Third-party Software Research Articles

Comparative analysis of NTRUEncrypt modified post-quantum cryptographic system and standard RSA cryptosystem

Introduction. The NTRUEncrypt cryptographic system, the calculation of the algorithmic complexity of the development of the NTRUEncrypt cryptosystem and its modifications are considered. The study objectives are to develop NTRUEncrypt, an efficient post-quantum cryptographic algorithm, which has high cryptographic resistance to quantum computer attacks, to work out a modification of the proposed algorithm, to analyze and experimentally validate its advantages. Materials and Methods . A description of the NTRUEncrypt encryption system is proposed. The modification of the considered algorithm is studied; the block diagram of the implementation of the software based on it is presented. An example of the software operation and its characteristic is given. The reliability of the results is proved using the Mann-Whitney U test. During the experiment, the third-party software implementation of the RSA cryptosystem was used. A Stopwatch class element was introduced in the source code of all three programs of NTRUEncrypt, RSA, and NTRUEncrypt modifications. This class provides a set of methods and properties that can be used for the precise measurement of the execution time. Thus, it became possible to record the results of the time spent on all three basic stages: key creation, encryption and decryption of the message. Research Results . The advantages of the developed cryptosystems in terms of the performance characteristics are proved. An experimental comparison of the implemented NTRUEncrypt algorithm and its modification is performed. All advantages of the latter are indicated. Discussion and Conclusions. The advantage of using the NTRUEncrypt algorithm modification is experimentally validated. The new application is 25% faster to perform general work on key generation, encryption and decryption. In addition, the internal memory usage is optimized through reducing the weight of the source program file and the size of the secret key. When attempting to crack a ciphertext, cryptographic robustness and complexity of using quantum algorithms are shown.

Pygenprop: a Python library for programmatic exploration and comparison of organism genome properties.

A critical step in comparative genomics is the identification of differences in the presence/absence of encoded biochemical pathways among organisms. Our library, Pygenprop, facilitates these comparisons using data from the Genome Properties database. Pygenprop is written in Python and, unlike existing libraries, it is compatible with a variety of tools in the Python data science ecosystem, such as Jupyter Notebooks for interactive analyses and scikit-learn for machine learning. Pygenprop assigns YES, NO, or PARTIAL support for each property based on InterProScan annotations of open reading frames from an organism's genome. The library contains classes for representing the Genome Properties database as a whole and methods for detecting differences in property assignments between organisms. As the Genome Properties database grows, we anticipate widespread adoption of Pygenprop for routine genome analyses and integration within third-party bioinformatics software. Pygenprop is written in Python and is compatible with versions 3.6 or higher. Source code is available under Apache Licence Version 2 at https://github.com/Micromeda/pygenprop. The package can be installed from both PyPi (https://pypi.org/project/pygenprop) and Anaconda (https://anaconda.org/lbergstrand/pygenprop). Documentation is available on Read the Docs (http://pygenprop.rtfd.io/).

Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers

High-quality and high-throughput prediction of enzyme commission (EC) numbers is essential for accurate understanding of enzyme functions, which have many implications in pathologies and industrial biotechnology. Several EC number prediction tools are currently available, but their prediction performance needs to be further improved to precisely and efficiently process an ever-increasing volume of protein sequence data. Here, we report DeepEC, a deep learning-based computational framework that predicts EC numbers for protein sequences with high precision and in a high-throughput manner. DeepEC takes a protein sequence as input and predicts EC numbers as output. DeepEC uses 3 convolutional neural networks (CNNs) as a major engine for the prediction of EC numbers, and also implements homology analysis for EC numbers that cannot be classified by the CNNs. Comparative analyses against 5 representative EC number prediction tools show that DeepEC allows the most precise prediction of EC numbers, and is the fastest and the lightest in terms of the disk space required. Furthermore, DeepEC is the most sensitive in detecting the effects of mutated domains/binding site residues of protein sequences. DeepEC can be used as an independent tool, and also as a third-party software component in combination with other computational platforms that examine metabolic reactions.

