Web Server Software Research Articles

PIDS: A User-Friendly Plant DNA Fingerprint Database Management System.

The high variability and somatic stability of DNA fingerprints can be used to identify individuals, which is of great value in plant breeding. DNA fingerprint databases are essential and important tools for plant molecular research because they provide powerful technical and information support for crop breeding, variety quality control, variety right protection, and molecular marker-assisted breeding. Building a DNA fingerprint database involves the production of large amounts of heterogeneous data for which storage, analysis, and retrieval are time and resource consuming. To process the large amounts of data generated by laboratories and conduct quality control, a database management system is urgently needed to track samples and analyze data. We developed the plant international DNA-fingerprinting system (PIDS) using an open source web server and free software that has automatic collection, storage, and efficient management functions based on merging and comparison algorithms to handle massive microsatellite DNA fingerprint data. PIDS also can perform genetic analyses. This system can match a corresponding capillary electrophoresis image on each primer locus as fingerprint data to upload to the server. PIDS provides free customization and extension of back-end functions to meet the requirements of different laboratories. This system can be a significant tool for plant breeders and can be applied in forensic science for human fingerprint identification, as well as in virus and microorganism research.

Attacks on Newly Registered Content Management Websites – A Comparison

Web Content Management Systems (CMSs) are tools for creating and maintaining commercial-quality websites. Their popularity has increased, but so has their complexity and the number of third-party modules. These, however, increase the risk of vulnerabilities. This paper presents a case study of hacker/intrusion activities on CMS websites. We study how much of the incoming traffic is potentially malicious and where it originates from. Additionally, we study if CMS’s based on different CMS software attract different kinds of traffic. To implement our study, we have registered and launched three virtual websites (running on the same computer). Each site runs its own popular CMS software, but their content is identical (a weblog with a simple template). The sites run for six months on a platform of a commercial web hosting provider. Our methodology is empirical, and our analysis is based on logging every HTTP request that was sent to the sites. This was done using the logging capabilities of the webserver software, Apache. We compare the sites with each other, with an established website, and an empty website. Our analysis shows that more than 90% of all traffic to the websites (both old and new) is potentially malicious. Further, we find that a large majority of the intrusion attempts are very unsophisticated: they do not try to exploit any specific vulnerabilities of the underlying CMS. Therefore, keeping the CMS up-to-date and following CMS hardening practices is enough to repel these attacks.

A server-side accelerator framework for multi-core CPUs and Intel Xeon Phi co-processor systems

Processing-intensive web server requests can lead to low Quality of Service (QoS), such as longer mean response time and lower throughput, which calls for a new web server software framework that can improve the performance of web servers. The characteristic of request-level parallelism in web servers is fit for many-core architecture accelerators, such as GPU and Intel Xeon Phi co-processors, but traditional web server model cannot make full use of the performance of these accelerators. We proposed a new web server software framework— called MIC-based Server-side Accelerator Framework (MSAF)—for a machine with not only multi-core CPUs but also Intel Xeon Phi co-processors based on Staged Event Driven Architecture (SEDA). The framework can fully exploit the performance of Intel Xeon Phi co-processors and multi-core CPUs, and improve power/energy efficiency by offloading the stage of handling requests to Intel Xeon Phi co-processors. We implemented the web server simulation software based on MSAF framework on a machine with multi-core CPUs and Intel Xeon Phi co-processors, and evaluated it by means of Apache Benchmark (AB). Our evaluation of MSAF shows its performance is about equivalent to that of a web server cluster consisting of four to five computing nodes. This paper indicates that if MSAF is applied to, Intel Xeon Phi co-processors are suitable for server side software, such as web servers, DNS servers, and database servers, because of its characteristic of lower communication latency between Intel Xeon Phi co-processors and host, more powerful logic processing ability, and more energy efficiency.

DALI and the persistence of protein shape.

DALI is a popular resource for comparing protein structures. The software is based on distance-matrix alignment. The associated web server provides tools to navigate, integrate and organize some data pushed out by genomics and structural genomics. The server has been running continuously for the past 25 years. Structural biologists routinely use DALI to compare a new structure against previously known protein structures. If significant similarities are discovered, it may indicate a distant homology, that is, that the structures are of shared origin. This may be significant in determining the molecular mechanisms, as these may remain very similar from a distant predecessor to the present day, for example, from the last common ancestor of humans and bacteria. Meta-analysis of independent reference-based evaluations of alignment accuracy and fold discrimination shows DALI at top rank in six out of 12 studies. The web server and standalone software are available from http://ekhidna2.biocenter.helsinki.fi/dali.

