This document provides an introduction to UNIX commands presented at a workshop on March 17, 2015. It covers navigating file systems, wildcards and shortcuts, file permissions, compression and networking commands, text file manipulation, command line pipelines, and an introduction to bash scripts. The document explains that most biological data analysis software uses UNIX command lines, data analysis on servers is faster, and NGS files require command line tools due to their large size.
The document provides tips for improving productivity when using the Unix command line. It discusses advantages of the shell like flexibility and chaining commands together. It then gives examples of using shell commands in scripting languages. The majority of the document provides examples of specific Unix commands like grep, find, less and their usage for tasks like file searching, viewing files and directory listings. It concludes with tips on aliases, environment variables and symbolic links.
Slides from the Introduction to UNIX Command-Lines class from the BTI Plant Bioinformatics course 2014. This is a course teach by the Sol Genomics Network researchers at the Boyce Thompson Institute.
The document provides an overview of various Unix/Linux command line concepts across 5 chapters. It describes commands for listing files and directories (ls), creating directories (mkdir), changing directories (cd), viewing the current directory (pwd), copying, moving and removing files (cp, mv, rm), searching files (grep), viewing processes (ps), running jobs in background (&), managing jobs (jobs, fg, bg) and killing processes (kill). It also covers file permissions (chmod), symbolic and hard links (ln), input/output redirection (> ,|), piping (|) and getting help (man, whatis).
This document provides instructions for various exercises to be completed as part of an Operating Systems lab manual. It includes exercises on system calls like fork, exec, wait; I/O system calls; simulating commands like ls and grep; scheduling algorithms like FCFS, SJF, priority, round robin; inter-process communication using shared memory, pipes, message queues; the producer-consumer problem using semaphores; and memory management schemes including paging, segmentation, and file allocation techniques. Example code is provided for implementing different memory management algorithms using concepts like free space list, allocated space list, and block merging.
50 most frequently used unix linux commands (with examples)Rodrigo Maia
This document provides examples for 50 common Linux commands, including tar, grep, find, ssh, sed, awk, vim, diff, sort, and more. It explains practical uses for each command and provides short code snippets to demonstrate basic functionality. The commands cover a wide range of tasks like archiving, searching, editing, comparing, and managing files, processes and system resources.
This Operating System lab manual is designed strictly according to BPUT Syllabus.Any suggestions or comments are well come at neelamani.samal@gmail.com
The document provides tips for improving productivity when using the Unix command line. It discusses advantages of the shell like flexibility and chaining commands together. It then gives examples of using shell commands in scripting languages. The majority of the document provides examples of specific Unix commands like grep, find, less and their usage for tasks like file searching, viewing files and directory listings. It concludes with tips on aliases, environment variables and symbolic links.
Slides from the Introduction to UNIX Command-Lines class from the BTI Plant Bioinformatics course 2014. This is a course teach by the Sol Genomics Network researchers at the Boyce Thompson Institute.
The document provides an overview of various Unix/Linux command line concepts across 5 chapters. It describes commands for listing files and directories (ls), creating directories (mkdir), changing directories (cd), viewing the current directory (pwd), copying, moving and removing files (cp, mv, rm), searching files (grep), viewing processes (ps), running jobs in background (&), managing jobs (jobs, fg, bg) and killing processes (kill). It also covers file permissions (chmod), symbolic and hard links (ln), input/output redirection (> ,|), piping (|) and getting help (man, whatis).
This document provides instructions for various exercises to be completed as part of an Operating Systems lab manual. It includes exercises on system calls like fork, exec, wait; I/O system calls; simulating commands like ls and grep; scheduling algorithms like FCFS, SJF, priority, round robin; inter-process communication using shared memory, pipes, message queues; the producer-consumer problem using semaphores; and memory management schemes including paging, segmentation, and file allocation techniques. Example code is provided for implementing different memory management algorithms using concepts like free space list, allocated space list, and block merging.
50 most frequently used unix linux commands (with examples)Rodrigo Maia
This document provides examples for 50 common Linux commands, including tar, grep, find, ssh, sed, awk, vim, diff, sort, and more. It explains practical uses for each command and provides short code snippets to demonstrate basic functionality. The commands cover a wide range of tasks like archiving, searching, editing, comparing, and managing files, processes and system resources.
This Operating System lab manual is designed strictly according to BPUT Syllabus.Any suggestions or comments are well come at neelamani.samal@gmail.com
This document provides an overview of basic Linux commands, including man for accessing manual pages, ls for listing directory contents, mkdir for creating directories, cd for changing directories, pwd for printing the working directory, and ~ for accessing the home directory. It also covers commands for copying, moving, removing files, clearing the screen, viewing file contents, searching within files, counting words, piping commands together, using wildcards, and changing file permissions with chmod. The document encourages learning through manual pages and understanding error messages.
The document provides an overview of Linux commands and the command line interface. It discusses:
1. Why the command line interface is useful and how to open the terminal emulator.
2. The different types of shells available in Linux and how to check the current shell or change shells.
3. Common Linux directory structures like /bin and /usr/bin that contain executable programs and commands.
This document provides commands for basic file management and system utilities in Linux/Unix systems. It includes commands for listing, moving, copying, deleting and changing permissions of files and directories. It also includes commands for editing files, finding files, archiving files, printing files, managing processes, debugging programs, I/O redirection and setting environment variables.
