Rapid Software Development Research Articles

Orchestrating high-throughput genomic analysis with Bioconductor.

Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors.

Proactive Software Engineering Approach to Ensure Rapid Software Development and Scalable Production with Limited Resources

Nowadays, the need for building scalable systems in narrow time window is needed. While the efforts and accuracy usually required for building high scale systems is not simple, the agile nature of system requirements spawn a need for enhancing some software engineering practices. These practices should be integrated together in order to help software (SW) development teams to build, and test scalable systems rapidly with a high confidence level in their scalability. This research explains the proposed Proactive Approach, which presents a set of software engineering practices that could help in producing scalable system while minimizing the wasted time within the production cycle. This set of practices have been validated, verified and tested through building 46 releases of one of the most important, mission critical and scalable systems. Applying these practices succeeded to enhance average response time of web pages by %1921.5, test code churn by more than % 5000, time to release by % 300, and succeeded to produce a system that could stand against 95375 users with % 99.921 scalability ratio.

The phylogenetic likelihood library.

We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements appropriate data structures and functions that allow users to quickly implement common, error-prone, and labor-intensive tasks, such as likelihood calculations, model parameter as well as branch length optimization, and tree space exploration. The highly optimized and parallelized implementation of the phylogenetic likelihood function and a thorough documentation provide a framework for rapid development of scalable parallel phylogenetic software. By example of two likelihood-based phylogenetic codes we show that the PLL improves the sequential performance of current software by a factor of 2–10 while requiring only 1 month of programming time for integration. We show that, when numerical scaling for preventing floating point underflow is enabled, the double precision likelihood calculations in the PLL are up to 1.9 times faster than those in BEAGLE. On an empirical DNA dataset with 2000 taxa the AVX version of PLL is 4 times faster than BEAGLE (scaling enabled and required). The PLL is available at http://www.libpll.org under the GNU General Public License (GPL).

Relation between Game Motivation and Preference to Cutscenes

Following rapid development of software and hardware technologies and increasing enhancement in arithmetic capability, there are more and more content that can be accommodated and processed in video games, which is also increasingly complex and fine. Cutscene as a main narrative method have been developed, which have become necessary to express some key plots and important scenarios in games. Good cutscene can strengthen engagement of players with virtual world in games and make players share affection and sorrow with roles in games; while badly-designed cut-scene or overused cut-scene will impair immersion of players and affect players' gaming experience; for this reason, developers should not continue cut-scene design just from opinions of designers nor make players passive receivers, instead, they should reduce as much as possible interruption by cut-scene to players' immersion and grant players with better immersion. After all, only designs depending on demands and preferences of players by having some knowledge of impacts of cut-scene on players' immersion can be accepted by players.

Current status of stress echocardiography: is it a required procedure for every sonographer?

Stress echocardiography is a versatile modality in the clinical cardiology. In its earlier days, its sole indication was restricted to diagnosing coronary artery disease. However, in response to the rapid development of ultrasound technology and analysis software, the indications have now evolved with expansion to several fields of cardiovascular disease. I reviewed previous stress echocardiography publications, and discussed the current status of stress echocardiography in routine clinical setting. Although its portability and online assessment make possible for immediate diagnosis even at the bedside, establishment of an appropriate procedure and an accurate assessment require some experience. Other imaging competitors, such as multidetector computed tomography and cardiac magnetic resonance are gradually replacing the role of stress echocardiography in some fields. However, stress echocardiography has a potential for other new fields, including valvular heart disease and congestive heart failure. Although primary indication of stress echocardiography for coronary artery disease seems to be not relevant especially in Japan, novel indication of stress echocardiography in other field of cardiovascular disease is rapidly expanding in conjunction with the advent of new technology. Stress echocardiography is not a tool for limited researchers, but rather a fundamental routine method of choice for every sonographer.

Large Data Visualization Analysis and Application in Scientific Computing

With the rapid development of computer hardware, software and network technology, the size of data is growing exponentially. Recently, large scientific computing data visualization becomes one of the important researches in scientific computing. This paper introduces the definition of big data, visualization analysis field and the significance of scientific computing for large data visualization. In the following part, we analyze and discuss the traditional scientific visualization methods, and introduce the algorithms in classification according to different types of datasets. We analyze the weak points of traditional methods in visualization of scientific computing, and then introduce the method of large data parallel computing and rendering based on GPU. Finally, combining the research of our group on scientific computing theory and application, we point out the direction for future work of scientific computing visualization with large data development.

JMVC: A Java Framework for Rapidly Developing Desktop Application Software Based on MVC

Java is one of the leading software development languages. However, the development model of existing Java organizes without structure, mixing the programming code for data access, the processes of business logic, and the graphical user interface layer together. This disorganization creates many problems for software developers, and prevents Java from meeting todays’ requirements for rapid application software development. A model-view-controller framework is a tool for facilitating the rapid development of software in a concurrent software development environment. In this paper, we propose a Java-based model-view-controller framework that we dub JMVC for developing desktop-based applications that can separate the data, view, and controller of the software to enhance the efficiency, reliability, maintainability, and scalability of application software.

