetrix Power Tools) and related libraries. Consequently, μ-CS offers four main advantages: (i) it avoids to waste time for searching the correct libraries, (ii) it reduces possible errors in the preprocessing and further analysis phases, e.g. due to the incorrect choice of parameters or the use of old libraries, (iii) it implements the annotation of preprocessed data, and finally, (iv) it may enhance the quality of further analysis since it provides the most updated annotation libraries. The μ-CS client is freely available as a plugin of the TM4 platform as well as a standalone application at the project web site (http://bioingegneria.unicz.it/M-CS).

The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.

BackgroundWith the vast amounts of biomedical data being generated by high-throughput analysis methods, controlled vocabularies and ontologies are becoming increasingly important to annotate units of information for ease of search and retrieval. Each scientific community tends to create its own locally available ontology. The interfaces to query these ontologies tend to vary from group to group. We saw the need for a centralized location to perform controlled vocabulary queries that would offer both a lightweight web-accessible user interface as well as a consistent, unified SOAP interface for automated queries.ResultsThe Ontology Lookup Service (OLS) was created to integrate publicly available biomedical ontologies into a single database. All modified ontologies are updated daily. A list of currently loaded ontologies is available online. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A programmatic interface is available to query the webservice using SOAP. The service is described by a WSDL descriptor file available online. A sample Java client to connect to the webservice using SOAP is available for download from SourceForge. All OLS source code is publicly available under the open source Apache Licence.ConclusionThe OLS provides a user-friendly single entry point for publicly available ontologies in the Open Biomedical Ontology (OBO) format. It can be accessed interactively or programmatically at .

CRITON: A Hypermedia Design Tool

The WWW has turned into a development and run-time environment for large-scale and complex applications. Such sophisticated applications are being deployed in increasing numbers without having been developed according to appropriate methodologies, tools and quality standards. The reason is not only that the hypermedia industry resists to utilize formal methods, but also that these methods and corresponding tools are very few and of dubious standards. The consequence is that the hypermedia applications being developed are of poor functionality and lack qualities such as modifiability, usability and maintainability. Especially the design phase is one of the phases that lack sufficient support from methods and CASE tools. This paper presents CRITON, a cross platform tool, built to support a hypermedia design method within an integrated environment. CRITON manages all three aspects of hypermedia design: conceptual design, navigational design and graphical user interface design, utilizing well-established theories and practices from software as well as hypermedia engineering. It employs these designs to generate a preliminary, exemplary form of the hypermedia application for the purpose of assessing the designs before the implementation phase.

A Remarkable Example of Catastrophic Cancellation Unraveled

In this paper we reinvestigate a well-known expression first published in [7], which is often used to illustrate catastrophic cancellation as well as the fact that identical output in different precisions does not imply reliability. The purpose of revisiting this expression is twofold. First, we show in Section 2 that the effect of the cancellation is very different on different IEEE 754 compliant platforms, and we unravel the underlying (hardware) reasons which are unknown to many numerical analysts. Besides illustrating cancellation, this expression also counters the common misbelief among many numerical analysts that a same program will deliver identical results on all IEEE conforming systems. Second, in Section 3 we use, illustrate and comment upon the cross-platform didactical tool Arithmetic Explorer developed at the University of Antwerp, by means of which we performed the bit level analysis of the expression evaluation under investigation on the different machines. We believe that this tool, which is freely available from the authors, can be of use to all of us teaching a first numerical analysis course.