Domain Software Research Articles

A Speculative Control Mechanism of Cloud Computing Systems Based on Emergency Disaster Information Using SDN

In recent years, a Cloud computing system has been popularly used. Among them, a hybrid Cloud is focused, which combined a public Cloud operated by service providers and a private Cloud constructed inside a company. Because a private Cloud is considered to be secure and a public Cloud is scalable, it is possible to build a Cloud computing system that works effectively by combining the both types of Clouds. However, when a big disaster occurrs, huge volume of data is produced by monitoring censors and users, and flowed into such an information infrastructure. In addition, enormous number of people access to the system in such a case, thus a load of the system becomes extremely high in a short time. Therefore, it is important to change an environment dynamically among inter-Cloud and intra-Cloud to deal with the load. In this paper, bursty increasing load is predicted based on Earthquake Early Warning (EEW), and a speculative control is performed in a short time between a time of occurrence of an earthquake and a time when the system is heavily loaded actually. In addition, network traffic is controlled to give a higher priority to important data replication. The system is constructed on a Cloud computing platform using public domain software, OpenStack in this experiment. Network traffic of the system is controlled by Software Defined Network (SDN), which is controlled by the OpenFlow protocol. As a result of an evaluation, our proposed system works fine and achieves good performance.

Monitoring Wnt Signaling in Zebrafish Using Fluorescent Biosensors.

In this chapter, we are presenting methods to monitor and quantify in vivo canonical Wnt signaling activities at single-cell resolution in zebrafish. Our technology is based on artificial enhancers, obtained by polymerization of TCF binding elements, cloned upstream to ubiquitous or tissue-specific promoters. The different promoter/enhancer combinations are used to drive fluorescent protein reporter constructs integrated in the zebrafish germline by microinjection of fertilized zebrafish eggs. Fish with a single integration site are selected by Mendelian analysis of fluorescent carriers, and heterozygous offspring are used to monitor and quantify canonical Wnt activities. Open source public domain software such as ImageJ/Fiji is used to calculate the integrated densities in the region of interest and compare the effect of experimental conditions on control and treated animals.

Bright-Field Imaging and Optical Coherence Tomography of the Mouse Posterior Eye.

Noninvasive live imaging has been used extensively for ocular phenotyping in mouse vision research. Bright-field imaging and optical coherence tomography (OCT) are two methods that are particularly useful for assessing the posterior mouse eye (fundus), including the retina, retinal pigment epithelium, and choroid, and are widely applied due to the commercial availability of sophisticated instruments and software. Here, we provide a guide to using these approaches with an emphasis on post-acquisition image processing using Fiji, a bundled version of the Java-based public domain software ImageJ. A bright-field fundus imaging protocol is described for acquisition of multi-frame videos, followed by image registration to reduce motion artifacts, averaging to reduce noise, shading correction to compensate for uneven illumination, filtering to improve image detail, and rotation to adjust orientation. An OCT imaging protocol is described for acquiring replicate volume scans, with subsequent registration and averaging to yield three-dimensional datasets that show reduced motion artifacts and enhanced detail. The Fiji algorithms used in these protocols are designed for batch processing and are freely available. The image acquisition and processing approaches described here may facilitate quantitative phenotyping of the mouse eye in drug discovery, mutagenesis screening, and the functional cataloging of mouse genes by individual laboratories and large-scale projects, such as the Knockout Mouse Phenotyping Project and International Mouse Phenotyping Consortium.

Open Source Software for 1D Airborne Electromagnetic Inversion

SUMMARY Geoscience Australia is releasing into the public domain software for the inversion of airborne electromagnetic (AEM) data to a 1D conductivity depth structure. The software includes two different algorithms for 1D inversion of AEM data. The first is a gradient based deterministic inversion code for multi-layer (smooth model) and few-layered (blocky-model) inversions. The second is a reversible-jump Markov chain Monte Carlo stochastic inversion algorithm suitable for assessing model uncertainty. A forward modelling program and some other ancillary programs are also included. The code is capable of inverting data from all of the commercial time-domain systems available in Australia today, including dual moment systems. The software is accessible in three forms. As C++ source code, as binary executables for 64 bit Windows® PCs, and as a service on the Virtual Geophysics Laboratory (VGL). The code is fully parallelized for execution on a high performance cluster computer system via MPI or a multi-core shared memory workstation via OpenMP.