A combination of LCPUFAs regulates the expression of miRNA-146a-5p in a murine asthma model and human alveolar cells

BackgroundLCPUFAs are suggestive of having beneficial effects on inflammatory diseases such as asthma. However, little is known about the modulative capacity of omega-(n)-3 and n-6 LCPUFAs within the epigenetic regulation of inflammatory processes. ObjectiveThe aim of this study was to investigate whether a specific combined LCPUFA supplementation restores disease-dysregulated miRNA-profiles in asthmatic mice. In addition, we determined the effect of the LCPUFA supplementation on the interaction of the most regulated miRNA expression and oxygenase activity in vitro. MethodsSequencing of miRNA was performed by NGS from lung tissue of asthmatic and control mice with normal diet, as well as of LCPUFA supplemented asthmatic mice. Network analysis and evaluation of the biological targets of the miRNAs were performed by DIANA- miRPath v.3 webserver software, TargetScanMouse 7.2, and tool String v.10, respectively. Expression of hsa-miRNA-146a-5p and activity of COX-2 and 5-LO in LCPUFA-treated A549 cells were assessed by qPCR and flow cytometry, respectively. ResultsIn total, 62 miRNAs were dysregulated significantly in murine allergic asthma. The LCPUFA combination restored 21 of these dysregulated miRNAs, of which eight (mmu-miR-146a-5p, -30a-3p, -139-5p, -669p-5p, -145a-5p, -669a-5p, -342-3p and -15b-5p) were even normalized compared to the control levels. Interestingly, six of the eight rescued miRNAs are functionally implicated in TGF-β signaling, ECM-receptor interaction and fatty acid biosynthesis. Furthermore, in vitro experiments demonstrated that upregulation of hsa-miRNA-146a-5p is accompanied by a reduction of COX-2 and 5-LO activity. Moreover, transfection experiments revealed that LCPUFAs inhibit 5-LO activity in the presence and absence of anti-miR-146a-5p. ConclusionOur results demonstrate the modulative capacity of LCPUFAs on dysregulated miRNA expression in asthma. In addition, we pointed out the high regulative potential of LCPUFAs on 5-LO regulation and provided evidence that miR-146a partly controls the regulation of 5-LO.

ВЕБ-ДОДАТОК ДЛЯ СЕРВІСУ СКЛАДАННЯ РАЦІОНУ ЗДОРОВОГО ХАРЧУВАННЯ ТА ДОСТАВКИ ПРОДУКТІВ

У статті обґрунтована необхідність створення веб-додатку, що об’єднує процеси складання здорового раціону харчування з урахуванням потреб людини та доставки продуктів. Проведено аналіз проблем автоматизації та інформатизації в Україні звичних для людини повсякденних справ, таких як забезпечення продуктами харчування, складання правильного раціону. Розглянуте питання актуальності даної проблеми, на основі якої проведено аналіз існуючих сервісів доставки продуктів в Україні. Були виявлені ключові недоліки та функції, яких не вистачає у кожному з них. Проведено аналіз дизайнів кожного ресурсу задля створення більш сучасного інтерактивного сервісу, який би задовольняв не тільки функціональні потреби користувачів, а й позитивно впливав на психоемоційний стан людини. Розглянуте питання зі створення сучасного веб-додатку, який поєднує в собі функції вибору продуктів харчування відповідно до насиченості поживними речовинами та калорійністю і реалізовує можливість доставки обраних товарів до клієнта. Представлені та аргументовані вимоги до дизайну ресурсу та інтерактивних елементів на сторінці. Визначено функції веб-сервісу, вимоги до контенту та програм для реалізації проекту. Веб-додаток розроблено за допомогою сучасних веб-технологій, що цілком відповідають прописаним специфікаціям. Визначені умови до адаптації та кросбраузерності додатку, задля можливості доступу до нього з усіх можливих пристроїв. Описано послідовність програмної реалізації веб-сервісу: розмітка, стилізація ресурсу, розробка модуля логіки та модуля інтерактивності. Сформульовано вимоги до програмного коду. Особливу увагу приділено функціональним можливостям ресурсу, аналогів яких, на українському ринку, знайдено не було, а саме, можливості обирати конкретні продукти, відповідно до вмісту в них поживних елементів, можливості бачити загальну калорійність продукту, відповідно до обраної ваги, та функцію зручного оформлення доставки замовлення, з можливістю додавання власного коментаря клієнта, що дозволяє приділити особливу увагу кожному замовнику та підвищити якість надання послуг у сфері продажу товарів.

