Linux Server Research Articles

Quantifying medical student clinical experiences via an ICD Code Logging App

ObjectivesThe logging of ICD Diagnostic, Procedure and Drug codes is one means of tracking the experience of medical students’ clinical rotations. The goal is to create a web-based computer and mobile application to track the progress of trainees, monitor the effectiveness of their training locations and be a means of sampling public health status.Materials and MethodsWe have developed a web-based app in which medical trainees make entries via a simple and quick interface optimized for both mobile devices and personal computers. For each patient interaction, users enter ICD diagnostic, procedure, and drug codes via a hierarchical or search entry interface, as well as patient demographics (age range and gender, but no personal identifiers), and free-text notes. Users and administrators can review and edit input via a series of output interfaces. The user interface and back-end database are provided via dual redundant failover Linux servers. Results and discussionStudents master the interface in ten minutes, and thereafter complete entries in less than one minute. Five hundred-forty 3rd year VCOM students each averaged 100 entries in the first four week clinical rotation. Data accumulated in various Appalachian clinics and Central American medical mission trips has demonstrated the public health surveillance utility of the application. ConclusionPC and mobile apps can be used to collect medical trainee experience in real time or near real-time, quickly, and efficiently. This system has collected 75,596 entries to date, less than 2% of trainees have needed assistance to become proficient, and medical school administrators are using the various summaries to evaluate students and compare different rotation sites.

Diseño y desarrollo de un prototipo robótico con orange PI

En este artículo se presenta el desarrollo de un robot móvil controlado vía web, diseñado para ejecutar tareas de monitoreo. El sistema es controlado mediante la tarjeta Orange Pi+ 2E y una tarjeta Arduino. El Robot está construido en acrílico, posee Una pantalla LCD touch para la comunicación con el usuario, 4 motores (para mover el vehículo), un controlador de carga, Sensores ultrasónicos para medir la distancia entre otros dispositivos de control. Se programó el sistema para que efectuará las tareas de manera óptima transmitiendo las imágenes de la cámara, la respuesta de los sensores y las órdenes de control del usuario cada 100 ms, la herramienta empleada es el framework ROS (Robot Operating System). En este caso se empleó el sistema operativo Linux server en la Orange Pi; que permite usar múltiples lenguajes de programación como lo son Java, PHP, Xajax y SH, en conjunto se ejecutan en un solo programa o interfaz de usuario que, a través de HTML5 y un navegador WEB permiten: captar video de la cámara, leer los comandos del usuario y hacer la petición a la Arduino para que dé la orden a los motores de efectuar el movimiento, leer el sensor y publicar en la pantalla LCD.

Testing Internet applications and services using PlanetLab

In this paper we evaluate a commonly used testing tool of Internet applications and services – PlanetLab. PlanetLab is a large-scale network of Linux servers used for Internet development and research. The geographical diversity of the servers allows engineers and researchers to test networking applications in the real Internet worldwide. In the paper we evaluate PlanetLab from different points of view we identified based on its long-term use. We specifically deal with the problematic aspects, such as PlanetLab service availability, networking performance, geographical accuracy, and DNS addressing correctness. Some of the PlanetLab ‘negative’ properties evaluated in this paper are required and needed as PlanetLab was established to reflect the real (erroneous) communication in the Internet. Nevertheless, one should be aware of them to set-up experiments correctly, run them smoothly, and not to misinterpret the results. Based on the observations presented, we give a set of simple conclusions that should help engineers to achieve valid Internet experiment results.

Fast H-DROP: A thirty times accelerated version of H-DROP for interactive SVM-based prediction of helical domain linkers.