Healthy Community and Healthy Commons: ‘Opensourcing’ as a Sustainable Model of Software Production

Many commercial software firms rely on opensourcing as a viable model of software production. Opensourcing is a specific form of interaction between firms and open source software (OSS) communities for collaboratively producing software. The existing literature has identified opensourcing as a viable form of software production, which could be a substitute for “in-house” or “outsourced” software development. However, little is known about how opensourcing works or is sustained in the long term. The objective of this research is to explain the factors affecting the sustainability of opensourcing as a model of software production. The study employs a single case study of hospital software in Thailand to understand how firms and the communities can live symbiotically and sustain their collaboration to peer-produce vertical domain software. The analysis reveals six mechanisms (positive experience, trust in the leadership of the project leader, the demonstration of reciprocity, marketing the community, enriching knowledge, and face-to-face meetings) and demonstrates how they operate in conjunction with each other to sustain opensourcing.

An Optimum Wind Solar Hybrid System for Stand –Alone Power Generation

The dynamic behaviour and simulation results of a stand – alone hybrid power generation system comprising of a wind turbine, solar array and battery storage are presented in this Paper. The objective of this study is to review the state of the simulation, optimization and control technologies of the stand-alone hybrid solar–wind energy system with the inclusion of battery storage. The hybrid system used for the simulation consisted of a 100W wind turbine, 150W solar array and a 70Ah lead acid battery. A Fuzzy Logic Maximum Power Point Tracker (MPPT) controller was applied to the variable–speed, fixed–pitch small scale wind turbine while maximum power point tracking (MPPT) method based on Perturb & Observation (P&O) searching algorithm was applied to the stand–alone solar photovoltaic system. MATLAB SimulinkTM 7.2 / Simpower system software environment was utilized to accomplish and simulate individual wind and PV dynamic models of the hybrid system. The public domain software, Hybrid Optimization Model for Electric Renewables (HOMER) produced by the National Renewable Energy Laboratory was used to optimize the hybrid system with data taken from a feasibility study together with meteorological data obtained from a selected area in Sri Lanka ENGINEER, Vol. 48, No.04, pp. 1-15, 2015

Porosity Characterization of Aluminium Castings by Using Particular Non-destructive Techniques

In this paper is presented an analysis of a comparison of particular non-destructive techniques: radiographic, ultrasonic, eddy current and pulsed infrared thermography to detect flaws in pressure die casting. Furthermore, a new way of the image segmentation method for porosity detection in aluminium pressure die casting using results from X-ray analysis and public domain software is proposed. The results of the research allowed verifying the possibility of using the aforesaid methods in controlled technological parameters of the casting process, and thus permitted confirming the quality of the manufactured castings. It was found that the radiographic method was the most preferred means for evaluating the quality of products and for optimizing the technological process for aluminium pressure casting. It permits a fast analysis of casting defects in the finished products, and when combined with the computer image analysis (the porosity segmentation algorithm as described in the article) it allows drawing conclusions regarding their causes (e.g. based on the size and shape analysis of the pores detected). The ultrasonic testing method can also be used to evaluate the quality of the casting (to detect it but without the possibility of interpreting the size or source of origin). The results obtained via this method allow for proper control of die casting parameters.

Using Photobleaching to Measure Spindle Microtubule Dynamics in Primary Cultures of Dividing Drosophila Meiotic Spermatocytes.

In dividing animal cells, a microtubule (MT)-based bipolar spindle governs chromosome movement. Current models propose that the spindle facilitates and/or generates translocating forces by regionally depolymerizing the kinetochore fibers (k-fibers) that bind each chromosome. It is unclear how conserved these sites and the resultant chromosome-moving mechanisms are between different dividing cell types because of the technical challenges of quantitatively studying MTs in many specimens. In particular, our knowledge of MT kinetics during the sperm-producing male meiotic divisions remains in its infancy. In this study, I use an easy-to-implement photobleaching-based assay for measuring spindle MT dynamics in primary cultures of meiotic spermatocytes isolated from the fruit fly Drosophila melanogaster. By use of standard scanning confocal microscopy features, fiducial marks were photobleached on fluorescent protein (FP)-tagged MTs. These were followed by time-lapse imaging during different division stages, and their displacement rates were calculated using public domain software. I find that k-fibers continually shorten at their poles during metaphase and anaphase A through the process of MT flux. Anaphase chromosome movement is complemented by Pac-Man, the shortening of the k-fiber at its chromosomal interface. Thus, Drosophila spermatocytes share the sites of spindle dynamism and mechanisms of chromosome movement with mitotic cells. The data reveal the applicability of the photobleaching assay for measuring MT dynamics in primary cultures. This approach can be readily applied to other systems.