This document contains 49 multiple choice questions about various Linux commands and concepts. The questions cover topics such as common commands (e.g. ls, cd), file system navigation, permissions, processes, networking and system administration tasks. Each question is followed by 4 possible answer choices.
This program implements the First Come First Serve (FCFS) CPU scheduling algorithm in C. It takes the arrival time and service time of each process as input, calculates the start time, finish time, waiting time and turnaround time of each process, and outputs these values along with the average waiting time and average turnaround time. The processes are scheduled in the order of their arrival, with no preemption, following the FCFS principle.
The document provides an overview of the history and development of the UNIX operating system from 1965 to 1983. It describes how UNIX originated from the Multics project at Bell Labs and MIT in 1965. It was further developed by AT&T in the 1970s and rewritten in C by Dennis Ritchie in 1973. The document also discusses the development of BSD and System V UNIX variants in the 1980s.
This document provides an overview of the UNIX operating system and some basic UNIX commands. It discusses what UNIX is, its origins at Bell Laboratories in 1969, and some of its core functions like providing a filing system and loading/executing programs. It also covers the UNIX kernel and layers, file system structure, shells, logging in, and examples of common commands like ls, cat, more, pr, grep, passwd, who, and man.
This document provides an overview of basic Unix commands including ls, cd, pwd, mkdir, rm, rmdir, cp, find, touch, echo, cat, who, and du. It explains what each command is used for and provides examples of common usages. The document serves as a beginner's guide to learning Unix commands.
The document provides an overview of common Linux commands, including commands for executing other commands, navigating directories, listing and copying files, managing users and permissions, searching for files, processing text, managing archives, and compressing files. Examples are given for commands like ls, cd, cp, mv, rm, who, echo, alias, awk, chown, diff, grep, pushd, kill, df, cat, tar, gzip, su. Brief descriptions are provided for most commands and references are given at the end for additional Linux resources.
The document provides information on basic Linux commands for working with files, permissions, users and running levels. Some key points:
- Commands like ls, du, df, free are used to view disk usage, files, permissions and available memory. chmod, chown, chgrp change file/folder permissions and ownership.
- Permissions are represented by rwx for read, write and execute for the user, group and others. Numerical values like 755 can set complex permission schemes.
- Linux has 7 run levels from 0-6 for different system states like shutdown, single-user mode, multi-user with networking. Services are started via links in run level directories.
- Common commands
This document provides an index of 21 coding topics that include performing arithmetic operations, comparison of numbers, compound interest calculation, prime number checking, and palindrome checking. It also includes displaying a Fibonacci series, calculating simple interest, and swapping numbers without using three variables. The index provides the topic name and number for each item.
This document provides an overview of Linux commands for redirecting standard input, output, and error streams. Some key points covered include:
- Redirecting input (<), output (> and >>), and pipes (|) to send output as input to another command
- Common redirection operators like tee to send output to both a file and stdout, and xargs to expand input to command line arguments
- Redirecting standard error (2>) independently from standard output using 2>, 2>>, 2>&1
- Using command substitution (`command` and $(command)) to capture output and use as arguments
- Chaining commands together in pipelines (|) to filter and transform text streams
- Examples of
Piping into PHP
Not the kind of pipe you smoke :) Though traditionally used to build websites, PHP has a great deal of often unused functionality. In this talk we will explore Unix named pipes and how we can start a PHP process which listens for input while it is running.
The document provides an overview of basic Linux commands organized into the following sections:
1. General purpose utilities such as date, echo, printf, calculator applications
2. Linux file system structure and commands for viewing file attributes, permissions, ownership
3. Commands for file handling, concatenation, pagination and comparing files
This document provides an overview of common Linux commands organized into categories such as file handling, process management, disk usage, searching, editing, and remote access. It describes the purpose and basic usage of commands like vi, ls, grep, find, scp, and more. Examples are given for piping output, redirection, appending, and searching/replacing text within files. Links to additional online resources on Linux basics and tips are also included.
This document provides summaries of 30 common Unix commands. It begins with an introduction explaining the purpose and scope of the document. The commands are then listed alphabetically, with each getting a brief 1-2 sentence description. For some commands, simple examples of usage are also provided. The document aims to give beginners a quick overview of the basic usage of important Unix commands.
This document provides information about creating partitions and filesystems in Linux. It discusses various Linux filesystem types like ext2, ext3, xfs, reiserfs v3, and vfat. It covers the commands and tools used to create partitions (fdisk, mkfs), filesystems (mkfs), and swap spaces (mkswap, swapon). It also discusses viewing filesystem information, mounting filesystems, and the Filesystem Hierarchy Standard for directory structure in Linux.
The document lists various Linux commands and provides a brief description of each command. Some common commands listed include mkdir to create folders, cd to change directories, ls to list files, cat to view file contents, date to view the date, cal to display a calendar, echo to display messages, and pwd to print the working directory. Other commands mentioned are tail and head to view parts of files, history to see previously run commands, and id to print user and group IDs.
This document provides a summary of useful Linux commands for starting and stopping the system, accessing and mounting file systems, finding files and text, moving, copying, deleting, and viewing files, installing software, user administration, and the X Window System. It lists commands such as shutdown, halt, reboot, mount, umount, find, locate, updatedb, which, grep, ls, rpm, tar, adduser, passwd, su, and exit along with brief explanations of their functions.