Designing and Synthesis of a siRNA against Angiopoietin‐2 for the Treatment of Neovascularization Associated to Diabetic Retinopathy

Diabetic retinopathy (RD) is a pathology that causes changes in the retina, for example exudates, microhemorrhages, neovascularizations, etc., which leads to loss of sight and is the third cause of blindness in the world. Among the mechanisms involved in neovascularization are angiogenic factors like angiopoietins (Angpt), especially angiopoietin‐2 (Angpt2), which has been reported that increase the formation of new vessels. For this reason, the aim of this study is to design and synthesize an siRNA against to Angpt2. Male Wistar rats were administered with streptozotocin (STZ) to induce diabetes, after 4 weeks the biochemical parameters, the neovascularization (junctions and lacunarity) and the expression of the Angpt2 were determined in the retina. The siRNA was designed with the siRNA Wizard v3.1 and RNA fold webserver software programs and was synthesized by MERMADE 8 equipment. The results showed that the number of junctions and the levels of Angpt2 of the diabetic rats were higher than the controls significantly, while the lacunarity was significantly lower than controls, on the other hand, the region susceptible to silencing could be from 1416 to 1436. Thus, we can conclude that early diabetes produces an increase in Angpt2 and neovascularization, which could be reduced by the siRNA to Angpt2.Support or Funding InformationGrants: Instituto Politécnico Nacional (SIP‐20194983), Programa Institucional de Formación de Investigadores del IPN (BEIFI No. 2177), Scholarship by Consejo Nacional de Ciencia y Tecnología (CONACYT No.418913) and Comisión de Operación y Fomento de Actividades del IPN (COFAA).This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Cancer Gene Discovery by Network Analysis of Somatic Mutations Using the MUFFINN Server.

Identifying genes that are capable of inducing tumorigenesis has been a major challenge in cancer research. In many cases, such genes frequently show somatic mutations in tumor samples; thus various computational methods for predicting cancer genes have been developed based on "significantly mutated genes." However, this approach is intrinsically limited by the fact that there are many cancer genes infrequently mutated in cancer genomes. Therefore, we recently developed MUFFINN (Mutations For Functional Impact on Network Neighbors), a method for cancer gene prediction based not only on mutation occurrences in each gene but also those of neighbors in functional networks. This enables the identification of cancer genes with infrequent mutation occurrence. We demonstrated that MUFFINN could retrieve known cancer genes more efficiently than gene-based methods and predicted cancer genes with low mutation occurrences in tumor samples. Users can freely access a web server ( http://www.inetbio.org/muffinn ) and run predictions with either public or private data of cancer somatic mutations. For given information of mutation occurrence profiles, the MUFFINN server returns lists of candidate cancer genes by four distinct predictions with different combinations between gene networks and scoring algorithms. Stand-alone software is also available, which allows MUFFINN to be run on local machines with a custom gene network. Here, we present an overall guideline for using the MUFFINN web server and stand-alone software for the discovery of novel cancer genes.

Software reusability metrics estimation: Algorithms, models and optimization techniques

ObjectiveIn this paper, the proposed model is intended to employ a novel evolutionary computing-based artificial intelligence or machine learning scheme for regression tests to be used for reusability estimation. Such enhancement can lead to accurate reusability pattern estimation, which can be effective for optimal software design purposes. This model is popularly called an aging-resilient software reusability forecast representation. The proposed system employs predominant object-oriented software metrics, such as Chidamber and Kemerer's metrics to examine reusability. Here, cumulative metrics, object-oriented metrics, McCabe's metrics, cohesion and a coupling-based reusability assessment model have been proposed which could be of paramount significance in software design optimization. In this paper, software metrics algorithms and their primary constructions have been developed for estimating the metrics from the UML/class diagrams. It is feasible to derive an efficient and robust reusability prediction model for web-service products using object-oriented metrics. Here, it was also found that OO-CK metrics, particularly complexity, cohesion and coupling-related metrics can be helpful in predicting reusability in web-service software products. Considering the above-mentioned key contributions, it can be stated that the proposed research could be of paramount significance in next-generation software computation systems, primarily for software component reusability, reliability, survivability, aging prediction and stability, and for software excellence assurance purposes.

Current and Voltage Measurement on Mobile Device

IoT (Internet of Things) technologies will change the traditional instruments and meters. A device combines wireless communication chip can transmit data to net. This paper aims at the IoT applied in instruments and meters. A Mobile multimeter is designed. It can provide necessary infrastructure to enable the data collection and dissemination to all stakeholders. Then mobile device record and process data. Also the mobile device install web server software, other computer can acquire data from WIFI net. In this framework WIFI and Bluetooth are default wireless communication style in mobile devices, and Android system is used in the most mobile devices. So the framework also can be used in other similar instruments and meters.