Efficient and rapid prediction of domain regions from amino acid sequence information alone is often required for swift structural and functional characterization of large multi-domain proteins. Here we introduce Fast H-DROP, a thirty times accelerated version of our previously reported H-DROP (Helical Domain linker pRediction using OPtimal features), which is unique in specifically predicting helical domain linkers (boundaries). Fast H-DROP, analogously to H-DROP, uses optimum features selected from a set of 3000 ones by combining a random forest and a stepwise feature selection protocol. We reduced the computational time from 8.5min per sequence in H-DROP to 14s per sequence in Fast H-DROP on an 8 Xeon processor Linux server by using SWISS-PROT instead of Genbank non-redundant (nr) database for generating the PSSMs. The sensitivity and precision of Fast H-DROP assessed by cross-validation were 33.7 and 36.2%, which were merely ~2% lower than that of H-DROP. The reduced computational time of Fast H-DROP, without affecting prediction performances, makes it more interactive and user-friendly. Fast H-DROP and H-DROP are freely available from http://domserv.lab.tuat.ac.jp/ .

A quantitative model of application slow-down in multi-resource shared systems

Scheduling multiple jobs onto a platform enhances system utilization by sharing resources. The benefits from higher resource utilization include reduced cost to construct, operate, and maintain a system, which often include energy consumption. Maximizing these benefits comes at a price-resource contention among jobs increases job completion time. In this paper, we analyze slow-downs of jobs due to contention for multiple resources in a system; referred to as dilation factor. We observe that multiple-resource contention creates non-linear dilation factors of jobs. From this observation, we establish a general quantitative model for dilation factors of jobs in multi-resource systems. A job is characterized by a vector-valued loading statistics and dilation factors of a job set are given by a quadratic function of their loading vectors. We demonstrate how to systematically characterize a job, maintain the data structure to calculate the dilation factor (loading matrix), and calculate the dilation factor of each job. We validate the accuracy of the model with multiple processes running on a native Linux server, virtualized servers, and with multiple MapReduce workloads co-scheduled in a cluster. Evaluation with measured data shows that the D-factor model has an error margin of less than 16%. We extended the D-factor model to capture the slow-down of applications when multiple identical resources exist such as multi-core environments and multi-disks environments. Validation results of the extended D-factor model with HPC checkpoint applications on the parallel file systems show that D-factor accurately captures the slow down of concurrent applications in such environments.

Performance Enhancement of Multipath TCP for Wireless Communications With Multiple Radio Interfaces

Multipath transmission control protocol (MPTCP) allows a TCP connection to operate across multiple paths simultaneously and becomes highly attractive to support the emerging mobile devices with various radio interfaces and to improve resource utilization as well as connection robustness. The existing multipath congestion control algorithms, however, are mainly loss-based and prefer the paths with lower drop rates, leading to severe performance degradation in wireless communication systems, where random packet losses occur frequently. To address this challenge and improve the performance of MPTCP in wireless networks, this paper proposes a new mVeno algorithm, which makes full use of the congestion information of all the subflows belonging to a TCP connection in order to adaptively adjust the transmission rate of each subflow. Specifically, mVeno modifies the additive increase phase of Veno so as to effectively couple all subflows by dynamically varying the congestion window increment based on the receiving ACKs. The weighted parameter of each subflow for tuning the congestion window is determined by distinguishing packet losses caused by random error of wireless links or by network congestion. We implement mVeno in a Linux server and conduct extensive experiments both in test bed and in real WAN to validate its effectiveness. The performance results demonstrate that compared with the existing schemes, mVeno increases the throughput significantly, achieves load balancing, and can keep the fairness with regular TCP.

Development of a web-based tool for automated processing and cataloging of a unique combinatorial drug screen