This document provides an overview of common Linux commands used to process text streams and filter output, including cat, cut, head, tail, and split. It discusses how these commands can be used to select, sort, reformat, and summarize data by printing certain parts of files like columns, lines, or characters. Redirection is also covered as a way to modify command input and output. The goal is to explain the key knowledge areas and objectives for the Junior Level Linux Certification exam related to GNU and Unix commands.
Summary of UNIX commands used in the BTI Plant Bioinformatics Course in 2014. It includes a description of these common commands and some useful options.
The document provides an introduction to Linux file systems and navigation, basic Linux commands, and users and groups. It describes:
1) The Linux file system uses a tree structure with root ("/") at the bottom and directories like /bin, /boot, /etc, /home, /lib, /opt, /proc, /sbin, /tmp, /usr, and /var.
2) Basic Linux commands include ls, cd, mkdir, rmdir, mount, df, ps, kill, touch, cat, head, cp, mv, comm, ln, history, wget, curl, find, which, echo, sort, man, tar, printenv, sleep, vi/vim
This document provides an overview of basic Linux commands, including man for accessing manual pages, ls for listing directory contents, mkdir for creating directories, cd for changing directories, pwd for printing the working directory, and ~ for accessing the home directory. It also covers commands for copying, moving, removing files, clearing the screen, viewing file contents, searching within files, counting words, piping commands together, using wildcards, and changing file permissions with chmod. The document encourages learning through manual pages and understanding error messages.
The document provides an overview of Linux commands and the command line interface. It discusses:
1. Why the command line interface is useful and how to open the terminal emulator.
2. The different types of shells available in Linux and how to check the current shell or change shells.
3. Common Linux directory structures like /bin and /usr/bin that contain executable programs and commands.
This document provides commands for basic file management and system utilities in Linux/Unix systems. It includes commands for listing, moving, copying, deleting and changing permissions of files and directories. It also includes commands for editing files, finding files, archiving files, printing files, managing processes, debugging programs, I/O redirection and setting environment variables.
This document contains 49 multiple choice questions about various Linux commands and concepts. The questions cover topics such as common commands (e.g. ls, cd), file system navigation, permissions, processes, networking and system administration tasks. Each question is followed by 4 possible answer choices.
This program implements the First Come First Serve (FCFS) CPU scheduling algorithm in C. It takes the arrival time and service time of each process as input, calculates the start time, finish time, waiting time and turnaround time of each process, and outputs these values along with the average waiting time and average turnaround time. The processes are scheduled in the order of their arrival, with no preemption, following the FCFS principle.
The document provides an overview of the history and development of the UNIX operating system from 1965 to 1983. It describes how UNIX originated from the Multics project at Bell Labs and MIT in 1965. It was further developed by AT&T in the 1970s and rewritten in C by Dennis Ritchie in 1973. The document also discusses the development of BSD and System V UNIX variants in the 1980s.
This document provides an overview of the UNIX operating system and some basic UNIX commands. It discusses what UNIX is, its origins at Bell Laboratories in 1969, and some of its core functions like providing a filing system and loading/executing programs. It also covers the UNIX kernel and layers, file system structure, shells, logging in, and examples of common commands like ls, cat, more, pr, grep, passwd, who, and man.
This document provides an overview of basic Unix commands including ls, cd, pwd, mkdir, rm, rmdir, cp, find, touch, echo, cat, who, and du. It explains what each command is used for and provides examples of common usages. The document serves as a beginner's guide to learning Unix commands.
The document provides an overview of common Linux commands, including commands for executing other commands, navigating directories, listing and copying files, managing users and permissions, searching for files, processing text, managing archives, and compressing files. Examples are given for commands like ls, cd, cp, mv, rm, who, echo, alias, awk, chown, diff, grep, pushd, kill, df, cat, tar, gzip, su. Brief descriptions are provided for most commands and references are given at the end for additional Linux resources.
The document provides information on basic Linux commands for working with files, permissions, users and running levels. Some key points:
- Commands like ls, du, df, free are used to view disk usage, files, permissions and available memory. chmod, chown, chgrp change file/folder permissions and ownership.
- Permissions are represented by rwx for read, write and execute for the user, group and others. Numerical values like 755 can set complex permission schemes.
- Linux has 7 run levels from 0-6 for different system states like shutdown, single-user mode, multi-user with networking. Services are started via links in run level directories.
- Common commands
This document provides an index of 21 coding topics that include performing arithmetic operations, comparison of numbers, compound interest calculation, prime number checking, and palindrome checking. It also includes displaying a Fibonacci series, calculating simple interest, and swapping numbers without using three variables. The index provides the topic name and number for each item.
This document provides an overview of Linux commands for redirecting standard input, output, and error streams. Some key points covered include:
- Redirecting input (<), output (> and >>), and pipes (|) to send output as input to another command
- Common redirection operators like tee to send output to both a file and stdout, and xargs to expand input to command line arguments
- Redirecting standard error (2>) independently from standard output using 2>, 2>>, 2>&1
- Using command substitution (`command` and $(command)) to capture output and use as arguments
- Chaining commands together in pipelines (|) to filter and transform text streams
- Examples of
Piping into PHP
Not the kind of pipe you smoke :) Though traditionally used to build websites, PHP has a great deal of often unused functionality. In this talk we will explore Unix named pipes and how we can start a PHP process which listens for input while it is running.