MoRFchibi SYSTEM: software tools for the identification of MoRFs in protein sequences.

Molecular recognition features, MoRFs, are short segments within longer disordered protein regions that bind to globular protein domains in a process known as disorder-to-order transition. MoRFs have been found to play a significant role in signaling and regulatory processes in cells. High-confidence computational identification of MoRFs remains an important challenge. In this work, we introduce MoRFchibi SYSTEM that contains three MoRF predictors: MoRFCHiBi, a basic predictor best suited as a component in other applications, MoRFCHiBi_Light, ideal for high-throughput predictions and MoRFCHiBi_Web, slower than the other two but best for high accuracy predictions. Results show that MoRFchibi SYSTEM provides more than double the precision of other predictors. MoRFchibi SYSTEM is available in three different forms: as HTML web server, RESTful web server and downloadable software at: http://www.chibi.ubc.ca/faculty/joerg-gsponer/gsponer-lab/software/morf_chibi/

A Web Server and Mobile App for Computing Hemolytic Potency of Peptides

Numerous therapeutic peptides do not enter the clinical trials just because of their high hemolytic activity. Recently, we developed a database, Hemolytik, for maintaining experimentally validated hemolytic and non-hemolytic peptides. The present study describes a web server and mobile app developed for predicting, and screening of peptides having hemolytic potency. Firstly, we generated a dataset HemoPI-1 that contains 552 hemolytic peptides extracted from Hemolytik database and 552 random non-hemolytic peptides (from Swiss-Prot). The sequence analysis of these peptides revealed that certain residues (e.g., L, K, F, W) and motifs (e.g., “FKK”, “LKL”, “KKLL”, “KWK”, “VLK”, “CYCR”, “CRR”, “RFC”, “RRR”, “LKKL”) are more abundant in hemolytic peptides. Therefore, we developed models for discriminating hemolytic and non-hemolytic peptides using various machine learning techniques and achieved more than 95% accuracy. We also developed models for discriminating peptides having high and low hemolytic potential on different datasets called HemoPI-2 and HemoPI-3. In order to serve the scientific community, we developed a web server, mobile app and JAVA-based standalone software (http://crdd.osdd.net/raghava/hemopi/).

Search engines crawling process optimization: a webserver approach

Purpose – The purpose of this paper is to decrease the traffic created by search engines’ crawlers and solve the deep web problem using an innovative approach. Design/methodology/approach – A new algorithm was formulated based on best existing algorithms to optimize the existing traffic caused by web crawlers, which is approximately 40 percent of all networking traffic. The crux of this approach is that web servers monitor and log changes and communicate them as an XML file to search engines. The XML file includes the information necessary to generate refreshed pages from existing ones and reference new pages that need to be crawled. Furthermore, the XML file is compressed to decrease its size to the minimum required. Findings – The results of this study have shown that the traffic caused by search engines’ crawlers might be reduced on average by 84 percent when it comes to text content. However, binary content faces many challenges and new algorithms have to be developed to overcome these issues. The proposed approach will certainly mitigate the deep web issue. The XML files for each domain used by search engines might be used by web browsers to refresh their cache and therefore help reduce the traffic generated by normal users. This reduces users’ perceived latency and improves response time to http requests. Research limitations/implications – The study sheds light on the deficiencies and weaknesses of the algorithms monitoring changes and generating binary files. However, a substantial decrease of traffic is achieved for text-based web content. Practical implications – The findings of this research can be adopted by web server software and browsers’ developers and search engine companies to reduce the internet traffic caused by crawlers and cut costs. Originality/value – The exponential growth of web content and other internet-based services such as cloud computing, and social networks has been causing contention on available bandwidth of the internet network. This research provides a much needed approach to keeping traffic in check.

Coarse-Graining of Volumes for Modeling of Structure and Dynamics in Electron Microscopy: Algorithm to Automatically Control Accuracy of Approximation

Coarse-graining (or granularization) of structures from transmission electron microscopy (EM volumes) has been shown to be useful for a variety of structural analysis applications. Several methods perform coarse-graining of EM volumes using hard spheres or 3D Gaussian functions but they do not allow controlling automatically the volume approximation accuracy. To tackle this problem, we recently developed such a method. It is currently used by 3DEM Loupe web server and HEMNMA software to study macromolecular dynamics based on coarse-grained representations of EM volumes. In this paper, we give a detailed description of the implemented algorithm and fully analyze its performance, which was out of scope of our previous papers. The performance is analyzed in a controlled environment, in the context of studying structure and dynamics of macromolecular complexes. We show that this technique allows computing structures that are similar to atomic structures, by analyzing intermediate-resolution volumes. Additionally, we show that it allows sharpening of intermediate-resolution volumes. The full algorithm description allows its implementation in any other software package.