Automatic Tool for Fast Generation of Custom Convolutional Neural Networks Accelerators for FPGA

This paper presents a platform that automatically generates custom hardware accelerators for convolutional neural networks (CNNs) implemented in field-programmable gate array (FPGA) devices. It includes a user interface for configuring and managing these accelerators. The herein-presented platform can perform all the processes necessary to design and test CNN accelerators from the CNN architecture description at both layer and internal parameter levels, training the desired architecture with any dataset and generating the configuration files required by the platform. With these files, it can synthesize the register-transfer level (RTL) and program the customized CNN accelerator into the FPGA device for testing, making it possible to generate custom CNN accelerators quickly and easily. All processes save the CNN architecture description are fully automatized and carried out by the platform, which manages third-party software to train the CNN and synthesize and program the generated RTL. The platform has been tested with the implementation of some of the CNN architectures found in the state-of-the-art for freely available datasets such as MNIST, CIFAR-10, and STL-10.

Watson for Oncology applied to teaching and remote consulting model.

6545 Background: IBM Watson for Oncology (WFO) is developed with artificial intelligence to assist the oncologists in treatment decision-making by providing evidence-based treatment recommendations with priority and personality. We have been exploring the value of applying WFO in teaching and remote consulting among members in the hospital union to improve medical quality and conformity. Methods: Four modes were followed to apply WFO to teaching and remote consulting. Firstly, a teaching hospital conducted instructional teaching for a primary hospital through WFO, or a primary hospital consulted with a teaching hospital on cancer treatment combined with WFO. Secondly, a teaching hospital conducted conference-based teaching and remote consulting for two or three primary hospitals through demonstrating WFO. Thirdly, we cooperated with other teaching hospitals to carry out interactive discussions on cases through WFO with several primary hospitals. Fourthly, we cooperated with other teaching hospitals to conduct WFO demonstration and discussion for several primary hospitals. Remote communication was performed by using third-party video conference software. A survey was conducted to collect feedback from 56 primary hospitals in our hospital union. Results: More than 80% of primary hospitals were willing to learn the standardized treatment and recent treatment progress of tumors by participating in WFO remote consulting in our hospital. The value of four modes to promote the standardized cancer treatment and improve the medical quality and conformity in primary hospitals were all recognized. WFO also contributed to academic exchanges and learning among high-level teaching hospitals, and facilitated the use of artificial intelligence in oncology therapy more rational and appropriate. Conclusions: Non-standardization in cancer care remains to be a big problem in primary hospitals in China. Although limitation of WFO exists in the complex cases of certain tumor types, the rational use of WFO in the teaching and remote consulting could help and promote the standardized cancer treatment in China.

Comparison of 3 Surveillance Methods to Detect Potential Controlled Substance Diversion in an Academic Medical Center.

Objectives: To compare 3 methods of detecting potential diversion of controlled substances (CS) by health care personnel from inpatient units in a large, academic medical center. Methods: Three different reports were retrospectively analyzed and evaluated to determine which employees are "high-risk" for diversion over a 30-day period using defined criteria. Reports were derived from automated dispensing machines (ADMs), purchased third-party software (TPS), and the electronic health record (EHR). The primary outcome was the percentage of employees in each report who were deemed to be high-risk for CS diversion (positive predictive value [PPV]). Secondary outcomes included the number of false positives and description of high-risk users on each report. Descriptive statistics were used to analyze differences between methods. Results: The PPV was highly variable between reports. The PPVs among the ADM, TPS, and EHR reports were 3.28%, 6.82%, and 23.88%, respectively. False positives were high among all reports (96.72%, 93.18%, and 76.12% for the ADM, TPS, and EHR reports, respectively). Conclusions: A report from the EHR has the highest PPV to detect high-risk employees who may be diverting CS. However, false positives were high for all reports, indicating that significant improvements are needed in the development of accurate and reliable software to detect potential and actual CS diversion.

