Linux Scripts Research Articles

ChronoBak: Automated cost-effective incremental backup software for large-scale data

Background: Data backup is an important component of data protection and management. It is especially imperative to back up large-scale data to guard against losses due to hardware failure, unauthorized access, software/system malfunction, and unintended deletion. However, businesses and organizations suffer from the financial investment required for data backup and recovery systems. Health-care systems suffer from data breaches and hacking incidents, which increase annually. Therefore, a cost-effective and highly secure backup approach is necessary. Methods: Seven different backup scripts were written in bash within Linux, and Crontab was used as the core chronological scheduler to execute the backup scripts on specific dates and times. These bash scripts, together with Crontab as their scheduler, were used to implement automated incremental backups on a Unix/Linux-based system. Results: ChronoBak is a collection of bash scripts that are compiled and executed through Crontab, which is a standard Unix/Linux function used to schedule hourly, daily, weekly, and monthly maintenance routines using Linux scripts. This strategy enabled us to implement cost-effective incremental backups within any time range. Conclusion: We developed ChronoBak software, which executes an automated incremental backup that is scheduled efficiently and systematically using standard and hidden directories, thereby providing an additional layer of security against cyber threats and system malfunctions.

Controlling user access with scripting to mitigate cyber-attacks

With the growing threats in the dynamic digital landscape, organizations are grappling with the difficult task of managing cyber-attacks by restricting user accessibility to most communication systems. This study aimed to develop a Linux script as a proactive response to the growing of cyber-attacks in organizational settings to prevent attacking vectors based on user negligence. The primary objective was to devise inventive solutions through script automation to restrict user access to the organizational network within predefined time frames, thereby mitigating potential cyber threats. The criteria used to define predefined time frames for user access, include the restriction of users on off duty times, The scripting seeks to address cyber-attacks targeted such as cross-site scripting (XSS) and SQL injection. To achieve the goal of this paper, the necessary steps and logic required to develop the scripts were taken. For instance, there are several suitable languages such as Bash, Python, or Perl, that can be used to write script. The paper selected Bash because it excels at scripting existing command-line tools and utilities, making it a great choice for automating tasks by using Vim text editor tool. The final scripts were run, some errors were identified, and modified as needed to ensure it worked correctly. This phase was necessary to improve the script's performance, readability, and maintainability by refining code, using efficient algorithms, by incorporating best practices. Finally, the various user inputs and scenarios were deployed to put the script into production for user access management. The adopted script metrics deployed such as Script Execution Time, Resources Utilization, Success Rate and Error Rate helped in evaluating the performance, efficiency, and effectiveness of the scripts. The implementation of the script achieved an executive time of 0.032 s, success rate was 1 and error rate was 0. The practical implementation in organizations can be scaled up or down depending on the organization's size and infrastructure. The compatibility of the developed Linux script with different operating systems, hardware platforms and network architectures will have no impact in adapting to various organizational environments. The script did not show any challenges, but real-world deployment may exhibit some potential challenges and limitations that may be associated with implementing the solution, such as resource constraints and legacy system compatibility.

Acetyl‐CoA Electron Density: Acyl‐CoA Reactivity and Crystallographic Data

Acetyl‐CoA and other acyl‐CoAs are the building blocks used in carbon‐carbon bond forming reactions underlying fatty acid and polyketide biosynthesis and many other biological activities. Since many enzymes use acetyl‐CoA, understanding how the substrate binds in the active site is key to determining interactions leading to enzymatic catalysis and substrate selectivity. We examined all of the PDB deposited crystal structures that report acetyl‐CoA bound and report stats for the reactive acetyl‐thioester moiety. We quantified this data by generating the real‐space R‐factor (RSR) and real‐space correlation coefficient (RSCC) by running a few rounds of refinement with Refmac to normalize the data. We examined the modeled thioester ends in comparison to the rest of CoA by creating a Linux script that splits acetyl‐CoA into the nucleic acid, pantetheine, and acetyl‐thioester moieties. We also analyzed the 3’phosphate of acetyl‐CoA to examine how splitting the molecule affects the RSR/RSCC values of small portions of the molecules along with the ribonucleotide containing substrates NAD+, NADH, NADP, and NADPH. Preliminary analysis of the output data reveals the nucleic acid and pantetheine RSR/RSCC values indicate good fits of models to electron density, but there is a portion of structures where RSR/RSCC values indicate the acetyl‐thioester moiety is poorly fit. We also find that the RSR method of calculation shows a significant difference between the acetyl‐CoA thioester and the 3’phosphate where the 3’phosphate is better than the average of the entire structure while the thioester is poorly fit. This is also consistent with the RSR values of NADP and NADPH 3’ phosphates. Conversely, the RSCC values of the acetyl‐CoA thioester end and the 3’phosphate were both equally lower than the entire structure. It appears there is an overfitting of the acetyl‐thioester fitting in crystal structures, likely due to a pressure to claim mechanistic inference from the structures.

