Linux Commands Research Articles

HMM-Based Blockchain Visual Automatic Deployment System

The traditional blockchain deployment process is too complicated and has high technical requirements for blockchain deployers. Deploying a blockchain requires building a complex software-dependent environment, being able to use Linux commands for cumbersome parameter configurations, as well as the need to consider whether the hardware meets the requirements for running a blockchain. To address these current challenges in blockchain deployment both domestically and internationally, a web-based automatic deployment system with an interactive front-end and back-end has been developed. This system streamlines the process by automatically configuring and deploying blockchains while providing deployers with a graphical interface to monitor the entire deployment procedure. Meanwhile, in order to improve the efficiency of blockchain deployment, a Hidden Markov Model has been designed for blockchain deployment, which can predict the best deployment method for blockchain deployment under the current software environment. As one of the excellent blockchain platforms in China, Chainmaker has the outstanding features of independent control, flexible assembly, software and hardware integration, open source, and openness. The system takes Chainmaker as an experimental object and after a lot of tests, it can easily build a blockchain network on the server.

Step-by-Step Bacterial Genome Comparison.

Thanks to advancements in genome sequencing and bioinformatics, thousands of bacterial genome sequences are available in public databases. This presents an opportunity to study bacterial diversity in unprecedented detail. This chapter describes a complete bioinformatics workflow for comparative genomics of bacterial genomes, including genome annotation, pangenome reconstruction and visualization, phylogenetic analysis, and identification of sequences of interest such as antimicrobial-resistance genes, virulence factors, and phage sequences. The workflow uses state-of-the-art, open-source tools. The workflow is presented by means of a comparative analysis of Salmonella enterica serovar Typhimurium genomes. The workflow is based on Linux commands and scripts, and result visualization relies on the R environment. The chapter provides a step-by-step protocol that researchers with basic expertise in bioinformatics can easily follow to conduct investigations on their owngenome datasets.

Turnstile File Transfer: A Unidirectional System for Medium-Security Isolated Clusters

Data transfer between isolated clusters is imperative for cybersecurity education, research, and testing. Such techniques facilitate hands-on cybersecurity learning in isolated clusters, allow cybersecurity students to practice with various hacking tools, and develop professional cybersecurity technical skills. Educators often use these remote learning environments for research as well. Researchers and students use these isolated environments to test sophisticated hardware, software, and procedures using full-fledged operating systems, networks, and applications. Virus and malware researchers may wish to release suspected malicious software in a controlled environment to observe their behavior better or gain the information needed to assist their reverse engineering processes. The isolation prevents harm to networked systems. However, there are times when the data is required to move in such quantities or speeds that it makes downloading onto an intermediate device untenable. This study proposes a novel turnstile model, a mechanism for one-way file transfer from one enterprise system to another without allowing data leakage. This system protects data integrity and security by connecting the isolated environment to the external network via a locked-down interconnection. Using medium-security isolated clusters, the researchers successfully developed a unidirectional file transfer system that acts as a one-way “turnstile” for secure file transfer between systems not connected to the internet or other external networks. The Turnstile system (source code available at github.com/monnin/turnstile) provides unidirectional file transfer between two computer systems. The solution enabled data to be transferred from a source system to a destination system without allowing any data to be transferred back in the opposite direction. The researchers found an automated process of transferring external files to isolated clusters optimized the transfer speed of external files to isolated clusters using Linux distributions and commands.

Leveraging Browser-Based Virtual Machines to Teach Operating System Fundamentals

In this paper, we identify challenges in delivering cybersecurity labs, including the overhead costs of delivering virtual machines to students. We propose instead to use JavaScript driven Browser-Based Virtual Machines (BBVMs) to overcome the challenges of Type I and II hypervisors, as well as vendor- specific cybersecurity lab ranges. BBVMs deliver configured VMs at lower cost to the student’s web browser and are much easier for students to use. BBVMs require no hardware or infrastructure for students besides an Internet-connected device. As such, labs delivery via BBVMs can be run on mobile phones, tablets, or computers with limited resources. With this in mind, the authors detail BBVM implementation for cybersecurity labs. With very little physical infrastructure, programming, and systems administration, an educational institution at any level may implement a cybersecurity lab in such an environment. Our examples focus on addressing learning the Linux command line, introducing different Linux commands, and deepen student understanding of the Linux operating system itself. We combine BBVMs with previous work to address configuration, repeatability, assessment, academic integrity/cheating, and other similar constraints using our polymorphic configuration methodology called PolyLab. Lastly, we include a step-by-step procedure to implement BBVMs and show use-cases for cybersecurity education.

