Bash Script Research Articles

Exploitation with Reverse_tcp Method on Android Device using Metasploit

Android is a popular operating system on smartphone which run on linux kernel. Android operating system allows developers to access and modify source code, but this advantage also increases the security issue. One of the various attack is exploit, that many attacker carry out this type of attack to get sensitive user information. In this research, exploit attacks are done used some tool such as metasploit framework and this experiment is done on android device which one be a target attack. The result obtained from this exploit attack in the form of an understanding of how to conduct exploit attack, analyze the interaction of attacker with victim, analyze the workings of exploit attack and how long will it take to set up a payload with bash script shell. All the details of the analyze will give us the conclusions and strategies to make the android operating system more secure.

A Machine Learning-based Pipeline for the Classification of CTX-M in Metagenomics Samples

Bacterial infections are a major global concern, since they can lead to public health problems. To address this issue, bioinformatics contributes extensively with the analysis and interpretation of in silico data by enabling to genetically characterize different individuals/strains, such as in bacteria. However, the growing volume of metagenomic data requires new infrastructure, technologies, and methodologies that support the analysis and prediction of this information from a clinical point of view, as intended in this work. On the other hand, distributed computational environments allow the management of these large volumes of data, due to significant advances in processing architectures, such as multicore CPU (Central Process Unit) and GPGPU (General Propose Graphics Process Unit). For this purpose, we developed a bioinformatics workflow based on filtered metagenomic data with Duk tool. Data formatting was done through Emboss software and a prototype of a workflow. A pipeline was also designed and implemented in bash script based on machine learning. Further, Python 3 programming language was used to normalize the training data of the artificial neural network, which was implemented in the TensorFlow framework, and its behavior was visualized in TensorBoard. Finally, the values from the initial bioinformatics process and the data generated during the parameterization and optimization of the Artificial Neural Network are presented and validated based on the most optimal result for the identification of the CTX-M gene group.

NaRIBaS—A Scripting Framework for Computational Modeling of Nanomaterials and Room Temperature Ionic Liquids in Bulk and Slab

Computational modeling is more and more often used in studies of novel ionic liquids. The inevitable side-effect is the growing number of similar computations that require automation. This article introduces NaRIBaS (Nanomaterials and Room Temperature Ionic Liquids in Bulk and Slab)—a scripting framework that combines bash scripts with computational codes to ease modeling of nanomaterials and ionic liquids in bulk and slab. NaRIBaS helps to organize and document all input and output data, thus, improving the reproducibility of computations. Three examples are given to illustrate the NaRIBaS workflows for density functional theory (DFT) calculations of ionic pairs, molecular dynamics (MD) simulations of bulk ionic liquids (ILs), and MD simulations of ILs at an interface.

The onboard software of the EUSO‐SPB pathfinder experiment

SummaryIn this paper, the flight software architecture of the EUSO‐SPB mission is described. The JEM‐EUSO program aims at developing an advanced large space‐borne UV telescope designed to detect ultra high energy cosmic rays. In this framework, the EUSO‐SPB experiment is the third pathfinder mission of the JEM‐EUSO program, the second that has been launched on a stratospheric balloon to test the technological readiness of the detectors and to carry out some preliminary scientific observations. The EUSO‐SPB software has a modular structure conceived to control all the instruments and the ancillary subsystems, to acquire data, and to manage data transfer to ground. System programming in C and C++ languages and Bash scripts have been used to implement and run the modules. The software runs on the data processor, an onboard computer that communicates with several payload blocks, the UV sensor, and the synchronization and time tagging board. The control software module controls all the subsystems, provides communication to ground through the NASA telemetry or the Internet, runs the acquisition control and download software, and manages the execution of the acquisition software. The acquisition software module directly operates the subsystems for the data acquisition activity. The acquisition control and download software module runs the acquisition software upon request of the control software and transfers scientific data to ground. The software system performed as expected during the flight on April 2017.