The document provides an overview of basic Linux commands organized into the following sections:
1. General purpose utilities such as date, echo, printf, calculator applications
2. Linux file system structure and commands for viewing file attributes, permissions, ownership
3. Commands for file handling, concatenation, pagination and comparing files
This document provides an overview of common Linux commands organized into categories such as file handling, process management, disk usage, searching, editing, and remote access. It describes the purpose and basic usage of commands like vi, ls, grep, find, scp, and more. Examples are given for piping output, redirection, appending, and searching/replacing text within files. Links to additional online resources on Linux basics and tips are also included.
This document provides summaries of 30 common Unix commands. It begins with an introduction explaining the purpose and scope of the document. The commands are then listed alphabetically, with each getting a brief 1-2 sentence description. For some commands, simple examples of usage are also provided. The document aims to give beginners a quick overview of the basic usage of important Unix commands.
This document provides information about creating partitions and filesystems in Linux. It discusses various Linux filesystem types like ext2, ext3, xfs, reiserfs v3, and vfat. It covers the commands and tools used to create partitions (fdisk, mkfs), filesystems (mkfs), and swap spaces (mkswap, swapon). It also discusses viewing filesystem information, mounting filesystems, and the Filesystem Hierarchy Standard for directory structure in Linux.
The document lists various Linux commands and provides a brief description of each command. Some common commands listed include mkdir to create folders, cd to change directories, ls to list files, cat to view file contents, date to view the date, cal to display a calendar, echo to display messages, and pwd to print the working directory. Other commands mentioned are tail and head to view parts of files, history to see previously run commands, and id to print user and group IDs.
This document provides a summary of useful Linux commands for starting and stopping the system, accessing and mounting file systems, finding files and text, moving, copying, deleting, and viewing files, installing software, user administration, and the X Window System. It lists commands such as shutdown, halt, reboot, mount, umount, find, locate, updatedb, which, grep, ls, rpm, tar, adduser, passwd, su, and exit along with brief explanations of their functions.
This document provides an overview of common Linux commands used to process text streams and filter output, including cat, cut, head, tail, and split. It discusses how these commands can be used to select, sort, reformat, and summarize data by printing certain parts of files like columns, lines, or characters. Redirection is also covered as a way to modify command input and output. The goal is to explain the key knowledge areas and objectives for the Junior Level Linux Certification exam related to GNU and Unix commands.
Summary of UNIX commands used in the BTI Plant Bioinformatics Course in 2014. It includes a description of these common commands and some useful options.
The document provides an introduction to Linux file systems and navigation, basic Linux commands, and users and groups. It describes:
1) The Linux file system uses a tree structure with root ("/") at the bottom and directories like /bin, /boot, /etc, /home, /lib, /opt, /proc, /sbin, /tmp, /usr, and /var.
2) Basic Linux commands include ls, cd, mkdir, rmdir, mount, df, ps, kill, touch, cat, head, cp, mv, comm, ln, history, wget, curl, find, which, echo, sort, man, tar, printenv, sleep, vi/vim
Linux is an open-source operating system based on Unix, designed for multi-user environments. The document provides an overview of basic Linux commands like ls, mkdir, cd for navigating files and directories, as well as more advanced commands for manipulating files, checking system resources, and getting system information. It also lists and describes many common Linux commands and their functions.
Linux is an open source operating system initially created by Linus Torvalds in 1991. It has since grown significantly with hundreds of companies and individuals developing their own versions based on the Linux kernel. The kernel is developed under the GNU GPL license and its source code is freely available. Basic Linux commands allow users to navigate directories, manage files and permissions, transfer files, and get system information. More advanced commands provide additional control and functionality.
The document provides an overview of command line basics, including X Windows, consoles and terminals, UNIX commands, the UNIX filesystem, and the vi editor. It describes the anatomy of commands, getting help with man pages, basic account and file management commands, viewing and editing files, and installing applications. It emphasizes that the command line is always available and more efficient than GUIs.
This document provides a summary of Linux command line cheat sheet covering topics such as:
- Simple commands like date, cal, df, free for displaying system information
- Navigation commands like cd, ls
- Exploring and manipulating files and directories using commands like cp, mv, mkdir, rm
- Finding files using locate, find
- Process commands like ps, top, kill
- Networking commands like ping, traceroute, netstat
- Archiving files using gzip, bzip2, tar, zip
- User permissions and ownership with chmod, chown, su
This document provides instructions for 27 common Linux commands: mkdir, rmdir, ls, cd, cat, touch, wc, who, pwd, rm, mv, chmod, cp, grep, cal, date, vi, tput, ps, export, type, tail, sudo, head, man, clear, and adduser. For each command, it lists the syntax and provides 1-3 examples of common uses. The document is presented over 28 pages with the commands organized topic-by-topic and includes formatting like headings and indentation to aid readability.
This document provides an introduction to Linux, including:
- What Linux is and where it came from, as an open source operating system created by Linus Torvalds in 1991.
- How to get Linux through downloading a distribution like Red Hat and the packages it includes.
- Why Linux has become significant due to its growing popularity, ability to run on multiple hardware platforms, and being free.
- An overview of Linux commands and utilities for file management, processes, users and permissions.
This document contains a list of common Linux commands and their brief descriptions. It includes commands for managing files, directories, users, processes, networking, installing software, editing text, and more. The list spans from a to z and contains over 100 commands in total that cover many essential tasks in Linux systems.