Facing totally resistant bacteria, traditional drug discovery efforts have proven to be of limited use in replenishing our depleted arsenal of therapeutic antibiotics. Recently, the natural anti-bacterial properties of metal ions in synergy with metal-coordinating ligands have shown potential for generating new molecule candidates with potential therapeutic downstream applications. We recently developed a novel combinatorial screening approach to identify compounds with copper-dependent anti-bacterial properties. Through a parallel screening technique, the assay distinguishes between copper-dependent and independent activities against Mycobacterium tuberculosis with hits being defined as compounds with copper-dependent activities. These activities must then be linked to a compound master list to process and analyze the data and to identify the hit molecules, a labor intensive and mistake-prone analysis. Here, we describe a software program built to automate this analysis in order to streamline our workflow significantly. We conducted a small, 1440 compound screen against M. tuberculosis and used it as an example framework to build and optimize the software. Though specifically adapted to our own needs, it can be readily expanded for any small- to medium-throughput screening effort, parallel or conventional. Further, by virtue of the underlying Linux server, it can be easily adapted for chemoinformatic analysis of screens through packages such as OpenBabel. Overall, this setup represents an easy-to-use solution for streamlining processing and analysis of biological screening data, as well as offering a scaffold for ready functionality expansion.

CANEapp: a user-friendly application for automated next generation transcriptomic data analysis.

BackgroundNext generation sequencing (NGS) technologies are indispensable for molecular biology research, but data analysis represents the bottleneck in their application. Users need to be familiar with computer terminal commands, the Linux environment, and various software tools and scripts. Analysis workflows have to be optimized and experimentally validated to extract biologically meaningful data. Moreover, as larger datasets are being generated, their analysis requires use of high-performance servers.ResultsTo address these needs, we developed CANEapp (application for Comprehensive automated Analysis of Next-generation sequencing Experiments), a unique suite that combines a Graphical User Interface (GUI) and an automated server-side analysis pipeline that is platform-independent, making it suitable for any server architecture. The GUI runs on a PC or Mac and seamlessly connects to the server to provide full GUI control of RNA-sequencing (RNA-seq) project analysis. The server-side analysis pipeline contains a framework that is implemented on a Linux server through completely automated installation of software components and reference files. Analysis with CANEapp is also fully automated and performs differential gene expression analysis and novel noncoding RNA discovery through alternative workflows (Cuffdiff and R packages edgeR and DESeq2). We compared CANEapp to other similar tools, and it significantly improves on previous developments. We experimentally validated CANEapp’s performance by applying it to data derived from different experimental paradigms and confirming the results with quantitative real-time PCR (qRT-PCR). CANEapp adapts to any server architecture by effectively using available resources and thus handles large amounts of data efficiently. CANEapp performance has been experimentally validated on various biological datasets. CANEapp is available free of charge at http://psychiatry.med.miami.edu/research/laboratory-of-translational-rna-genomics/CANE-app.ConclusionsWe believe that CANEapp will serve both biologists with no computational experience and bioinformaticians as a simple, timesaving but accurate and powerful tool to analyze large RNA-seq datasets and will provide foundations for future development of integrated and automated high-throughput genomics data analysis tools. Due to its inherently standardized pipeline and combination of automated analysis and platform-independence, CANEapp is an ideal for large-scale collaborative RNA-seq projects between different institutions and research groups.

サーバ管理者養成を目的とした学習支援システムの開発と評価

サーバ管理者養成を目的とした学習支援システムの開発と評価

홍보 효과 증진을 위한 페이스북 팬페이지 분석 시스템 개발

소셜 네트워크 서비스의 등장과 급속한 성장은 정보의 생산과 소비로 이어지는 유통 프레임의 변화를 가져왔다. 소비자들은 소셜 네트워크를 통하여 다양한 정보를 빠르게 얻을 수 있게 되었고 기업은 소셜 네트워크를 홍보 채널로 활용하고 있다. 소셜 네트워크를 통한 홍보 활동의 효과를 높이기 위해서는 홍보 활동의 결과를 평가하고 분석하여 홍보 전략을 수립하고 적용하는 과정이 요구된다. 본 논문에서는 낮은 비용으로 소셜 네트워크를 통한 홍보 활동의 결과를 평가하고 분석할 수 있는 시스템 개발 방법을 제안한다. 리눅스 기반 서버에 MySQL 데이터베이스와 PHP를 이용하여 소셜 네트워크상의 대표적인 기업 홍보 채널인 페이스북 팬페이지 데이터를 수집하고 분석하는 시스템을 구축하고 운영하여 제안된 방법의 효율성을 검증하였다. Appearance and rapid growth of the social network services (SNS) have led to changes in the distribution structure of information. Consumers can obtain various information quickly via the social network services and companies make use of a new advertising channel in them. In order to increase the effect of publicity activities through the social network services, development and application of public relations strategy by evaluating and analyzing the results of the activities is required. In this paper, a method for developing a low cost system to evaluate and analyze the results of public relations through the social networks is proposed. The proposed method was verified through building and running a demo system to collect and analyze data in the Facebook fan pages using MySQL database and PHP script on a Linux server.

