The adoption of next generation sequencing based methods in cancer research allowed for the investigation of the complex genetic structure of tumor samples. In the last few years, considerable ...importance was given to the research of somatic variants and several computational approaches were developed for this purpose. Despite continuous improvements to these programs, the validation of their results it's a hard challenge due to multiple sources of error. To overcome this drawback different simulation approaches are used to generate synthetic samples but they are often based on the addition of artificial mutations that mimic the complexity of genomic variations. For these reasons, we developed a novel software, Xome-Blender, that generates synthetic cancer genomes with user defined features such as the number of subclones, the number of somatic variants and the presence of copy number alterations (CNAs), without the addition of any synthetic element. The singularity of our method is the "morphological approach" used to generate mutation events. To demonstrate the power of our tool we used it to address the hard challenge of evaluating the performance of nine state-of-the-art somatic variant calling methods for small and large variants (VarScan2, MuTect, Shimmer, BCFtools, Strelka, EXCAVATOR2, Control-FREEC and CopywriteR). Through these analyses we observed that by using Xome-Blender data it is possible to appraise small differences between their performance and we have designated VarScan2 and EXCAVATOR2 as best tool for this kind of applications. Xome-Blender is unix-based, licensed under the GPLv3 and freely available at https://github.com/rsemeraro/XomeBlender.
OneLOop is a program to evaluate the one-loop scalar 1-point, 2-point, 3-point and 4-point functions, for all kinematical configurations relevant for collider-physics, and for any non-positive ...imaginary parts of the internal squared masses. It deals with all UV and IR divergences within dimensional regularization. Furthermore, it provides routines to evaluate these functions using straightforward numerical integration.
Program title: OneLOop
Catalogue identifier: AEJO_v1_0
Program summary URL:
http://cpc.cs.qub.ac.uk/summaries/AEJO_v1_0.html
Program obtainable from: CPC Program Library, Queenʼs University, Belfast, N. Ireland
Licensing provisions: Standard CPC licence,
http://cpc.cs.qub.ac.uk/licence/licence.html
No. of lines in distributed program, including test data, etc.: 12 061
No. of bytes in distributed program, including test data, etc.: 74 163
Distribution format: tar.gz
Programming language: Fortran
Computer: Workstations
Operating system: Linux, Unix
RAM: Negligible
Classification: 4.4, 11.1
Nature of problem: In order to reach next-to-leading order precision in the calculation of cross sections of hard scattering processes, one-loop amplitudes have to be evaluated. This is done by expressing them as linear combination of one-loop scalar functions. In a concrete calculation, these functions eventually have to be evaluated. If the scattering process involves unstable particles, consistency requires the evaluation of these functions with complex internal masses.
Solution method: Expressions for the one-loop scalar functions in terms of single-variable analytic functions existing in literature have been implemented.
Restrictions: The applicability is restricted to the kinematics occurring in collider-physics.
Running time: The evaluation of the most general 4-point function with 4 complex masses takes about 180 μs, and the evaluation of the 4-point function with 4 real masses takes about 18 μs on a 2.80 GHz Intel Xeon processor.
► Implementation of the one-loop scalar 1-, 2-, 3-, and 4-point functions. ► Both UV and IR divergences are treated within dimensional regularization. ► Internal squared masses may have non-zero imaginary parts. ► Also provided is evaluation using numerical integration, as means of cross-check.