Subject identification via ECG fiducial-based systems: Influence of the type of QT interval correction

Electrocardiography (ECG) has been recently proposed as biometric trait for identification purposes. Intra-individual variations of ECG might affect identification performance. These variations are mainly due to Heart Rate Variability (HRV). In particular, HRV causes changes in the QT intervals along the ECG waveforms. This work is aimed at analysing the influence of seven QT interval correction methods (based on population models) on the performance of ECG-fiducial-based identification systems. In addition, we have also considered the influence of training set size, classifier, classifier ensemble as well as the number of consecutive heartbeats in a majority voting scheme. The ECG signals used in this study were collected from thirty-nine subjects within the Physionet open access database. Public domain software was used for fiducial points detection. Results suggested that QT correction is indeed required to improve the performance. However, there is no clear choice among the seven explored approaches for QT correction (identification rate between 0.97 and 0.99). MultiLayer Perceptron and Support Vector Machine seemed to have better generalization capabilities, in terms of classification performance, with respect to Decision Tree-based classifiers. No such strong influence of the training-set size and the number of consecutive heartbeats has been observed on the majority voting scheme.

WE-D-204-07: Development of An ImageJ Plugin for Renal Function Quantification: RenalQuant

Purpose: Commercial workstations usually have their own software to calculate dynamic renal functions. However, usually they have low flexibility and subjectivity on delimiting kidney and background areas. The aim of this paper is to present a public domain software, called RenalQuant, capable to semi-automatically draw regions of interest on dynamic renal scintigraphies, extracting data and generating renal function quantification parameters. Methods: The software was developed in Java and written as an ImageJ-based plugin. The preprocessing and segmentation steps include the user’s selection of one time frame with higher activity in kidney’s region, compared with background, and low activity in the liver. Next, the chosen time frame is smoothed using a Gaussian low pass spatial filter (σ = 3) for noise reduction and better delimitation of kidneys. The maximum entropy thresholding method is used for segmentation. A background area is automatically placed below each kidney, and the user confirms if these regions are correctly segmented and positioned. Quantitative data are extracted and each renogram and relative renal function (RRF) value is calculated and displayed. Results: RenalQuant plugin was validated using retrospective 20 patients’ 99mTc-DTPA exams, and compared with results produced by commercial workstation software, referred as reference. The renograms intraclass correlation coefficients (ICC) were calculated and false-negative and false-positive RRF values were analyzed. The results showed that ICC values between RenalQuant plugin and reference software for both kidneys’ renograms were higher than 0.75, showing excellent reliability. Conclusion: Our results indicated RenalQuant plugin can be trustingly used to generate renograms, using DICOM dynamic renal scintigraphy exams as input. It is user friendly and user’s interaction occurs at a minimum level. Further studies have to investigate how to increase RRF accuracy and explore how to solve limitations in the segmentation step, mainly when background region has higher activity compared to kidneys. Financial support by CAPES

A Faulty Synchronous Machine Model for Efficient Interface with Power System

This paper presents a new approach for simulating the internal faults of synchronous machines using distributed computing and Large Change Sensitivity (LCS) analysis. LCS analysis caters for a parallel solution of 3-phase model of a faulted machine within the symmetrical component- based model of interconnected network. The proposed method considers dynamic behavior of the faulty machine and connected system and tries to accurately solve the synchronous machine's internal fault conditions in the system. The proposed method is implemented in stand-alone FORTRAN-based phasor software and the results have been compared with available recordings from real networks and precisely simulated faults by use of the ATP/EMTP as a time domain software package. An encouraging correlation between the simulation results using proposed method, ATP simulation and measurements was observed and reported. The simplified approach also enables engineers to quickly investigate their particular cases with a reasonable precision.