The document provides an introduction to Linux commands and lists the top 50 commands. It includes brief descriptions of common commands like ls, cd, mkdir, rmdir, ps, kill, cat, head, cp, mv, comm, ln, history, wget, curl, find, grep, sed and more. It then provides a lab exercise with 17 steps to practice basic file navigation and directory creation/deletion using these commands.
Quick guide of the most common linux commandsCarlos Enrique
This document provides a quick guide to the most common Linux commands organized in alphabetical order. It lists over 100 commands and briefly describes the basic function of each one such as manipulating files and directories, running processes, viewing system information, and more.
The document summarizes the usage of various Linux commands like cd, bc, man, who, whoami, pwd, mkdir, rmdir, ls, touch, mv, date, cat, more, less, print, echo, lp, rm, cp and their options. It provides the syntax and examples of using each command. The commands covered are for directory navigation, file manipulation, text processing and printing files in Linux operating system.
This document provides a tutorial on Unix/Linux. It begins with an overview of the Unix system including the kernel, shell, multi-user and multi-process capabilities, and important directory structures. It then covers basic commands, relative and absolute paths, redirecting and piping output, permissions, process management, installing software, text editors, running jobs in the foreground and background, and remote login/file transfer. The goal is to introduce fundamental Unix concepts and commands to new users.
The document provides descriptions of various Linux commands for basic usage and pentesting. It describes commands for making directories (mkdir), deleting empty directories (rmdir), viewing processes (ps), checking username (whoami), checking disk space (df), displaying date and time (date), checking connectivity (ping), downloading files (wget), looking up domain registration records (whois), navigating directories (cd), listing directory contents (ls), displaying command manuals (man), displaying text files (cat), copying files (cp), moving and renaming files (mv), removing files and directories (rm), creating empty files (touch), searching files (grep), using administrative privileges (sudo), viewing start of files (head), viewing end of files (
Unix , Linux Commands
Unix, which is not an acronym, was developed by some of the members of the Multics team at the bell labs starting in the late 1960's by many of the same people who helped create the C programming language.
This document provides an overview of basic Unix commands, including:
- Commands for navigating directories (cd, pwd, ls), creating/removing directories and files (mkdir, rmdir, cp, rm)
- Commands for viewing file contents (cat, more, less) and comparing files (diff)
- Commands for searching files (grep) and counting elements (wc)
- Commands for changing file permissions (chmod) and moving/renaming files (mv)
It also briefly describes shells, files and pathnames in Unix systems. The document is intended as an introduction for new Unix users to understand basic file management and navigation.
This document provides a cheat sheet of common Linux commands and their usage. It covers basic file operations like copying, moving, deleting files and directories. It also includes commands for viewing files, compressing/decompressing files, finding files, remote access, and getting system information. The commands are explained over 3 pages with examples of proper syntax and usage for each one.
The document provides information about an upcoming UNIX and Shell Scripting workshop, including contact information for the workshop instructor R. Chockalingam, and covers topics that will be discussed such as the architecture and components of the UNIX operating system, basic UNIX commands, text editors, the file system structure, flags and arguments, and more.
The document discusses Linux commands for file management, viewing and shell programming. It describes common commands like ls, cd, cp, mv, rm, mkdir which allow navigating and manipulating files and directories. It also covers commands for viewing file contents like cat, head, tail, grep. Commands for compression like tar, gzip, zip and decompression like gunzip, unzip are mentioned. The document also has a section on shell programming which explains how to write shell scripts using commands and variables. It provides examples of using pipes, redirections and command options.
Similaire à SGN Introduction to UNIX Command-line 2015 part 1 (20)
This document summarizes the Solanum lycopersicum Heinz 1706 genome assembly SL4.0 and its annotation ITAG4.0 from the Sol Genomics Network. Key points include: SL4.0 has an improved assembly compared to previous versions with longer contigs and less unplaced sequence. It was generated using PacBio and Illumina sequencing. The annotation ITAG4.0 contains 34,075 protein-coding genes compared to 34,725 in the previous version, with improvements in 5' and 3' UTR identification. Novel genes in ITAG4.0 are enriched for stress response functions. Validation was performed using various omics datasets and optical mapping.
This document summarizes a presentation on breeding data management and analysis tools using the Cassavabase database. It describes how Cassavabase collects phenotypic and genotypic data from various programs and ensures data quality. Over 9 million phenotypic observations, 2488 trials and 34,000 genotypes have been collected. It also discusses expanding interoperability through APIs and partnerships with other crop databases. The presentation demonstrates using Cassavabase to access trial data, visualize genotypes, perform statistical analysis, genomic prediction and multi-trait selection to increase genetic gain.
This document provides instructions for sampling cassava plants for genotyping using the Cassavabase database and Coordinate mobile app. It describes how to:
1. Design a field trial and generate barcodes in Cassavabase
2. Use the Coordinate app to collect samples according to the trial template and export the sample data
3. Upload the template and sample data to Cassavabase
4. Submit the genotyping order to the service provider
The goal is to efficiently collect samples from the field trial and prepare the data for genotyping.
The document discusses breeding informatics solutions provided by the Sol Genomics Network (SGN). SGN aims to create a one-stop digital ecosystem for high-throughput breeding data. It provides database, field work tools, trial design and analysis tools to facilitate efficient data collection, sharing, analysis and knowledge discovery. Key features include linking genetic data to genomes and maps through ontologies, registering genetic material and designing trials and plates, field phenotype data collection apps, exploratory data analysis tools, and genomic selection tools. The goal is an integrated system for access, analysis and utilization of genetic data.