A framework and architecture for rapid software development: a success story

In this paper, we present the experience of applying Empirical Software Engineering to create a new improved global architecture and framework for Computer Integrated Manufacturing in Freescale® Semiconductor Inc. The architecture and framework described in this paper have been utilized to create three software applications that run in all the interconnected probe and final test floors in Freescale around the world. These applications successfully and efficiently have increased automation and have significantly enhanced manufacturing processes, specifically in the fields of latent defects detection and equipment utilization improvement.

The Development of Basketball Assistant Training System Based on Kinect Motion Capture

With the rapid development of sensor technology, access software, body movements and facial expressions to capture system on the development cost, operation effect and efficiency to obtain the optimal balance point, has wide application prospect. This article through to access motion capture analyzing the basic techniques of basketball, basketball developed auxiliary training system, guide the basketball player to carry on the scientific, systematic and comprehensive teaching and training, so as to directly promote the improvement of the overall level of basketball.

The Implement of Interior 3D Navigation based on VRML

With the rapid development of computer software and hardware, the virtual reality is applied more widely. Interior 3D navigation, being as an important part of virtual reality and especially for 3D virtual roaming system, has become a hot research topic in recent years. In this paper, we propose a novel method to implement interior 3D navigation based on Virtual Reality Model Language (VRML). Firstly, the 3D tree routing map of an office building is obtained fro m the accurate AutoCAD model and with the support of block management strategy. Then, the roaming path by waypoint navigation method is generated. Finally, the interior 3D navigation system based on VRML is developed. By the automatic navigation, user can realistically experience the 3D indoor scene and the results test the validity of the proposed method in the engineering project.

Magnetic Resonance Neurography

Magnetic resonance (MR) neurography has progressed in the past 2 decades because of rapid technological developments in both hardware and software. In addition to improvements in high-resolution anatomic pulse sequences, functional techniques are becoming feasible. This article presents the current state-of-the-art three-dimensional anatomic techniques, discusses the advantages of functional techniques being exploited, and portrays novel contrast types and molecular techniques that are under development and promise a bright future for this rapidly evolving technique.

THE HUMAN ACTIVITY DETECTION FROM VIDEO SURVEILLANCE BASED ON HMM FOR FUTURE DEVELOPMENT IN COMPUTER ENVIRONMENT

Visual investigation of human activities related to the detection, tracking and recognition of people, and, more generally, the perceptive of human activities, from image sequences. Recognizing human activities from image sequences is an active area of research in computer vision. Human activity recognition (HAR) research has been on the rise because of the rapid technological development of the image-capturing software and hardware. In this paper, we propose a new approach for human action recognition from video. Here we use the HMM algorithm for recognition of activity from video. The result of this method is good as compare to other method. It consume less time as compare with other method. This result can be useful in future development as an automatic human machine interaction.

Application on the Virtual Campus Making with 3D Max and VRP Technology

With the rapid development of computer software and hardware technology, 3D technology and virtual reality technology is acquiring a greater growing space. Three-dimensional virtual campus environment compared with the traditional two-dimensional campus graphics more intuitive, vivid, true-to-life. More convenient to operate, you can choose a different camera pan any, the viewpoint conversion, angle rotation.

Detection of significantly differentially methylated regions in targeted bisulfite sequencing data

Bisulfite sequencing is currently the gold standard to obtain genome-wide DNA methylation profiles in eukaryotes. In contrast to the rapid development of appropriate pre-processing and alignment software, methods for analyzing the resulting methylation profiles are relatively limited so far. For instance, an appropriate pipeline to detect DNA methylation differences between cancer and control samples is still required. We propose an algorithm that detects significantly differentially methylated regions in data obtained by targeted bisulfite sequencing approaches, such as reduced representation bisulfite sequencing. In a first step, this approach tests all target regions for methylation differences by taking spatial dependence into account. A false discovery rate procedure controls the expected proportion of incorrectly rejected regions. In a second step, the significant target regions are trimmed to the actually differentially methylated regions. This hierarchical procedure detects differentially methylated regions with increased power compared with existing methods. R/Bioconductor package BiSeq. Supplementary Data are available at Bioinformatics online.

Using cloud technologies to check and record programming tasks

The rapid development of hardware and software and the bandwidth of telecommunications networks has provided extraordinary opportunities in the use of cloud technology in many areas of life, especially in education. For example, there are many Internet resources that offer peculiar web-based software development environments (IDEs). Such IDEs allow storing the source codes of programs, debugging them, compiling and executing them.Intensification of the learning process stimulates the search for new approaches to teaching disciplines, creating new and using ready-made software to support the learning process at a high level. At the same time, an important role in the study of programming-related disciplines is played by automated information systems of verification of solutions and accounting of the results of the verification.