PWR advanced fuel high burnup-dependent xenon oscillation controllability assessment

The controllability of xenon oscillations in a Pressurized Water Reactor (PWR) fuel assembly was evaluated using the MCNP and ORIGEN-2 codes. Burnup-dependent symmetrical cosine depleted nuclide profiles were generated for advanced high burnup uranium oxide (UO2) and mixed oxide (MOX) fuels. A Monte Carlo burnup coupling BASH script (MCOS) was used to calculate burnup-dependent neutron Fission Tally and 135Xe axial relative oscillation profiles. Burnup-dependent xenon oscillation controllability was then assessed for the advanced high-burnup UO2 and MOX fuels using MCOS-calculated xenon reactivity worth swing bands (ΔK) with respect to the mean. The advanced fuels xenon oscillation bands ΔK are bounded by the typical PWR uranium oxide fuel with 235U enrichment of 3.0 wt%. It has demonstrated that the typical PWR full/partial length control rod banks system’s reactivity can adequately control the high burnup advanced fuels xenon oscillation in full power operation.

SL-quant: a fast and flexible pipeline to quantify spliced leader trans-splicing events from RNA-seq data.

BackgroundThe spliceosomal transfer of a short spliced leader (SL) RNA to an independent pre-mRNA molecule is called SL trans-splicing and is widespread in the nematode Caenorhabditis elegans. While RNA-sequencing (RNA-seq) data contain information on such events, properly documented methods to extract them are lacking.FindingsTo address this, we developed SL-quant, a fast and flexible pipeline that adapts to paired-end and single-end RNA-seq data and accurately quantifies SL trans-splicing events. It is designed to work downstream of read mapping and uses the reads left unmapped as primary input. Briefly, the SL sequences are identified with high specificity and are trimmed from the input reads, which are then remapped on the reference genome and quantified at the nucleotide position level (SL trans-splice sites) or at the gene level.Conclusions SL-quant completes within 10 minutes on a basic desktop computer for typical C. elegans RNA-seq datasets and can be applied to other species as well. Validating the method, the SL trans-splice sites identified display the expected consensus sequence, and the results of the gene-level quantification are predictive of the gene position within operons. We also compared SL-quant to a recently published SL-containing read identification strategy that was found to be more sensitive but less specific than SL-quant. Both methods are implemented as a bash script available under the MIT license [1]. Full instructions for its installation, usage, and adaptation to other organisms are provided.

Accurate mapping of tRNA reads.

Motivation Many repetitive DNA elements are transcribed at appreciable expression levels. Mapping the corresponding RNA sequencing reads back to a reference genome is notoriously difficult and error-prone task, however. This is in particular true if chemical modifications introduce systematic mismatches, while at the same time the genomic loci are only approximately identical, as in the case of tRNAs. Results We therefore developed a dedicated mapping strategy to handle RNA-seq reads that map to tRNAs relying on a modified target genome in which known tRNA loci are masked and instead intronless tRNA precursor sequences are appended as artificial 'chromosomes'. In a first pass, reads that overlap the boundaries of mature tRNAs are extracted. In the second pass, the remaining reads are mapped to a tRNA-masked target that is augmented by representative mature tRNA sequences. Using both simulated and real life data we show that our best-practice workflow removes most of the mapping artefacts introduced by simpler mapping schemes and makes it possible to reliably identify many of chemical tRNA modifications in generic small RNA-seq data. Using simulated data the FDR is only 2%. We find compelling evidence for tissue specific differences of tRNA modification patterns. Availability and implementation The workflow is available both as a bash script and as a Galaxy workflow from https://github.com/AnneHoffmann/tRNA-read-mapping. Contact fabian@tbi.univie.ac.at. Supplementary information Supplementary data are available at Bioinformatics online.