Musabase is a phenotyping and breeding database for bananas that aims to connect data within and between banana breeding projects. It digitizes field data collection through tools like barcoding and digital forms. The database integrates data from various sources like field trials, surveys, sequencing data and tissue culture. It links this in situ breeding data to ex situ conservation resources to create a "digital ecosystem" for banana breeders and researchers. Future work will expand collaboration and train local partners to continue developing open-source tools to improve banana improvement for smallholder farmers.
This document outlines an agenda for a Cassavabase workshop to be held in Ibadan, Nigeria in March 2017. It provides details on the workshop objectives, audience, attendees, an overview of Cassavabase, and exercises for days 1 and 2. The objectives are to train attendees on using Cassavabase for data loading, visualization, analysis and breeding management through hands-on examples. The audience includes trial managers, data curators/analysts, and scientists/PhD students. Details are provided on checking accounts, tablets, and websites for training. The agenda covers searching, downloading accessions, list management, barcoding, fieldbook use, phenotype analysis including selection indices and genomic selection, and solving issues.
Improvements in the Tomato Reference Genome (SL3.0) and Annotation (ITAG3.0)solgenomics
The document describes improvements made to the tomato reference genome sequence (SL3.0) and its annotation (ITAG3.0). Over 1,000 BAC sequences were integrated which reduced contig gaps by 11 Mb. Optical maps from BioNano helped assemble the genome into 57 scaffolds with an N50 of 25.4 Mb. The ITAG3.0 annotation includes over 5,800 novel genes identified through RNA sequencing evidence and ab initio prediction. The updated annotation shows improvements in gene structures and functional annotations compared to the previous version.
This document describes solGS, a web-based tool for genomic selection analysis. solGS allows users to store phenotypic and genotypic data, perform pre-modeling data processing like handling missing values, build prediction models using methods like RR-BLUP and GBLUP, estimate breeding values of selection candidates, and conduct additional analyses like estimating genetic correlations and calculating selection indices. The tool aims to make genomic selection more accessible for plant breeders by providing a platform for organizing and analyzing genomic data.
This document outlines the steps and procedures for demonstrating the Musabase phenotyping workflow, including:
1) Creating trials, accessions, crosses, and lists in Musabase
2) Designing fieldbook layouts and trait lists for phenotyping
3) Using the Android Fieldbook app to record phenotypes in the field
4) Uploading the exported phenotype data into Musabase
solGS is a web-based tool for genomic selection analysis that allows users to store data, build prediction models, and estimate breeding values. It offers three options for composing a training population: searching by trait, searching for trials, or using a custom list. Models can then be applied to estimate breeding values for selection candidates, analyze genetic correlations, and calculate selection indices. The tool aims to advance genomic selection in plant breeding.
The document summarizes a NextGen Cassava workshop held at IITA Ibadan in October 2016. The workshop aimed to train attendees in using Cassavabase for cassava breeding data management and analysis. Over two days, participants learned how to search and manage data, design trials, record phenotypes using Fieldbook, analyze data, and utilize genomic selection and crossing tools. Hands-on exercises helped attendees practice the various Cassavabase functions. Support was provided for using the tool and participants received homework assignments.
This document provides a cheat sheet for using SQL commands to interact with PostgreSQL databases, schemas, tables, and data. It lists commands for connecting to databases (\c) and schemas (\dn), viewing table details (\d), and sending output to a file (\o). It also summarizes commands for data manipulation like INSERT, UPDATE, DELETE, and transactions using BEGIN and COMMIT. Finally, it outlines common SQL queries using SELECT, WHERE, ORDER BY, LIMIT, JOIN and other clauses.
The document provides an overview of relational and non-relational databases as well as SQL syntax and commands. It discusses PostgreSQL and how to connect to databases, create and alter roles and permissions, and perform basic SQL commands. It also covers database development topics like creating, importing, exporting, and deleting databases and schemas. Table structures, relationships, and normalization are explained.
- The document demonstrates the YamBase workflow for phenotyping, which includes creating a cross with progenies, listing accessions and traits, making a trial, generating fieldbook files, recording data on a tablet, exporting phenotypes, and uploading to YamBase.
- It also shows how to create a genotyping trial in YamBase and upload historic phenotype data from existing trials by importing the trial information and phenotype files.
- The goal is to provide an end-to-end demonstration of the YamBase platform for managing yam breeding data.
This document provides an outline for a YamBase workshop held in Cotonou, Benin in March 2016. The workshop agenda covers an overview of YamBase, account creation and login, searching YamBase, working with lists, the search wizard, managing data, and uploading various types of data including accessions, images, pedigrees, crosses, and field trial data. The document explains what YamBase is, its benefits, and how to access and use the YamBase test site. It also covers the YamBase data structure and account privileges, and includes exercises for participants to complete hands-on with the YamBase test server during the workshop.
Cassavabase general presentation PAG 2016solgenomics
CASSAVABASE is a central data store for genomic and phenotypic data from the NEXTGEN CASSAVA project, which aims to accelerate breeding of African cassava through genomic selection. It currently contains over 80,000 accessions and 2.5 billion phenotypic observations. CASSAVABASE allows users to search, manage, analyze and visualize diverse data types to support cassava breeding. Ongoing work involves developing new analysis tools, improving existing tools, and establishing mirror sites for African users.