Comparison among operators for detecting and/or extracting or roads using the matlab software and the cartomorph software

Abstract. FCT / UNESP has been developing CARTOMORPH to be a public domain software which can be operated by users needing to extract and / or detect features from digital images. In this work, two methods were applied for the extraction and / or detection of the contours of the feature of interest (the highway) using a digital image containing part of a highway. One method was applied through the use of operators contained in the Mathematical Morphology toolbox, which is a private domain, SDC Information Systems, and the other was applied using the routine contained in the CARTOMORPH software. In the toolbox, the operators used were mmreadgray, responsible for opening the original image, mmhisteq, which softens the image, mmneg which can reverse the grayscale of pixels, and mmareaclose, which aims to remove image segmentation. This set of operators has resulted in a routine capable of extracting and / or detecting the contour of a road. The Blur and Minimum (Gblur) operator was used in the process using the CARTOMORPH software. This can detect the edges of objects present in the original blurred image, and transform them into an ideal edge ramp. Results from both methods were compared and the conclusion is that the blur and minimum (GBlur) operator gave a better performance. This finding indicates that the set of operators implemented in CARTOMORPH will be able to be operated by users in the field of cartography and related fields, thus enabling the use of a public domain software with efficient results.

Simulation and Analysis of Light Scattering by Air Bubble in Optical Glass

Mie scattering theory is used in this paper to analyze the forward scattered light intensity distribution of an air bubble in the subsurface of optical glass, shining by a monochrome laser with a wavelength of 632.8um. The scattering process can be classified as uncorrelated single scattering .according to the properties of optical media. The finite difference time domain (FDTD) software is used to establish a 3-d simulation model to calculate for forward scattered intensity distribution of different sized air bubbles. Moreover, according to the relationship between Mie scattering intensity pattern and the size of bubbles, the size of bubbles are figured out with the help of neural network algorithm. The errors are lower than 10%. The simulation results can improve the precision of defects detection in optical glass.

The Role of Tissue Resection Length in the Determination of Post-Operative Eyelid Position for Muller’s Muscle-Conjunctival Resection Surgery

Purpose: To investigate the relationships between pre-operative marginal reflex distance (MRD), tissue resection length, phenylephrine response, and change in MRD with surgery for a cohort of individuals undergoing Muller’s muscle conjunctival resection (MMCR) surgery.Methods: All cases of MMCR surgery performed over a 13-year period at a single institution were screened for entry. Individuals with adequate photographic documentation and follow up were included. Patients with previous or concurrent upper eyelid, orbital or eyebrow disease of surgery were excluded. Marginal reflex distance (MRD) was calculated based on photographs utilizing public domain software. Data was plotted for inspection and appropriate statistical tests were performed.Results: During the study period 198 eyes fit criteria for analysis. A loose association between tissue resection length and change in MRD with surgery was found (r = 0.176, p < 0.05); this relationship was not significant in ANOVA analysis (p = 0.367). There was a strong association between MRD change with surgery and pre-operative MRD (r = 0.498, p < 0.01). Approximately 28% of the sample responded to 2.5% phenylephrine drop instillation with a greater than 2 mm increase in MRD. The response to phenylephrine was strongly associated with pre-operative MRD (r = −0.441, p < 0.01). A regression on change in MRD with surgery with tissue resection, phenylephrine response >2 mm and pre-operative MRD as variables revealed a model with pre-operative MRD as the only significant predictor (p < 0.01).Conclusion: Tissue resection length and phenylephrine response play small roles relative to pre-operative MRD in the determination of change in MRD with MMCR surgery.

A Bayesian approach to removal of incoherent scattering from neutron total-scattering data

A Bayesian statistics approach for subtraction of incoherent scattering from neutron total-scattering data has been developed and implemented in a public domain software package. In this approach, the estimated background signal associated with incoherent scattering maximizes the posterior probability, which combines the likelihood of this signal in reciprocal and real spaces with the prior that favors smooth lines. The probability distributions are constructed according to the principle of maximum entropy. The method enables robust subtraction of incoherent-scattering backgrounds while providing estimated uncertainties for recovered signals. The developed procedure was first tested using simulated data and then demonstrated using three representative experimental data sets, collected on bulk materials and nanoparticles, featuring distinct ratios of coherent to incoherent scattering.