Experiences of Library Professionals on DSpace Installation

DSpace, a free and open-source software (FOSS) provides the digital platform for building collections of an institution. Due to the lack of the skills to install and configure DSpace, librarians are incapable to conduct it even after the awareness about it. Identifying challenges about DSpace installation is vital to increase its use by librarians. Hence, it aims to explore the understanding of DSpace installation among librarians and to identify aspects of their experiences and feelings while installing DSpace. Librarians' experiences and feelings are important for accepting the software. Librarians were interviewed during the training program conducted on digital library technology from December 2020 to January 2021. Two groups were distinguishing from each other: one is with a library science background and another is with computer science and engineering background. The second group aswas self-sustained to install DSpace, once they got the guidelines for installation. Their views were reflected with the code terms status, exploration, feeling, activities, preferences, and inadequacy. Through their experiences, the aspects of challenges are the less experience of using the command line in computer use, the unavailability of teaching courses on Linux operating system in Library and Information Science (LIS) education, and the lack of self-exploration habits. Practice to Linux commands, incorporate the Linux in the Library Science course, self-exploration, and consistent effort will help librarians in installing DSpace by themselves. Finally, librarians should internalize their goal to act as the administrator for the DSpace, not only as of the operator.

Extraordinary Command Line: Basic Data Editing Tools for Biologists Dealing with Sequence Data

The command line is a standard way of using the Linux operating system. It contains many features essential for efficiently handling data editing and analysis processes. Therefore, it is very useful in bioinformatics applications. Commands allow for rapid manipulation of large ASCII files or very numerous files, making basic command line programming skills a critical component in modern life science research. The following article is not a guide to Linux commands. In this manuscript, in contrast to many various Linux manuals, we aim to present basic command line tools helpful in handling biological sequence data. This manuscript provides a collection of simple and popular hacks dedicated to users with very basic experience in the area of the Linux command line. It includes a description of data formats and examples of editing of four types of data formats popular in bioinformatics applications.

Anomaly Detection in Control Data of Programming Execution by Context Sensitive Hidden Markov Model

The inconsistency is a major problem in security of information in computer is two ways: data inconsistency and application inconsistency. These two problems are raised due to bad structure of design in programming and create security breaches, vulnerable entries by exploiting application codes. So we can discover these anomalies by design of anomaly detection system (ADS) models at system programming (coding) levels with the help of machine learning. The security vulnerabilities (anomalies) are frequently occurred at potential code execution by exploitation or manipulation of instructions. So, in this paper we have specified various forms of extensions to our work to detect wide range of anomalies at coding exploits and use of a machine learning technique called Context Sensitive-Hidden Markov Model (CS-HMM) will improve the overall performance of ADS by discovering the correlations between control data instances. In this paper we are going to use Linux OS tracing kits to collect the necessary information such as control data instances (return addresses) collected from system as part of artificial learning. The results evaluated through practice on various programs developed for work and also uses of some Linux commands for tracing, finally compared performance of all those input datasets generated live (artificially). After that, the CS-HMM is applying to datasets to scrutinize the anomalies with similarity-search and correlation of function control data of program and classification process determines the anomalous outcomes.

Bioinformatics: the Power of Computers in Biology – a Practical Guide

This Practical Guide in the Bringing Bioinformatics into the Classroom series introduces simple bioinformatics approaches for database searching and sequence analysis. A ‘mystery’ gene is used as an exemplar: we first characterise the gene, then use it to explore the impact of gene loss in humans. Analyses are run both online and at the command line, the latter using Raspberry Pi computers running the 4273π variant of Linux ( 4273pi.org ). Specifically, this Guide introduces a popular Web-based tool for searching biological sequence databases, and shows how similar functionality can be achieved using the Linux command line. On reading the Guide and completing the exercises, users will be able to: search biological sequence databases using the online program BLAST, and navigate GenPept sequence records; execute some basic Linux commands to perform a set of simple file-manipulation tasks; perform BLAST searches via the Linux command line; and evaluate the biological implications of search results, with reference to mutations and function.

The effects of gamification elements in e-learning platforms

Gamification to perform tedious tasks in an enjoyable way is used in e-learning systems. This study examines in what manner gamification elements affect the e-learning experience in software studies. Two similar e-learning platforms were developed with the aim to teach basic Linux commands, one of them including gaming elements. One group (92 participants) studied using the gamified platform, and another group (47) using a non-gamified platform. The findings show that although the exam grades were not statistically different between the groups, the motivation to learn and continue learning after this experience was higher in the group using a gamified e-learning platform.

Penetration Testing Exploitation of Windows XP SP0

A penetration test is performed on an operating system with the expectation of discovering security weaknesses and exploiting target OS. The goal of this testing is to find all security vulnerabilities without any type of actually harming the computer system. In this research paper, we discuss the some phases of penetration testing on operating system. We are using some tools and techniques to penetrate the target system by using Nmap, Metasploit (msfconsole) and Meterpreter. We will make remove folders in host OS and also make and delete folders to the target OS through LINUX commands. And we will shut down the target operating system with using Linux commands. In this, we are using penetration testing tool to attack on particular operating system and to scan and also exploiting target OS. In the previous research paper, we had performed the work on scanning the target operating system with reconnaissance tool Nmap. In this research paper, we will work only on exploitations of our target operating system with Windows XP SP0 “Service Pack”. Keywords: Penetration Testing, VMware, Kali Linux, Nmap, Scanning, Metasploit, Meterpreter, Exploitation, msfconsole.