LQTA-R: A new 3D-QSAR methodology applied to a set of DGAT1 inhibitors

The rapid advances in computational methods for the drug design have resulted in the accurate predictions of biological activities of ligands with or without the availability of enzyme structures. 3D-QSAR is one of the computational methods used for such purpose. Currently, freely available 3D-QSAR methods suffer the limitations like complex methodologies, difficulty in the analysis of results, applying the statistical methods and validations of models built. Present work describes simple and novel 3D-QSAR methodology, which uses bash scripts LQTA_R_LJ, LQTA_R_QQ and LQTA_R_HB using freely available R statistical program. These scripts then generate Leenard-Jones, Coulomb and Hydrogen bond descriptors. These descriptors provide the steric 3D property, electrostatic property and hydrogen bond formation capacity respectively. These scripts have been tested for the set of DGAT1 inhibitors and results showed that the 3D-QSAR models built have better predictive abilities in terms of R2 0.735, Q2loo 0.635 and R2ext 0.715. The 3D-QSAR model suggested that the substitutions of the alkyl group at the oxadiazolyl ring at the 6th position of the pyrrolo-pyridazine ring is undesirable, on the contrary, substituted phenyl ring at 7th position is responsible for the improved DGAT1 inhibitory activity. The analysis also suggested that 6th position could be substituted with the oxadiazolyl ring or analogous heterocyclic rings, where the 3rd position of such heterocyclic rings substituted with rigid hydrophobic substitute can improve DGAT1 activity.

Implementación de una base de datos heterogénea distribuida entre los SGBDs ORACLE, MySQL y PostgreSQL con replicación, mediante un script bash implementado en el sistema operativo CentOS usando software libre.

El presente artículo permite obtener una base de datos distribuida heterogénea conreplicación en un ambiente CentOS en menos de 5 minutos, mediante un script bash, usandoúnicamente software libre. La idea se centra en tener un esclavo que será ORACLE y los nodosmaestros estarán en MySQL y PostgreSQL, con la finalidad de reducir costos a la hora dediseñar e implementar una base de datos distribuida ya que se aprovecha al máximo la potenciade un gestor de pago, el cual es Oracle, con la gratuidad y buen desempeño de MySQL yPostgreSQL. El resultado de este artículo será un ODBC que configure los dos gestores singastar un solo centavo y en tiempo récord, y así poder obtener una base de datos distribuidaconformada por distintos gestores, que trabajen como uno solo.

Scripting as an Approach to Automated CFD Simulation for Packed Bed Catalytic Reactor Modeling

AbstractIn recent years computational fluid dynamics (CFD) has become a widely applied tool for the simulation of catalytic fixed‐bed reactors and numerous authors have contributed towards methods for random packed bed generation and flow simulation. The presented approach focuses on an automated simulation routine realized through bash and python scripting covering multiple entire simulation runs including preprocessing, simulation as well as post‐processing based on open‐source software. As an example, the routine is demonstrated with a case study on catalytic fixed‐bed reactors.

Test Automation for eConnectsâ„¢

Manual testing of systems controlled by a single eConnectâ„¢ requires weeks to complete. With the use of test automation, the time required for testing will be reduced to requiring only a few hours. Test automation is done with the use of Bash scripts. The Bash scripts that were created for test automation include moving map, cabin lights, and a system configuration editor. Some minor edits were made to the previously created Bash scripts such as DVT-Menu. The new Bash scripts are explained in high level detail. The results files from the tests are used to verify that the eConnectâ„¢ meet customer requirements. The results files are also used for traceability.

Accurate mapping of tRNA reads.

Many repetitive DNA elements are transcribed at appreciable expression levels. Mapping the corresponding RNA sequencing reads back to a reference genome is notoriously difficult and error-prone task, however. This is in particular true if chemical modifications introduce systematic mismatches, while at the same time the genomic loci are only approximately identical, as in the case of tRNAs. We therefore developed a dedicated mapping strategy to handle RNA-seq reads that map to tRNAs relying on a modified target genome in which known tRNA loci are masked and instead intronless tRNA precursor sequences are appended as artificial 'chromosomes'. In a first pass, reads that overlap the boundaries of mature tRNAs are extracted. In the second pass, the remaining reads are mapped to a tRNA-masked target that is augmented by representative mature tRNA sequences. Using both simulated and real life data we show that our best-practice workflow removes most of the mapping artefacts introduced by simpler mapping schemes and makes it possible to reliably identify many of chemical tRNA modifications in generic small RNA-seq data. Using simulated data the FDR is only 2%. We find compelling evidence for tissue specific differences of tRNA modification patterns. The workflow is available both as a bash script and as a Galaxy workflow from https://github.com/AnneHoffmann/tRNA-read-mapping. fabian@tbi.univie.ac.at. Supplementary data are available at Bioinformatics online.