LTE 기반 모바일 DaaS 환경에서 비디오 스트리밍을 위한 Linux TCP 구현물의 실험적 성능 분석

Recent network environment has been rapidly evolved to cloud computing environment based on the development of the Internet technologies. Furthermore there is an increasing demand on mobile cloud computing due to explosive growth of smart devices and wide deployment of LTE-based cellular networks. Thus mobile Desktop-as-a-Service(DaaS) could be a pervasive service for nomadic users. In addition, video streaming traffic is currently more than two-thirds of mobile traffic and ever increasing. All such trends enable that video streaming in mobile DaaS could be an important concern for mobile cloud computing. It should be noted that the performance of the Transmission Control Protocol(TCP) on cloud host servers greatly affects Quality of Service(QoS) of video streams for mobile users. With widely deployed Linux server platforms for cloud computing, in this paper, we conduct an experimental analysis of the twelve Linux TCP variants in mobile DaaS environments. The results of our experiments show that the TCP Illinois outperforms the other TCP variants in terms of wide range of packet loss rate and propagation delay over LTE-based wireless links between cloud servers and mobile devices, even though TCP CUBIC is usually used in default in the current Linux systems.

리눅스 서버에서 인터렉티브 서비스 Stepping Stone 자가진단을 위한 brute-force 기법

인터넷을 통해 악의적으로 접근하는 공격자들은 자신의 노출을 최대한 감추기 위해 중간 호스트(소위, stepping stone으로 불림)를 경유한다. 본 논문에서는 텔넷, SSH, 그리고 rlogin 등 인터렉티브 서비스를 이용하여 리눅스 서버에 접근하여 다시 이러한 인터렉티브 서비스를 이용하여 다른 컴퓨터로 원격 접속을 시도하는 행위를 brute-force한 방법으로 검출하는 기법을 제안한다. 제안된 기법은 인터렉티브 서비스 데몬(Daemon) 프로세스의 시스템 콜(system call)을 감시하여 stepping stone 여부를 진단하기 때문에 ssh 접속과 같은 암호화 연결에서 대해서도 완벽한 검출 결과를 제공할 수 있다. 본 논문에서는 ptrace 시스템 콜과 간단한 쉘 스크립트를 작성하여 제안된 기법을 CentOS 6.5 64비트 환경에서 실질적으로 구현하였다. 마지막으로 몇몇 실험 시나리오를 대상으로 실시한 현장 운영을 통해 제안된 brute-force 기법을 검증하였다. In order to hide their identities, intruders on the Internet often attack targets indirectly by staging their attacks through intermediate hosts known as stepping stones. In this paper, we propose a brute-force technique to detect the stepping stone behavior on a Linux server where some shell processes remotely logged into using interactive services are trying to connect other hosts using the same interactive services such as Telnet, Secure Shell, and rlogin. The proposed scheme can provide an absolute solution even for the encrypted connections using SSH because it traces the system calls of all processes concerned with the interactive service daemon and their child processes. We also implement the proposed technique on a CentOS 6.5 x86_64 environment by the ptrace system call and a simple shell script using strace utility. Finally the experimental results show that the proposed scheme works perfectly under test scenarios.