The document describes solGS, a web-based tool for genomic selection in plant and animal breeding. solGS allows users to store genotype and phenotype data, compose training populations, build prediction models using RR-BLUP or GBLUP, predict breeding values for selection candidates, and perform additional analyses like estimating genetic correlations and calculating selection indices. The tool addresses challenges of large genomic data volumes and enables data cleaning, imputation, statistical modeling, and interactive visualization. Models are fitted using 10-fold cross-validation, and solGS provides options for composing training populations by trait, trial, or custom individual lists.
solGS is a web-based tool that addresses challenges in genomic selection including data management, analysis, and sharing results. It stores phenotype and genotype data in a database and provides an intuitive interface for statistical modeling, visualization, and estimating genomic breeding values. Breeders can build prediction models from training populations, validate models, and estimate genomic estimated breeding values for selection candidates to select best individuals. The open-source code can be adapted to any breeding program.
Cassavabase is a database for cassava and related crops that allows users to search accessions and trial plots, manage breeding programs and trials, analyze genomic selection tools, and visualize genomic data. It contains data for over 80,000 accessions, 300,000 trial plots, 8 million phenotypic observations, and 2 billion genotypic datapoints. Users must create an account to access full database privileges like submitting trials or phenotypic data. The database is open to all cassava breeders and part of a collaborative effort for genomic selection in African cassava breeding programs.
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
When I was asked to give a companion lecture in support of ‘The Philosophy of Science’ (https://shorturl.at/4pUXz) I decided not to walk through the detail of the many methodologies in order of use. Instead, I chose to employ a long standing, and ongoing, scientific development as an exemplar. And so, I chose the ever evolving story of Thermodynamics as a scientific investigation at its best.
Conducted over a period of >200 years, Thermodynamics R&D, and application, benefitted from the highest levels of professionalism, collaboration, and technical thoroughness. New layers of application, methodology, and practice were made possible by the progressive advance of technology. In turn, this has seen measurement and modelling accuracy continually improved at a micro and macro level.
Perhaps most importantly, Thermodynamics rapidly became a primary tool in the advance of applied science/engineering/technology, spanning micro-tech, to aerospace and cosmology. I can think of no better a story to illustrate the breadth of scientific methodologies and applications at their best.
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...Leonel Morgado
Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...Sérgio Sacani
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
The binding of cosmological structures by massless topological defectsSérgio Sacani
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
The cost of acquiring information by natural selectionCarl Bergstrom
This is a short talk that I gave at the Banff International Research Station workshop on Modeling and Theory in Population Biology. The idea is to try to understand how the burden of natural selection relates to the amount of information that selection puts into the genome.
It's based on the first part of this research paper:
The cost of information acquisition by natural selection
Ryan Seamus McGee, Olivia Kosterlitz, Artem Kaznatcheev, Benjamin Kerr, Carl T. Bergstrom
bioRxiv 2022.07.02.498577; doi: https://doi.org/10.1101/2022.07.02.498577
Immersive Learning That Works: Research Grounding and Paths ForwardLeonel Morgado
We will metaverse into the essence of immersive learning, into its three dimensions and conceptual models. This approach encompasses elements from teaching methodologies to social involvement, through organizational concerns and technologies. Challenging the perception of learning as knowledge transfer, we introduce a 'Uses, Practices & Strategies' model operationalized by the 'Immersive Learning Brain' and ‘Immersion Cube’ frameworks. This approach offers a comprehensive guide through the intricacies of immersive educational experiences and spotlighting research frontiers, along the immersion dimensions of system, narrative, and agency. Our discourse extends to stakeholders beyond the academic sphere, addressing the interests of technologists, instructional designers, and policymakers. We span various contexts, from formal education to organizational transformation to the new horizon of an AI-pervasive society. This keynote aims to unite the iLRN community in a collaborative journey towards a future where immersive learning research and practice coalesce, paving the way for innovative educational research and practice landscapes.
Or: Beyond linear.
Abstract: Equivariant neural networks are neural networks that incorporate symmetries. The nonlinear activation functions in these networks result in interesting nonlinear equivariant maps between simple representations, and motivate the key player of this talk: piecewise linear representation theory.
Disclaimer: No one is perfect, so please mind that there might be mistakes and typos.
dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
(June 12, 2024) Webinar: Development of PET theranostics targeting the molecu...Scintica Instrumentation
Targeting Hsp90 and its pathogen Orthologs with Tethered Inhibitors as a Diagnostic and Therapeutic Strategy for cancer and infectious diseases with Dr. Timothy Haystead.
The technology uses reclaimed CO₂ as the dyeing medium in a closed loop process. When pressurized, CO₂ becomes supercritical (SC-CO₂). In this state CO₂ has a very high solvent power, allowing the dye to dissolve easily.
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
6. Sol Genomics Network
Why use command-line?