Microseismic event location using global optimization algorithms: An integrated and automated workflow

We perform the location of microseismic events generated in hydraulic fracturing monitoring scenarios using two global optimization techniques: Very Fast Simulated Annealing (VFSA) and Particle Swarm Optimization (PSO), and compare them against the classical grid search (GS). To this end, we present an integrated and optimized workflow that concatenates into an automated bash script the different steps that lead to the microseismic events location from raw 3C data. First, we carry out the automatic detection, denoising and identification of the P- and S-waves. Secondly, we estimate their corresponding backazimuths using polarization information, and propose a simple energy-based criterion to automatically decide which is the most reliable estimate. Finally, after taking proper care of the size of the search space using the backazimuth information, we perform the location using the aforementioned algorithms for 2D and 3D usual scenarios of hydraulic fracturing processes. We assess the impact of restricting the search space and show the advantages of using either VFSA or PSO over GS to attain significant speed-ups.

BreakPoint Surveyor: a pipeline for structural variant visualization.

BreakPoint Surveyor (BPS) is a computational pipeline for the discovery, characterization, and visualization of complex genomic rearrangements, such as viral genome integration, in paired-end sequence data. BPS facilitates interpretation of structural variants by merging structural variant breakpoint predictions, gene exon structure, read depth, and RNA-sequencing expression into a single comprehensive figure. Source code and sample data freely available for download at https://github.com/ding-lab/BreakPointSurveyor, distributed under the GNU GPLv3 license, implemented in R, Python and BASH scripts, and supported on Unix/Linux/OS X operating systems. lding@wustl.edu. Supplementary data are available at Bioinformatics online.

MetaLIMS, a simple open-source laboratory information management system for small metagenomic labs.

Background: As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger sequencing projects and take on the complexity of data storage for high volumes of samples. This has created a need for low-cost laboratory information management systems (LIMS) that contain flexible fields to accommodate the unique nature of individual labs. Many labs do not have a dedicated information technology position, so LIMS must also be easy to setup and maintain with minimal technical proficiency. Findings: MetaLIMS is a free and open-source web-based application available via GitHub. The focus of MetaLIMS is to store sample metadata prior to sequencing and analysis pipelines. Initially designed for environmental metagenomics labs, in addition to storing generic sample collection information and DNA/RNA processing information, the user can also add fields specific to the user's lab. MetaLIMS can also produce a basic sequencing submission form compatible with the proprietary Clarity LIMS system used by some sequencing facilities. To help ease the technical burden associated with web deployment, MetaLIMS options the use of commercial web hosting combined with MetaLIMS bash scripts for ease of setup. Conclusions: MetaLIMS overcomes key challenges common in LIMS by giving labs access to a low-cost and open-source tool that also has the flexibility to meet individual lab needs and an option for easy deployment. By making the web application open source and hosting it on GitHub, we hope to encourage the community to build upon MetaLIMS, making it more robust and tailored to the needs of more researchers.

Kollector: transcript-informed, targeted de novo assembly of gene loci.