Energy‐efficient CPU frequency control for the Linux system

SummaryEfficiency of energy usage in computing systems improves, however, still not at the rate matching the climbing demand for computing capacity. To address this urging problem, computing elements of the latest generation, that is, CPUs/graphics processing units, memory units, and network interface cards, have been designed to operate in multiple modes with differentiated energy consumption levels. Mode switching and high‐frequency performance monitoring functions have also been exposed by co‐designed abstract programming interfaces. The challenge of energy‐efficient computing is to develop hardware control mechanisms taking advantage of the new capabilities. This paper aims at giving an insight into the structure of optimal energy‐aware CPU frequency scaling rules. It gives a characterization of solutions to the optimal control problem of energy‐efficient real‐time packet inspection performed by a Linux server. A class of CPU frequency switching rules, exploiting dynamic voltage and frequency scaling mechanisms, is constructed based on experimentally identified model of server operations. The control rules are demonstrated to outperform the default CPU frequency scaling governor for the Linux kernel, both in terms of achievable power savings and service quality. Copyright © 2015 John Wiley & Sons, Ltd.

Impact of Developer Choices on Energy Consumption of Software on Servers

The power cost of running a data center is a significant portion of its total annual operating budget. With the aim of reducing power bills of data centers, “Green Computing” has emerged with the primary goal of making software more energy efficient without compromising the performance. Developers play an important role in controlling the energy cost of data center software while writing code. In this paper, we show how software developers can contribute to energy efficiency of servers by choosing energy efficient APIs (Application Programming Interface) with the optimal choice of parameters while implementing file reading, file copy, file compression and file decompression operations in Java; that are performed extensively on large scale servers in data centers. We performed extensive measurements of energy cost of those operations on a Dell Power Edge 2950 machine running Linux and Windows servers. Measurement results show that energy costs of various APIs for those operations are sensitive to the bu ff er size selection. The choice of a particular Java API for file reading with different buffer sizes has significant impact on the energy cost, giving an opportunity to save up to 76%. To save energy while copying files, it is important to use APIs with tunable buffer sizes, rather than APIs using fixed size buffers. In addition, there is a trade off between compression ratio and energy cost: because of more compression ratio, xz compression API consumes more energy than zip and gzip compression APIs. Finally, we model the energy costs of APIs by polynomial regression to avoid repeated measurements.

The Multi-Server Load Balancing Systems Research in Large-Website Construction

The load balancing method based on the Linux server cluster is proposed in large-website construction. The load balancing of server cluster is achieved by SSH framework, Oracle database and Ajax technologies. The load balancing of server cluster method can’t only improve performance, scalability, availability of system and reduce the execution time of multi-tasking but also eliminates network bottlenecks and improve the flexibility and reliability of the network. In order to verify the validity of the algorithm, large number of experimental data is used in the experiment. We propose a method of load balancing algorithm is compared with the traditional non-load-balancing algorithm for CPU utilization and system response time in the experiments. The experimental results show that the load balancing technology can reduce system response time and CPU utilization of server.

Demonstrations of Efficient Online Spectrum Defragmentation in Software-Defined Elastic Optical Networks

Elastic optical networks (EONs) facilitate agile spectrum management in the optical layer. When coupling with software-defined networking, they function as software-defined EONs (SD-EONs) and provide service providers more freedom to customize their infrastructure dynamically. In this paper, we investigate how to overcome spectrum fragmentation in SD-EONs with OpenFlow-controlled online spectrum defragmentation (DF), and conduct system implementations to facilitate highly-efficient online DF. We first consider sequential DF, i.e., the scenario that involves a sequence of lightpath reconfigurations to progressively consolidate the spectrum utilization. We modify our previous DF algorithm to make sure that the reconfigurations can be performed in batches and the “make-before-break” scheme can be applied to all of them. The modified algorithm is implemented in an OpenFlow (OF) controller, and we design OF extensions to facilitate synchronous batch reconfiguration. Then, we further simplify the DF operations by designing and implementing parallel DF that can accomplish all the DF-related lightpath reconfigurations simultaneously. All these DF implementations are experimentally demonstrated in an SD-EON control plane testbed that consists of $14$ stand-alone OF agents and one OF controller, which are all implemented based on high-performance Linux servers. The experimental results indicate that our OF-controlled online DF implementations perform well and can improve network performance in an efficient way.