Text processing and pattern matching simplified Key Features * -Master the fastest and most elegant big data munging language * -Implement text processing and pattern matching using the advanced ...features of AWK and GAWK * -Implement debugging and inter-process communication using GAWK Book Description AWK is one of the most primitive and powerful utilities which exists in all Unix and Unix-like distributions. It is used as a command-line utility when performing a basic text-processing operation, and as programming language when dealing with complex text-processing and mining tasks. With this book, you will have the required expertise to practice advanced AWK programming in real- life examples. The book starts off with an introduction to AWK essentials. You will then be introduced to regular expressions, AWK variables and constants, arrays and AWK functions and more. The book then delves deeper into more complex tasks, such as printing formatted output in AWK, control flow statements, GNU's implementation of AWK covering the advanced features of GNU AWK, such as network communication, debugging, and inter-process communication in the GAWK programming language which is not easily possible with AWK. By the end of this book, the reader will have worked on the practical implementation of text processing and pattern matching using AWK to perform routine tasks. What you will learn * -Create and use different expressions and control flow statements in AWK * -Use Regular Expressions with AWK for effective text-processing * -Use built-in and user-defined variables to write AWK programs * -Use redirections in AWK programs and create structured reports * -Handle non-decimal input, 2-way inter-process communication with Gawk * -Create small scripts to reformat data to match patterns and process texts Who this book is for This book is for developers or analysts who are inclined to learn how to do text processing and data extraction in a Unix-like environment. Basic understanding of Linux operating system and shell scripting will help you to get the most out of the book.
## In Detail Zsh has become incredibly popular in recent times and reasonably so; the shell boasts some really great features such as command completion, filename generation, and history sharing ...among instances of the shell. Learning to use them to your advantage will prove to be really valuable and will save you from lots of tedious and overly-complex tasks. This hands-on guide will show you how to configure and use zsh for work and daily tasks. It provides a clear introduction to the more powerful features of the shell such as globbing and completion. This book will help you take advantage of the real power behind the UNIX shell on both desktops and servers through real-world examples. This book will help you understand the features of zsh and make it one of the most valuable assets in your toolbox. It will teach you how to use the shell history to look up and edit previously typed entries and take advantage of the line-editor module to speed up your typing and editing of commands. You will be able to create your own completion functions and ensure you never mistype a command or have to look at the manpages again. You will learn how to define your own aliases and learn about filename generation so you can do more by typing even less. You will also discover the essentials of zsh and go deeper with its more advanced features. When you are done with this book, your time with the command line will be much more enjoyable and productive. ## Approach A step-by-step tutorial that will teach you, through real-world examples, how to configure and use zsh and its various features. ## Who this book is for If you are a system administrator, developer, or computer professional involved with UNIX who are looking to improve on their daily tasks involving the UNIX shell, "Learning Shell Scripting with zsh" will be great for you. It's assumed that you have some familiarity with an UNIX command-line interface and feel comfortable with editors such as Emacs or vi.
With the rapid and steady increase of next generation sequencing data output, the mapping of short reads has become a major data analysis bottleneck. On a single computer, it can take several days to ...map the vast quantity of reads produced from a single Illumina HiSeq lane. In an attempt to ameliorate this bottleneck we present a new tool, DistMap - a modular, scalable and integrated workflow to map reads in the Hadoop distributed computing framework. DistMap is easy to use, currently supports nine different short read mapping tools and can be run on all Unix-based operating systems. It accepts reads in FASTQ format as input and provides mapped reads in a SAM/BAM format. DistMap supports both paired-end and single-end reads thereby allowing the mapping of read data produced by different sequencing platforms. DistMap is available from http://code.google.com/p/distmap/
We present an algorithm for the fast computation of the general N-point spatial correlation functions of any discrete point set embedded within an Euclidean space of . Utilizing the concepts of ...kd-trees and graph databases, we describe how to count all possible N-tuples in binned configurations within a given length scale, e.g., all pairs of points or all triplets of points with side lengths < rMAX. Through benchmarking, we show the computational advantage of our new graph-based algorithm over more traditional methods. We show measurements of the three-point correlation function up to scales of ∼200 Mpc (beyond the baryon acoustic oscillation scale in physical units) using current Sloan Digital Sky Survey (SDSS) data. Finally, we present a preliminary exploration of the small-scale four-point correlation function of 568,776 SDSS Constant (stellar) Mass (CMASS) galaxies in the northern Galactic cap over the redshift range of 0.43 < z < 0.7. We present the publicly available code GRAMSCI (GRAph Made Statistics for Cosmological Information; bitbucket.org/csabiu/gramsci), under a Gnu is Not Unix (GNU) General Public License.