We’re Working On It: Transferring the Sloan Digital Sky Survey from Laboratory to Library

This article reports on the transfer of a massive scientific dataset from a national laboratory to a university library, and from one kind of workforce to another. We use the transfer of the Sloan Digital Sky Survey (SDSS) archive to examine the emergence of a new workforce for scientific research data management. Many individuals with diverse educational backgrounds and domain experience are involved in SDSS data management: domain scientists, computer scientists, software and systems engineers, programmers, and librarians. These types of positions have been described using terms such as research technologist, data scientist, e-science professional, data curator, and more. The findings reported here are based on semi-structured interviews, ethnographic participant observation, and archival studies from 2011-2013. The library staff conducting the data storage and archiving of the SDSS archive faced two performance problems. The preservation specialist and the system administrator worked together closely to discover and implement solutions to the slow data transfer and verification processes. The team overcame these slow-downs by problem solving, working in a team, and writing code. The library team lacked the astronomy domain knowledge necessary to meet some of their preservation and curation goals. The case study reveals the variety of expertise, experience, and individuals essential to the SDSS data management process. A variety of backgrounds and educational histories emerge in the data managers studied. Teamwork is necessary to bring disparate expertise together, especially between those with technical and domain education. The findings have implications for data management education, policy and relevant stakeholders. This article is part of continuing research on Knowledge Infrastructures.

Towards component-based validation of GATE: Aspects of the coincidence processor

GATE is public domain software widely used for Monte Carlo simulation in emission tomography. Validations of GATE have primarily been performed on a whole-system basis, leaving the possibility that errors in one sub-system may be offset by errors in others. We assess the accuracy of the GATE PET coincidence generation sub-system in isolation, focusing on the options most closely modeling the majority of commercially available scanners.Independent coincidence generators were coded by teams at Toshiba Medical Research Unit (TMRU) and UC Davis. A model similar to the Siemens mCT scanner was created in GATE. Annihilation photons interacting with the detectors were recorded. Coincidences were generated using GATE, TMRU and UC Davis code and results compared to “ground truth” obtained from the history of the photon interactions. GATE was tested twice, once with every qualified single event opening a time window and initiating a coincidence check (the “multiple window method”), and once where a time window is opened and a coincidence check initiated only by the first single event to occur after the end of the prior time window (the “single window method”). True, scattered and random coincidences were compared. Noise equivalent count rates were also computed and compared.The TMRU and UC Davis coincidence generators agree well with ground truth. With GATE, reasonable accuracy can be obtained if the single window method option is chosen and random coincidences are estimated without use of the delayed coincidence option. However in this GATE version, other parameter combinations can result in significant errors.

Cyberinfrastructures: Bridging the Divide between Scientific Research and Software Engineering

Cyberinfrastructures--scientific research environments that span multiple institutions--require careful crafting and collaboration among domain specialists and software engineers, but several factors impede this collaboration. Recognizing five rules of thumb can help facilitate successful cyberinfrastructure creation and accelerate science in the disciplines they support.

REASONING UNDER UNCERTAINTY WITH BAYESIAN BELIEF NETWORKS ENHANCED WITH ROUGH SETS

The objective of this paper is to present a new approach to reasoning under uncertainty, based on the use of Bayesian belief networks (BBN’s) enhanced with rough sets. The role of rough sets is to provide additional reasoning to assist a BBN in the inference process, in cases of missing data or difficulties with assessing the values of related probabilities. The basic concepts of both theories, BBN’s and rough sets, are briefly introduced, with examples showing how they have been traditionally used to reason under uncertainty. Two case studies from the authors’ own research are discussed: one based on the evaluation of software tool quality for use in real-time safety-critical applications, and another based on assisting the decision maker in taking the right course of action, in real time, in the naval military exercise. The use of corresponding public domain software packages based on BBN’s and rough sets is outlined, and their application for real-time reasoning in processes under uncertainty is presented.

Three-Dimensional Reconstructions From Computed Tomographic Scans on Smartphones and Tablets: A Simple Tutorial for the Ward and Operating Room Using Public Domain Software

Handling 3-dimensional reconstructions of computed tomographic scans on portable devices is problematic because of the size of the Digital Imaging and Communications in Medicine (DICOM) stacks. The authors provide a user-friendly method allowing the production, transfer, and sharing of good-quality 3-dimensional reconstructions on smartphones and tablets.