APLIKASI SETTING DNS SERVER BERBASIS WEB PADA LINUX UBUNTU SERVER

With many Linux Operating System, automatically many Linux users. From the start of the installation of the Operating System, Linux has 2 modes for zoom (Interface), the TEXT mode and mode GUI (Graphic User Interface). To TEXT mode is usually used for servers that promotes speed and efficiency of hard drive capacity. For GUI mode is used for desktop computers, because it is easy to operate with excellence zoom an image. Based on the above background, it is concluded several issues, among others: 1.Bagaimana how application installation on Linux Ubuntu Server? 2.Bagaimana how to configure Ubuntu Server Linux server remotely? 3Bagaimana how WEB-based DNS server settings on Ubuntu Linux Server? The purpose of the study is as follows: 1.Mempermudah setting up a server without having to be in front of the server machine. 2.Mensetting server does not use the text but using the GUI. 3. No need additional applications, just using the WEB Browser to run it. Keywords : Ubuntu, mode text, mode gui, DNS, Web Server

NTP DRDoS Attack Vulnerability and Mitigation

The Network Time Protocol (NTP) is used to synchronize clocks of various computer devices such as personal computers, tablets, and phones based their set time zones. The network of devices that use these NTP servers form a huge distributed network that attracted a number of attacks from late 2013 towards early 2014. This paper presents a hands-on test of the Distributed Reflection Denial of Service (DRDoS) attack by the monlist command, provides more vulnerability in the protocol, and offers mitigation to these vulnerabilities. A Kali Linux server was used to test the monlist command on its localhost. The results showed that a request with a size of 234 bytes got a response of 4,680 bytes. A busy NTP server can return up to 600 addresses which were theoretically calculated to return approximately 48 kilobytes in 100 packets. Consequently, this results in an amplification factor of 206×. The knowledge of the way the attack can be propagated was an important step in thwarting the attack and mitigating more such threats in the same protocol.

Poster - Thur Eve - 52: A Web-based Platform for Collaborative Document Management in Radiotherapy

We describe DepDocs, a web-based platform that we have developed to manage the committee meetings, policies, procedures and other documents within our otherwise paperless radiotherapy clinic. DepDocs is essentially a document management system based on the popular Drupal content management software. For security and confidentiality, it is hosted on a linux server internal to our hospital network such that documents are never sent to the cloud or outside of the hospital firewall. We used Drupal's in-built role-based user rights management system to assign a role, and associated document editing rights, to each user. Documents are accessed for viewing using either a simple Google-like search or by generating a list of related documents from a taxonomy of categorization terms. Our system provides document revision tracking and an document review and approval mechanism for all official policies and procedures. Committee meeting schedules, agendas and minutes are maintained by committee chairs and are restricted to committee members. DepDocs has been operational within our department for over six months and has already 45 unique users and an archive of over 1000 documents, mostly policies and procedures. Documents are easily retrievable from the system using any web browser within our hospital's network.

NEMiD: A Web-Based Curated Microbial Diversity Database with Geo-Based Plotting

The majority of the Earth's microbes remain unknown, and that their potential utility cannot be exploited until they are discovered and characterized. They provide wide scope for the development of new strains as well as biotechnological uses. The documentation and bioprospection of microorganisms carry enormous significance considering their relevance to human welfare. This calls for an urgent need to develop a database with emphasis on the microbial diversity of the largest untapped reservoirs in the biosphere. The data annotated in the North-East India Microbial database (NEMiD) were obtained by the isolation and characterization of microbes from different parts of the Eastern Himalayan region. The database was constructed as a relational database management system (RDBMS) for data storage in MySQL in the back-end on a Linux server and implemented in an Apache/PHP environment. This database provides a base for understanding the soil microbial diversity pattern in this megabiodiversity hotspot and indicates the distribution patterns of various organisms along with identification. The NEMiD database is freely available at www.mblabnehu.info/nemid/.