Feasibility of remote administration of the fundamentals of laparoscopic surgery (FLS) skills test using Google wearable device.

The fundamentals of laparoscopic surgery (FLS) program is a simulation-based training program designed to teach and assess the basic skills necessary for laparoscopic surgery. Preliminary work has demonstrated the feasibility of using Skype™ as a telesimulation modality in reliably scoring the exam for remote centers. Google Glass (GG) (Mountain View, California) is referred to as a wearable computer containing a heads-up display and front-facing camera allowing point-of-view video transmission. The objective of this study was to evaluate the feasibility of GG in scoring the technical skills component of the FLS exam. Twenty-eight participants were asked to complete the peg transfer and intracorporeal knot tasks of FLS using both GG and Skype™ setups. GG employed a third-party HIPAA-compliant video software (Pristine; Austin, TX) for video transmission. Participants were alternated between setups and evaluated by onsite and remote proctors. Times and errors were recorded by both proctors. Interrater reliability of their FLS scores was compared using Intraclass Correlation Coefficients (ICCs). GG experience was evaluated based on participant survey responses using a 5-point Likert scale. Interrater reliability for GG demonstrated a statistically significant correlation between onsite (OP) and remote (RP) proctors with ICCs of 0.985 (95% Confidence Interval [CI], 0.969-0.993) and 0.997 (95% CI 0.993-0.998), respectively, for peg and suture tasks. Skype™ demonstrated ICCs of 1.0 (95% CI 1.0-1.0). Average Likert scale responses found GG to be distracting (2.71), obstructive of the view (2.79), and a limitation to task execution (2.75). Overall, there was no statistical difference in scores between GG and Skype™ setups for either the peg (t = 1.446, p = 0.154) or suture task (t = - 0.710, p = 0.480), only 1 participant found the use of GG superior to Skype™. Our findings suggest that although GG are feasible in remote assessment of FLS with strong interrater reliability (ICC > 0.95), Skype™ was the preferred modality.

Correction of Spatialization Issues in Acousmatic Music: Remedying Incompatibility Between SpatGRIS and Logic Pro X [Stetson University

In this project, a technical solution for incompatibility among software programs involved in the spatialization of sound in multichannel speaker arrays was designed and implemented. Acousmatic music is a genre of electronic music intended for playback by a group of loudspeakers with the central concept being calculated ideation by the composer on how sound moves in space. Dr. Robert Normandeau, a pioneer in both acousmatic composition and sound spatialization research, describes the genre as “Cinema for the Ear.” Through his efforts with Groupe de Recherche en Immersion Spatiale (GRIS), Dr. Normandeau created a software plugin, SpatGRIS, which allows composers to send sounds around the space to come seemingly from anywhere in relation to the listener. This allows acousmatic composers to send sounds around, over, or through the audience for a completely immersive experience. Through use of SpatGRIS in conjunction with Logic Pro X, one of the most globally popular Digital Audio Workstations, the plugin has proven useful to create complex sonic movements in acousmatic compositions produced throughout the completion of this research. However, when trying to export these projects in their entirety for playback and sharing, both programs labeled and exported channels differently in octophonic (eight channel) compositions. This difference resulted in sounds from the composition being spatialized incorrectly. Therefore, a method using a free third-party software, which can easily remedy this error and correct the final recordings to their originally intended state, was created to serve as solution.

Проблемы проектирования геопортальных интерфейсов

The article is devoted to a detailed analysis of the problem of designing graphic geoportal interfaces. The authors formulated the basic points for solving problems in this field, having given the rationale and detailed description of each of them. The emphasis is made on the flexible arrangement of the design and development of interfaces, aiming at the future realities, at the human centricity of the interface design process, at the need for cross-platform adaptive web interfaces, at the preference to use proprietary and third-party software modules over the implementation of spatial data management systems. Lists of basic functional and quality requirements for graphical interfaces of geoportals are given. The geoportal “Natural and cultural heritage of Mordovia” is presented as an illustrative example of the various implementation of graphical user web interfaces. An experimental assessment of the effectiveness of measures to improve geoportal graphical interfaces is given. It is shown that properly over-thought interfaces of geoportal systems can contribute to solving various kinds of problems in many fields.