MotivationDespite considerable advancements in sequencing and computing technologies, de novo assembly of whole eukaryotic genomes is still a time-consuming task that requires a significant amount of computational resources and expertise. A targeted assembly approach to perform local assembly of sequences of interest remains a valuable option for some applications. This is especially true for gene-centric assemblies, whose resulting sequence can be readily utilized for more focused biological research. Here we describe Kollector, an alignment-free targeted assembly pipeline that uses thousands of transcript sequences concurrently to inform the localized assembly of corresponding gene loci. Kollector robustly reconstructs introns and novel sequences within these loci, and scales well to large genomes—properties that makes it especially useful for researchers working on non-model eukaryotic organisms.ResultsWe demonstrate the performance of Kollector for assembling complete or near-complete Caenorhabditis elegans and Homo sapiens gene loci from their respective, input transcripts. In a time- and memory-efficient manner, the Kollector pipeline successfully reconstructs respectively 99% and 80% (compared to 86% and 73% with standard de novo assembly techniques) of C.elegans and H.sapiens transcript targets in their corresponding genomic space using whole genome shotgun sequencing reads. We also show that Kollector outperforms both established and recently released targeted assembly tools. Finally, we demonstrate three use cases for Kollector, including comparative and cancer genomics applications.Availability and ImplementationKollector is implemented as a bash script, and is available at https://github.com/bcgsc/kollectorSupplementary information Supplementary data are available at Bioinformatics online.

MDplot: Visualise Molecular Dynamics

The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project's GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license.

ARTc: Anisotropic reflectivity and transmissivity calculator

While seismic anisotropy is known to exist within the Earth's crust and even deeper, isotropic or even highly symmetric elastic anisotropic assumptions for seismic imaging is an over-simplification which may create artifacts in the image, target mis-positioning and hence flawed interpretation. In this paper, we have developed the ARTc algorithm to solve reflectivity, transmissivity as well as velocity and particle polarization in the most general case of elastic anisotropy. This algorithm is able to provide reflectivity solution from the boundary between two anisotropic slabs with arbitrary symmetry and orientation up to triclinic.To achieve this, the algorithm solves full elastic wave equation to find polarization, slowness and amplitude of all six wave-modes generated from the incident plane-wave and welded interface. In the first step to calculate the reflectivity, the algorithm solves properties of the incident wave such as particle polarization and slowness. After calculation of the direction of generated waves, the algorithm solves their respective slowness and particle polarization. With this information, the algorithm then solves a system of equations incorporating the imposed boundary conditions to arrive at the scattered wave amplitudes, and thus reflectivity and transmissivity.Reflectivity results as well as slowness and polarization are then tested in complex computational anisotropic models to ensure their accuracy and reliability. ARTc is coded in MATLAB® and bundled with an interactive GUI and bash script to run on single or multi-processor computers.

Building Pipelines for Heterogeneous Execution Environments for Big Data Processing

Many real-world data analysis scenarios require pipelining and integration of multiple (big) data-processing and data-analytics jobs, which often execute in heterogeneous environments, such as MapReduce; Spark; or R, Python, or Bash scripts. Such a pipeline requires much glue code to get data across environments. Maintaining and evolving these pipelines are difficult. Pipeline frameworks that try to solve such problems are usually built on top of a single environment. They might require rewriting the original job to take into account a new API or paradigm. The Pipeline61 framework supports the building of data pipelines involving heterogeneous execution environments. It reuses the existing code of the deployed jobs in different environments and provides version control and dependency management that deals with typical software engineering issues. A real-world case study shows its effectiveness. This article is part of a special issue on Software Engineering for Big Data Systems.

Parametric model of ventilators simulated in OpenFOAM and Elmer

The main goal of presented work was to develop parametric model of a ventilator for CFD and structural analysis. The whole model was designed and scripted in freely available open source programmes in particular in OpenFOAM and Elmer. The main script, which runs or generates other scripts and further control the course of simulation, was written in bash scripting language in Linux environment. Further, the scripts needed for a mesh generation and running of a simulation were prepared using m4 word pre-processor. The use of m4 allowed comfortable set up of the higher amount of scripts. Consequently, the mesh was generated for fluid and solid part of the ventilator within OpenFOAM. Although OpenFOAM offers also a few tools for structural analysis, the mesh of solid parts was transferred into Elmer mesh format with the aim to perform structural analysis in this software. This submitted paper deals namely with part concerning fluid flow through parametrized geometry with different initial conditions. As an example, two simulations were conducted for the same geometric parameters and mesh but for different angular velocity of ventilator rotation.