Raspberry Pi Touchscreen Tablet (Pi-Pad)

The Raspberry Pi is a credit card sized single-board computer developed in UK by Raspberry Pi foundation with the intention of promoting the teaching of basic computer science in school. Now a days none of the tablets that are available in the market are of Linux OS. In this paper we showcase our attempt at building a low cost stand-alone device called Pi-pad which is very much helpful for educational purpose using the Raspberry Pi as its brain with Bluetooth for connecting peripherals and communicating with local devices like Wi-Fi, keyboard and mouse. It has a touch screen display providing a user interface. The Raspberry Pi Tablet is controlled by a modified version of Debain Linux called Raspbian Wheezy OS optimized for the ARM architecture. The display contains a graphical interface which provides various fields for data entry via onscreen keyboard. Also, in this paper we use Linux commands and python programming for operating and interfacing the hardware. Keywords—Raspberry pi; Linux OS; Python; Wi-fi; ARM; Raspbian; Touchscreen. __________________________________________________*****_______________________________________________

Abstract C04: Comparative analysis of bioinformatic tools for the detection of viral DNA sequences in tumor cells

Abstract Cancer health disparities exist among different ethnicities and races. Various factors such as lifestyle, environmental exposure, genetics, and epigenetics are thought to play a role in the existence of these disparities. Viruses, which outnumber cells in the human body by 100-fold, have a major impact on human health. Viruses have been estimated to cause 15-20% of human cancers, and we expect that some of these oncogenic viruses may have the potential to impact health disparities. Next generation sequencing (NGS) technologies are being used to investigate novel virus-cancer associations and interactions, and several bioinformatics tools for the detection and analysis of virus sequences in human NGS data have recently become available. These tools have not been validated, however, for use in human cancers with extremely low levels of viral sequences. In this study, we have compared the sensitivity and specificity of READSCAN to a manually constructed analysis workflow in a common, commercial NGS web application. READSCAN is a freely available software application that utilizes automated “digital subtraction” to eliminate host reads and identify specific virus sequences in NGS data. The functionality of this tool was compared to a workflow constructed within the web interface for the commercially available NGS software Partek. This constructed workflow first subtracted human sequences and then aligned the remaining sequences against select viral genomes. The sensitivity of the various tools was compared using NGS data obtained from human cytomegalovirus (HCMV) infected cells. Specificity of the tools was determined by analyzing the same data set against the Epstein-Barr virus (EBV) and Human Papilloma virus type 16 (HPV-16). Partek and READSCAN detected 69.66% and 60.54% of the input number of reads as HCMV sequences. Under these conditions, neither bioinformatics tool detected EBV or HPV16 specific reads in the HCMV infected cell data. This indicated that both Partek and READSCAN were capable of readily detecting the presence of large amounts of virus reads in NGS data from infected cells in a specific manner. In order to test the ability of these tools to detect viral specific reads in NGS data from tumors, data obtained from the HPV16 positive cervical squamous cell carcinoma cell line SiHa were analyzed. Both Partek and READSCAN detected six reads out of 969,798 total reads as HPV16 sequences; EBV or HCMV sequences were not detected. Our results are in agreement with previously published observations for this SiHa cell line, in which five HPV16 specific reads were detected. While we are still in the process of testing additional bioinformatics tools and configurations, our results attest that the open–source bioinformatics tool READSCAN and the commercially available Partek are comparable in performance, but differ in utility. Partek is faster, has a user-friendly interface, and a knowledge of Linux commands is not required. READSCAN lacks these features, but it is free and has an algorithm more clearly proscribed in the literature for digital subtraction. Next steps include utilizing a wider range of digital subtraction software, evaluating a broader range of NGS data from demographically diverse origins, and investigating discordance as it is found between alternative tools and configuration parameters. Ultimately, an ensemble of tools and configuration contexts is expected to yield critical information on the role of viruses in cancer and associated health disparities Citation Format: Barbara Swanson, Scott Harrison, Dukka KC, Perpetua Muganda. Comparative analysis of bioinformatic tools for the detection of viral DNA sequences in tumor cells. [abstract]. In: Proceedings of the Sixth AACR Conference: The Science of Cancer Health Disparities; Dec 6–9, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2014;23(11 Suppl):Abstract nr C04. doi:10.1158/1538-7755.DISP13-C04

A practical guide to linux commands, editors, and shell-programming, third edition by Mark G. Sobell

A practical guide to linux commands, editors, and shell-programming, third edition by Mark G. Sobell