Gen2Epi: an automated whole-genome sequencing pipeline for linking full genomes to antimicrobial susceptibility and molecular epidemiological data in Neisseria gonorrhoeae

BackgroundRecent adva1nces in whole genome sequencing (WGS) based technologies have facilitated multi-step applications for predicting antimicrobial resistance (AMR) and investigating the molecular epidemiology of Neisseria gonorrhoeae. However, generating full scaffolds of N. gonorrhoeae genomes from short reads, and the assignment of molecular epidemiological information (NG-MLST, NG-MAST, and NG-STAR) to multiple assembled samples, is challenging due to required manual tasks such as annotating antimicrobial resistance determinants with standard nomenclature for a large number of genomes.ResultsWe present Gen2Epi, a pipeline that assembles short reads into full scaffolds and automatically assigns molecular epidemiological and AMR information to the assembled genomes. Gen2Epi is a command-line tool integrating third-party software and tailored specifically for N. gonorrhoeae. For its evaluation, the Gen2Epi pipeline successfully assembled the WGS short reads from 1484 N. gonorrhoeae samples into full-length genomes for both chromosomes and plasmids and was able to assign in silico molecular determinant information to each dataset automatically. The assemblies were generated using raw as well as trimmed short reads. The median genome coverage of full-length scaffolds and “N” statistics (N50, NG50, and NGA50) were higher than, or comparable to, previously published results and the scaffolding process improved the quality of the draft genome assemblies. Molecular antimicrobial resistant (AMR) determinants identified by Gen2Epi reproduced information for the 1484 samples as previously reported, including NG-MLST, NG-MAST, and NG-STAR molecular sequence types.ConclusionsGen2Epi can be used to assemble short reads into full-length genomes and assign accurate molecular marker and AMR information automatically from NG-STAR, NG-MAST, and NG-MLST. Gen2Epi is publicly available under “CC BY-NC 2.0 CA” Creative Commons licensing as a VirtualBox image containing the constituent software components running on the LINUX operating system (CentOS 7). The image and associated documentation are available via anonymous FTP at ftp://www.cs.usask.ca/pub/combi or ftp://ftp.cs.usask.ca/pub/combi

ADCP Discharge Measurements on the River Danube: Post-Processing and Correction of Data

Abstract Accurate measurements and analyses of river discharges are one of the key tasks of hydrology. Nowadays, the traditional methods of discharge measurements are being supplemented or even replaced by novel approaches that utilize state-of-the-art technologies. One approach, which has recently become very popular in the hydrological practice both in Slovakia and abroad, is a method utilizing the Doppler effect of sound waves. In this study, a dataset of 185 discharge measurements on the River Danube was created using a RiverRay portable Acoustic Doppler Current Profiler (ADCP). All the measurements were taken on the River Danube at four different cross-sections in Slovakia. The measurements were processed using the manufacturer’s WinRiver II software and further adjusted in Agila, which is a specialised third-party post-processing software aimed at correcting measurement errors from ADCP discharge measurements. Currently, some but not all countries lying in the Danube basin have included Agila post-processing in their methodologies. This causes problems and disputes between national water authorities when exchanging information about discharge measurements in the border regions. In order to respond to this problem, the main objective of this study was to compare the results of both original and corrected discharges, which were measured under a number of different circumstances, and to propose recommendations about the suitability of using Agila post-processing for discharge measurements of the River Danube.