Exploiting Mobile Devices to Assist Identification System of Photos for Social Relationship

With the popularity and prevalence of mobile devices, they have become indispensable daily necessities. The rapid development of software and hardware technology has made mobile devices increasingly powerful in function. Mobile devices have been inextricably linked with people’s lives. Moreover, as a result of the prevalence of social networking sites, the topic of people’s social relationship mining has attracted the attention of numerous researchers. This paper presented a mobile device-assisted determining social relationship system, which mainly uses the mobile device to collect geographic information about the surrounding people to determine whether they are within the angle of view of the mobile device's camera. The information is stored in the pictures as the basis for people relationship mining. The proposed approach has automatic and rapid processing capabilities for large amounts of photo data.

Multimedia Information Resource «The Church of the Savior on Ilyina Street in Novgorod the Great»

Rapid development of information technologies, related equipment and software makes it possible to achieve significant results in cultural heritage preservation. In recent times not only abroad but also in Russia more and more efforts and funds are allocated for development of cultural preservation innovative projects, which are aimed at establishing of information sources, virtual museums and large-scale educational portals where Internet-users could find information on different museums of many regions of the Russian Federation. Multimedia resources combine several advanced technologies: the technology of augmented reality (AR), GPS-navigation and recognition of QR-codes. These technologies are supported by smart phones on the basis of iOS and Android platforms and can be available in Android Market and the App Store as the most common products. One of such resources developed in recent years is about a unique world-famous church located in Novgorod the Great. The Church of the Savior on Ilyina street is located in Novgorod the Great, built in 1374. It is the only church in the world, where we can see the frescoes of the hand of Theophanes the Greek. The churched was decorated with frescoes in 1378. Painting of the church has not been completely preserved. Its greater part was destroyed due to numerous fires and repairs. But even small remaining pieces make it possible to appreciate general plan of the whole ensemble and unique style of Theophanes the Greek. Nowadays these pieces are the only in the world which can represent monumental work of Theophanes the Greek. Multimedia informational source is based on historical materials. It includes not only information on the Church of the Savior on Ilyina but also historical and cultural background of that period.One of the most important results of this project is so-called «e-passport» of the object. It is a number of architectural drawings developed on the basis of exact architectural and geodesic measurements. Images from archival photos and preserved painting fragments including original textures are superimposed on these drawings. Three-dimensional model of the monument can be now implemented with the use of finalized drawings

A cross-platform toolkit for mass spectrometry and proteomics

Mass-spectrometry-based proteomics has become an important component of biological research. Numerous proteomics methods have been developed to identify and quantify the proteins in biological and clinical samples1, identify pathways affected by endogenous and exogenous perturbations2, and characterize protein complexes3. Despite successes, the interpretation of vast proteomics datasets remains a challenge. There have been several calls for improvements and standardization of proteomics data analysis frameworks, as well as for an application-programming interface for proteomics data access4,5. In response, we have developed the ProteoWizard Toolkit, a robust set of open-source, software libraries and applications designed to facilitate proteomics research. The libraries implement the first-ever, non-commercial, unified data access interface for proteomics, bridging field-standard open formats and all common vendor formats. In addition, diverse software classes enable rapid development of vendor-agnostic proteomics software. Additionally, ProteoWizard projects and applications, building upon the core libraries, are becoming standard tools for enabling significant proteomics inquiries.

A Novel Integrated AHP-QFD Model for Software Project Selection under Fuzziness

Now-a-days software manufacturing companies usually try to capture market share with rapid software development. Actually the development of high quality software products can decrease cost by reducing rework and increasing productivity. For that, reason selection of software projects is an important task. Several factors come into consideration while selection of proper project for a specified job. To deal with this typical situation the current researchers combined the much known AHP(Analytic Hierarchy Process) with QFD (Quality Function Deployment). Here the AHP method redefined under fuzziness. Then QFD process is applied to identifying and ranking customer’s need and translating them into product / service specification. At the last sensitivity analysis has been done to make the process more robust from the characterization of integration of the fuzzy AHP & QFD. General Terms Software project selection; fuzziness; sensitivity analysis.

Approximation of COSMIC functional size to support early effort estimation in Agile

The demands in the software industry of estimating development effort in the early phases of development are met by measuring software size from user requirements. A large number of companies have adapted themselves with Agile processes, which, although, promise rapid software development, pose a huge burden on the development teams for continual decision making and expert judgement, when estimating the size of the software components to be developed at each iteration. COSMIC, on the other hand, is an ISO/IEC international standard that presents an objective method of measuring the functional size of the software from user requirements. However, its measurement process is not compatible with Agile processes, as COSMIC requires user requirements to be formalised and decomposed at a level of granularity where external interactions with the system are visible to the human measurer. This time-consuming task is avoided by agile processes, leaving it with the only option of quick subjective judgement by human measurers for size measurement that often tends to be erroneous. In this article, we address these issues by presenting an approach to approximate COSMIC functional size from informally written textual requirements demonstrating its applicability in popular agile processes. We also discuss the results of a preliminary experiment studying the feasibility of automating our approach using supervised text mining.