안전한 웹 서버 환경을 위한 시큐어코딩 도구, 웹쉘 탐지도구 간의 상호연동 시스템 설계

Recently, with the development of the ICT environment, the use of the software is growing rapidly. And the number of the web server software used with a variety of users is also growing. However, There are also various damage cases increased due to a software security vulnerability as software usage is increasing. Especially web shell hacking which abuses software vulnerabilities accounts for a very high percentage. These web server environment damage can induce primary damage such like homepage modification for malware spreading and secondary damage such like privacy. Source code weaknesses checking system is needed during software development stage and operation stage in real-time to prevent software vulnerabilities. Also the system which can detect and determine web shell from checked code in real time is needed. Therefore, in this paper, we propose the system improving security for web server by detecting web shell attacks which are invisible to existing detection method such as Firewall, IDS/IPS, Web Firewall, Anti-Virus, etc. while satisfying existing secure coding guidelines from development stage to operation stage.

The assembly and annotation of the complete Rufous-bellied thrush mitochondrial genome

Among known bird species, oscines are one of the few groups that produce complex vocalizations due to vocal learning. One of the most conspicuous oscine passerines in southeastern South America is the Rufous-bellied Thrush, Turdus rufiventris. The complete mitochondrial genome of this species was sequenced with the Illumina HiSeq platform (Illumina Inc., San Diego, CA), assembled using MITObim software and annotated by MITOS web server and Artemis software. This mitogenome contained 16 669 bases, organized as 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a control region (d-loop). The sequencing of the Rufous-bellied Thrush mitochondrial genome is of particular interest for better understanding of population genetics and phylogeography of the Turdidae family.

Optimizing RNA structures by sequence extensions using RNAcop.

A key aspect of RNA secondary structure prediction is the identification of novel functional elements. This is a challenging task because these elements typically are embedded in longer transcripts where the borders between the element and flanking regions have to be defined. The flanking sequences impact the folding of the functional elements both at the level of computational analyses and when the element is extracted as a transcript for experimental analysis. Here, we analyze how different flanking region lengths impact folding into a constrained structure by computing probabilities of folding for different sizes of flanking regions. Our method, RNAcop (RNA context optimization by probability), is tested on known and de novo predicted structures. In vitro experiments support the computational analysis and suggest that for a number of structures, choosing proper lengths of flanking regions is critical. RNAcop is available as web server and stand-alone software via http://rth.dk/resources/rnacop.

Using Node-HTTP-Proxy for Remote Experiment Data Transmission Traversing Firewall

In this paper, a novel real time experimental data transmission solution based on a new web server software architecture that allows the traversing of network firewalls is proposed. With this new software architecture, the public network port 80 can be shared between Node.js and the Apache web server software system. With this new solution, the Apache web server application still listens to the public network port 80, but any client requests for the Node.js web server application through the port will be forwarded to a special network port which Node.js web server application is listening to. Accordingly, a new solution in which both Apache and Node.js web server applications work together via HTTP proxy developed by the Node-HTTP-Proxy software package is implemented on the server-side. With this new real time experiment control and data transmission solution, the end user can control remote experiments and view experimental data on the web browser without firewall issues and without the need of third party plug-ins. It also provides a new approach for the remote experiment control and real time data transmission based on pure HTTP protocol. The solution will significantly benefit the development of remote laboratory technology.

A Distributed Measurement System for Power Quality Monitoring

This paper describes a distributed power quality (PQ) monitoring system. The structure of the measurement system, format of PQ database and web-server software are being discussed. The developed software can be used for PQ analysis and research activities. Examples of harmonic pollution measurements are being displayed.

Energy Efficiency of a Web and Database Server System

Energy-efficiency of server hardware, web server software and databases has been widely studied. However, studies that combine these aspects are rare. In this paper the authors present an energy-efficiency evaluation of a web and database application. They concentrate on the following aspects: server BIOS and operating system energy optimization and “bursting” i.e. queuing requests and then executing them in bursts. The authors have used the bursting method with both a database application and a web plus database application. Their results indicate about 10% energy savings using this method. They analyse the model by statistical tools and present an equation to express the quality of service versus burst wait time relationship.