Magnetohydrodynamic equations (MHD) generation code

A program to generate codes in Fortran and C of the full magnetohydrodynamic equations is shown. The program uses the free computer algebra system software REDUCE. This software has a package called EXCALC, which is an exterior calculus program. The advantage of this program is that it can be modified to include another complex metric or spacetime. The output of this program is modified by means of a LINUX script which creates a new REDUCE program to manipulate the magnetohydrodynamic equations to obtain a code that can be used as a seed for a magnetohydrodynamic code for numerical applications. As an example, we present part of the output of our programs for Cartesian coordinates and how to do the discretization.

TCP based-user control for adaptive video streaming

Nowadays, Media streaming services over TCP have become very popular because of the TCP's reliability, which provides remarkable stability to the Internet. However, in order to offer a high media quality and a good user satisfaction, the media streaming service requires that transport protocols can be adapted continuously with the network parameters. However, the diversity, of terminals (i.e., tablet, smart phones, laptop ź etc.) and their corresponding capabilities, means that users' agnostic solutions are inefficient to cope with such diverse contexts. Indeed, the intrinsic characteristics and parameters of the terminal users (i.e., devices) need to be taken into account on the video streaming adaptation process. The classic adaptive video streaming services do not consider the user parameters on the adaptation process. In this paper, we propose an adaptive video streaming solution to improve the user satisfaction factor by adapting the TCP parameters according to the user's parameters on mobile networks. The user satisfaction factor is calculated according to some metrics driven from the user's quality of experience (QoE). The work is validated through our proposal based on a new mobile agent (which does all the work) developed on a Linux script platform and tested on different kinds of devices with different scenarios.

YPHON: A package for calculating phonons of polar materials

In our recent works, we have developed a mixed-space approach within the framework of direct method for the first-principle calculation of phonon properties. It makes full use of the accuracy of the force constants calculated in the real space and the dipole–dipole interactions in the reciprocal space, making the accurate phonon calculation possible with the direct method for polar materials. In this paper, an efficient C++ implementation of the mixed-space approach, YPHON, is provided as open source, including demos and Linux scripts for extracting input data to YPHON from the output of VASP.5. The functions of the current package include the calculations of: (1) the phonon dispersions; (2) the phonon density of states; (3) the neutron scattering section weighted phonon density of state; (4) the phonons of the high symmetry structure using the force constants from low symmetry structure; (5) the phonon dispersions of random alloys; and (6) the analysis of the vibrational modes using the point group theory. Program summaryProgram title: YPHONCatalogue identifier: AETS_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AETS_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 567815No. of bytes in distributed program, including test data, etc.: 9763594Distribution format: tar.gzProgramming language: C++, Linux scripts.Computer: Linux systems with a g++ or C++ compiler.Operating system: Linux.RAM: Ranges from a few Mbytes to a few Gbytes, dynamically depending on the system size.Classification: 7.8.External routines: GSL—the GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. VASP.5 or later for the calculations of force constants and dielectric constants and Born effective charge for polar materials.Nature of problem:This package has the purpose of computing accurately phonon properties of polar materials within the small displacement approach.Solution method:Mixed-space approach to the vibration-induced dipole–dipole interaction.Running time:In the scale of a common Linux command.

A package of Linux scripts for the parallelization of Monte Carlo simulations

Despite the fact that fast computers are nowadays available at low cost, there are many situations where obtaining a reasonably low statistical uncertainty in a Monte Carlo (MC) simulation involves a prohibitively large amount of time. This limitation can be overcome by having recourse to parallel computing. Most tools designed to facilitate this approach require modification of the source code and the installation of additional software, which may be inconvenient for some users. We present a set of tools, named clonEasy, that implement a parallelization scheme of a MC simulation that is free from these drawbacks. In clonEasy, which is designed to run under Linux, a set of “clone” CPUs is governed by a “master” computer by taking advantage of the capabilities of the Secure Shell (ssh) protocol. Any Linux computer on the Internet that can be ssh-accessed by the user can be used as a clone. A key ingredient for the parallel calculation to be reliable is the availability of an independent string of random numbers for each CPU. Many generators—such as RANLUX, RANECU or the Mersenne Twister—can readily produce these strings by initializing them appropriately and, hence, they are suitable to be used with clonEasy. This work was primarily motivated by the need to find a straightforward way to parallelize PENELOPE, a code for MC simulation of radiation transport that (in its current 2005 version) employs the generator RANECU, which uses a combination of two multiplicative linear congruential generators (MLCGs). Thus, this paper is focused on this class of generators and, in particular, we briefly present an extension of RANECU that increases its period up to ∼ 5 × 10 27 and we introduce seedsMLCG, a tool that provides the information necessary to initialize disjoint sequences of an MLCG to feed different CPUs. This program, in combination with clonEasy, allows to run PENELOPE in parallel easily, without requiring specific libraries or significant alterations of the sequential code. Program summary 1