Mathematical approach to the validation of functional surface texture parameter software

A new method for performance validation of surface texture parameter calculation software is introduced, focussing on functional surface texture parameters. Material ratio curves are defined algebraically and used to calculate functional surface texture parameters mathematically. Discrete datasets are created from the material ratio curves and input into three third-party parameter calculation software packages. Comparisons are made between the software-obtained parameter values and the mathematical values, identifying significant differences between them. Work is carried out to highlight inaccuracies introduced by sampling discrete datasets from mathematical representations, and it is shown that the resulting variations in parameter values are insignificant compared to the differences from the mathematical values.

Reusability in multimedia softwares using structural and lexical dependencies

Software reuse focuses on developing software using reusability principles. Component Based Software Engineering (CBSE) is one of the approaches that support software reuse by utilizing reusable software components. Many approaches have been proposed in the literature to mine reusable components from existing object-oriented software. But, almost all of these approaches are dependent on the selection of third-party application software as clients. Therefore, this paper proposes a reusable component identification approach from the source-code of a singular object-oriented software system especially related to multimedia tools. The proposed approach is based on making use of two kinds of dependency relations among different software elements namely structural and lexical relations. These relations, help us to measure cohesion at the component level using two proposed cohesion metrics. The cohesion values are further used as objective functions in the multi-objective search-based evolutionary algorithm, namely NSGA-III to identify the set of reusable components as different clusters. The proposed approach is validated by applying it to six open source Java applications of different sizes and belonging to multimedia domains.

Addressing Crypto-Ransomware Attacks: Before You Decide whether To-Pay or Not-To

ABSTRACT Crypto-ransomware attacks have forced victims to part away with millions of dollars using various intimidation and scare tactics. Victims have made hasty decisions of whether to pay or not without adequate information. In this paper, we explore options to address ransomware attacks before considering whether to pay or not. We propose a ransomware categorization framework that classifies the virulence of a ransomware attack using a proposed classification algorithm that is based on data deletion and file encryption attack structures. The categories that increase in severity from CAT1 to CAT8 classify the technical prowess and the overall effectiveness of potential ways of retaining the data without paying the ransom demand. The framework provides an avenue for a deeper comprehension of potential inadequacies and flaws to be exploited for data recovery. Results show that poorly implemented attack structures make recovery of data possible via system volume shadow copies or third-party software without paying.

An empirical study of DLL injection bugs in the Firefox ecosystem

DLL injection is a technique used for executing code within the address space of another process by forcing the load of a dynamic-link library. In a software ecosystem, the interactions between the host and third-party software increase the maintenance challenges of the system and may lead to bugs. In this work, we empirically investigate bugs that were caused by third-party DLL injections into the Mozilla Firefox browser. Among the 103 studied DLL injection bugs, we found that 93 bugs (90.3%) led to crashes and 57 bugs (55.3%) were caused by antivirus software. Through a survey with third-party software vendors, we observed that some vendors did not perform any QA with pre-release versions nor intend to use a public API (WebExtensions) but insist on using DLL injection. To reduce DLL injection bugs, host software vendors may strengthen the collaboration with third-party vendors, e.g., build a publicly accessible validation test framework. Host software vendors may also use a whitelist approach to only allow vetted DLLs to inject.

Ін’єктивний метод отримання даних користувацького досвіду в ігрових симуляторах комп’ютерних мереж

In the paper the ways of organizing the simulator’s work of computer networks are described, as well as methods and approaches for harvesting user experience. The application of this technology for entertainment and educational purposes is described. The main goals of collecting user data in gaming simulators of computer networks, which are used in particular in the competitions and contests for programming and application of IT technologies, are defined. Attention is drawn to the issue of collecting user experience data in applications that use a remote terminal connection using third-party software. Features of application of software interfaces of technologies which functionality can be used as a basis for method development are reviewed: technologies of containerization of the user environment of the operating system LXC and User Mode Linux, technology of packet interception based on the NetFilter network firewall and Open vSwitch virtual switch. Attention is also paid to isolating user processes and traffic from the host operating system environment, as well as the risks that may arise in the absence of measures and technologies of the sandbox software isolation. In the paper described the sequence of software implementation of the injective method, as well as the features of its use in the production environment. Attention is paid to logging changes to log files and real-time user activity logging. The features of the method are described in each of two variants of the basic containerization technology: LXC and User Mode Linux. The ways of increasing the security and reliability of the method itself when it is integrated with User Mode Linux virtualization technology are presented. Also ways of improving this approach by using additional Linux kernel modules are provided.