Security logs are the key to understanding attacks and diagnosing vulnerabilities. Often coming in the form of text logs, their analysis remains a daunting challenge. Language Models (LMs) have ...demonstrated unmatched potential in understanding natural and programming languages. The question arises as to whether and how LMs could be also used to automatise the analysis of security logs. We here systematically study how to benefit from the state-of-the-art LM to support the analysis of text-like Unix shell attack logs automatically. For this, we thoroughly designed LogPrécis. LogPrécis receives as input malicious shell sessions. It then automatically identifies and assigns the attacker tactic to each portion of the session, i.e., unveiling the sequence of the attacker's goals. This creates a unique attack fingerprint. We demonstrate LogPrécis capability to support the analysis of two large datasets containing about 400,000 unique Unix shell attacks recorded in a 2-year-long honeypot deployment. LogPrécis reduces the analysis to about 3,000 unique fingerprints. Such abstraction lets us better understand attacks, extract attack prototypes, detect novelties, and track families and mutations. Overall, LogPrécis, released as open source, demonstrates the potential of adopting LMs for security analysis and paves the way for better and more responsive defence against cyberattacks.
Implementation of data mining, machine learning, and statistical data from educational department commonly known as educational data mining. Most of school systems require a teacher to teach a number ...of students at one time. Exam are regularly being use as a method to measure student’s achievement, which is difficult to understand because examination cannot be done easily. The other hand, programming classes makes source code editing and UNIX commands able to easily detect and store automatically as log-data. Hence, rather that estimating the performance of those student based on this log-data, this study being more focused on detecting them who experienced a difficulty or unable to take programming classes. We propose CLG clustering methods that can predict a risk of being dropped out from school using cluster data for outlier detection.
Open-source sofware and its components are widely used in various products, solutions, and applications, even in closed-source. Majority of them are made on Linux or Unix based systems. Netfilter ...framework is one of the examples. It is used for packet filtering, load-balancing, and many other manipulations with network traffic. Netfilter based packet filter iptables has been most common frewall tool for Linux systems for more than two decades. Successor of iptables nfables was introduced in 2014. It was designed to overcome various iptables limitations. However, it hasn't received wide popularity and transition is still ongoing. In recent years researchers and developers around the world are searching for solution to increase performance of packet processing tools. For that purpose, many of them trying to utilize eBPF (Extended Berkeley Packet Filter) with XDP (Express Data Path) data path. This paper focused on analyzing Linux OS packet filters and comparing their performances in different scenarios. Keywords: Linux, Netfilter, iptables, nfables, eBPF, XDP, frewalls, packet filters. Atvirojo kodo priemones placiau naudojamos skirtinguose produktuose ir programose. Dauguma is ju yra padaryta panaudojant Linux arba Unix sistemas. Netfler tvarkykle yra vienas is pavyzdziu. Ji naudojama paketams filtruoti, apkrovai paskirstyti ir kitoms manipuliacijoms su paketais atlikti. Netfilter paketu filtras ipatables jau du desimtmecius yra populiariausia Linux ugniasiene. Nauja ugniasiene nfables buvo pristatyta 2014 metais ir turejo iveikti iptables trukumus. Taciau nfables taip ir negavo visuotinio pripazinimo, daug sistemu taip ir nebuvo perkeltos i iptables. Todel pastaruosius metus mokslininkai ir programines irangos kurejai iesko naujo sprendimo padidinti paketu apdorojimo nasuma. Tam jie bando isnaudoti tokias technologijas kaip eBPF ir XDP. Sio straipsnio tikslas padaryti Linux OS paketu filtro analize ir palyginti ju nasuma skirtinguose scenarijuose. Reiksminiai zodziai: Linux, Netfilter, iptables, nfables, eBPF, XDP, ugniasiene, paketu filtrai.
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