M16 - PATHVIEW WEB: USER FRIENDLY PATHWAY VISUALIZATION AND DATA INTEGRATION

Background Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Pathview quickly became a leading tool in pathway visualization, and has been widely adopted by tens of thousands of scientists and dozens of dependent applications worldwide. Methods Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. We also provide a comprehensive online help system and multiple quick-start example analyses. Even with no special computing training and resources, users may still accomplish pathway based data visualization and integration independently. Results The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package: 1) The results graphs are interactive and hyperlinked to abundant external annotation data online; 2) The server provides the latest, most complete and accurate pathway definitions and graphs by regular synchronization with KEGG source databases; 3) Users can review, replicate and share their analyses easily with free registered user accounts, which enable collaborative research and reproducible science; 4) Useful user engagement features allow users make comments and suggestions, or ask for help in designated pages. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Discussion Pathview Web is openly and freely accessible at https://pathview.uncc.edu/ .

Specificity of editorial and publishing training of electronic textbooks for the New Ukrainian School

The article is based on the analysis of ten electronic textbooks for the first grade of the New Ukrainian Schools. It was put to the competition by the publishers and presented in the electronic library of the Institute for the Modernization of the Content of Education (four textbooks «I am exploring the world», three textbooks in art, two electronic and one electronic textbook, textbook «Ukrainian Language. ABC Book. Parts 1 and 2») two models of the editorial and publishing preparation of projects of multimedia interactive electronic textbooks are defined and described. The first is «outsourcing model» which means involvement a technology company or multimedia publishing house in the creating of electronic textbooks. The second is «standalone model» which means independent creation of multimedia electronic textbooks by specialists of traditional publishing who use the specialized third-party software. It’s concluded that the market for interactive multimedia electronic textbooks can develop in several directions: more publishers of printed textbooks enter the market (in case if technological platforms that are available for Ukrainian publishers on the criterion «price – quality» and software for interactive programming will be provided) or filling of the niche of this market by tech companies and digital multimedia publishers (the main example is multimedia publishing house «Розумники» («A Clever Ones»)).

Understanding Customer Voice of Project Portfolio Management Software

Project Portfolio Management (PPM) has gained success in many projects due to its large number of features that covers effective scheduling, risk management, collaboration, and third-party software integrations to mention a few. A broad range of PPM software is available; however, it is essential to select the PPM with minimum usage issues over time. While many companies use surveys and market research to get users feedback, the PPM product software reviews carry the voice of users; the positive and negative sentiments of the PPM software reviews. This paper collected 4,775 reviews of ten PPM software from Capttera.com. Our approach has these phases- text preprocessing, sentiment analysis, summarization, and categorizations. The software reviews are filtered and cleaned, then negative sentiments of user reviews are summarized into a set of factors that identify issues of adopted PPM software. We report the most important issues of PPM software which were related to missing technological features and lack of training. Results using Latent Dirichlet Allocation (LDA) model showed that the top ten common issues are related to software complexity and lack of required features.

Free-space Polygon Creation based on Occupancy Grid Maps for Trajectory Optimization Methods

Abstract In this paper, we present a strategy for incorporating occupancy grid maps into local trajectory optimization methods to allow for safe autonomous navigation. We construct polygons as surface representations of the locally visible area and merge them with the aid of third-party software to form connected free-spaces. The method can be applied to any two-dimensional environments and different representations of vehicle dimensions. It allows direct optimization methods to be used consistently for different problem levels from control to planning. The strategies developed are applied to a rover system that moves in the plane. We evaluate our algorithms on the basis of simulation results and real-world experiments.