• Most software for biological data analysis is used through
UNIX command-line terminal
• Most of the servers for biological data analysis use Linux as
operative system
• Data analysis on calculation servers are much faster since we
can use more CPUs and RAM than in a PC (e.g.: Boyce servers
has 64 cores and 1TB RAM)
• Large NGS data files can not be opened or loaded in most of
GUI-based software and web sites
• Compression commands are useful, since NGS large data files
usually are stored and shared as compressed files
7. Sol Genomics Network
Text handling commandsText handling commands
command > file saves STDOUT in a file
command >> file appends STDOUT in a file
cat file concatenate and print files
cat file1 file2 > file3 merges files 1 and 2 into file3
cat *fasta > all.fasta
concatenates all fasta files in
the current directory
head file prints first lines from a file
head -n 5 file prints first five lines from a file
tail file prints last lines from a file
tail -n 5 file prints last five lines from a file
less file view a file
less -N file includes line numbers
less -S file wraps long lines
grep ‘pattern’ file Prints lines matching a pattern
grep -c ‘pattern’ file counts lines matching a pattern
cut -f 1,3 file
retrieves data from selected
columns in a tab-delimited file
sort file sorts lines from a file
sort -u file sorts and return unique lines
uniq -c file filters adjacent repeated lines
wc file counts lines, words and bytes
paste file1 file2
concatenates the lines of input
files
paste -d “,”
concatenates the lines of input
files by commas
sed transforms text
File system CommandsFile system Commands
ls lists directories and files
ls -a lists all files including hidden files
ls -lh formatted list including more data
ls -t lists sorted by date
pwd returns path to working directory
cd dir changes directory
cd .. goes to parent directory
cd / goes to root directory
cd goes to home directory
touch file_name creates en empty file
cp file file_copy copy a file
cp -r copy files contained in directories
rm file deletes a file
rm -r dir deletes a directory and its files
mv file1 file2 moves or renames a file
mkdir dir_name creates a directory
rmdir dir_name deletes a directory
locate file_name searches a file
man command shows commands manual
top shows process activity
df -h shows disk space info
Networking CommandsNetworking Commands
wget URL download a file from an URL
ssh user@server connects to a server
scp copy files between computers
apt-get install installs applications in linux
Compression commandsCompression commands
gzip/zip compress a file
gunzip/unzip decompress a file
tar -cvf groups files
tar -xvf ungroups files
tar -zcvf groups and gzip files
tar -zxvf gunzip and ungroups files
UNIX Command-Line Cheat Sheet
BTI-SGN Bioinformatics Course 2014
•File system commands
File system navigation
http://www.slideshare.net/NoFernndezPozo/unix-command-sheet2014
https://btiplantbioinfocourse.files.wordpress.com/2014/02/unix_command_sheet_2014.pdf
Download the cheat sheet from:
9. Sol Genomics Network
Home and Root directories
/bin, /lib, /usr code and code libraries
/var logs and other data
/home user directories
/tmp temporary files
/etc configuration information
/proc special file system in Linux
/home/bioinfo
/home/noe
/home/noe/Desktop
Root directory
Home directory
10. Sol Genomics Network
Anatomy of a UNIX command
grep -c -A 3 --ignore-case file.txt
command
Simple option flag
(short form)
option (long form)option with
argument
argument
man grep
print grep manual
11. Sol Genomics Network
ls, cd and pwd to navigate the file system
• where am I? pwd
• how to change current directory cd
• what files and directories are in my current directory? ls
pwd
return current work directory
12. Sol Genomics Network
ls
list directories and files in current directory
ls lists directories and files
ls -a
list all directories and files, including hidden files
ls -l -h -t
time sorted
ls -lhS
size sorted
ls -l -h
list in long format
human readable
13. Sol Genomics Network
ls lists directories and files
r readable
w writable
x executable or searchable
- not rwx
d Directory
- Regular file
d rwx r-x r-x
user
group
other
owner user
permissions
owner group
date File namesizelinks #
14. Sol Genomics Network
Use up and down
arrows to navigate
the command
history
Wildcards, history and some shortcuts
ls *txt
ls P*s list files starting with P and ending with s,
e.g.: Pictures, Photos, Programs ...
list all txt files in current directory
ctrl-c stop process
ctrl-a go to begin of line
ctrl-e go to end of line
ctrl-r search in command history
15. Sol Genomics Network
Escaping special characters
Tip: file names in lower
case and with underscores
instead of spaces
! @ $ ^ & * ~ ? . | / [ ] < > ` " ;# ( )
Use tab key to
autocomplete names
ls my folder list a folder containing a space
ls my_folder list a folder
16. Sol Genomics Network
Use tab key to
autocomplete names
cd changes directory
cd Desktop
changes directory to Desktop
cd ..
goes to parent directory
cd goes to home directory
cd / goes to root directory
cd - goes to previous directory
17. Sol Genomics Network
Absolute and relative paths
ls /home/user/Desktop
list files in Desktop using an absolute path
ls Desktop/
list files in Documents using a relative path (from your home: /home/bioinfo)
ls ~/Desktop
list files in Desktop using your home as a reference
18. Sol Genomics Network
Absolute and relative paths
ls /home/bioinfo/Desktop
ls ~/Desktop
Absolute paths do not depend on where you are
~/ is equivalent to /home/bioinfo/
19. Sol Genomics Network
Absolute and relative paths
ls ../Documents
cd Desktop/
goes to Desktop from when you are in your home (/home/bioinfo)
list files from Documents when you are in Desktop
20. Sol Genomics Network
Create, copy, move and delete files
touch tmp_file.txt
creates an empty file called tmp_file.txt
cp tmp_file.txt file_copy.txt
copies tmp_file.txt in file_copy.txt
rm file.txt deletes file.txt
mv file1.txt file2.txt moves or rename a file
Tip: file names in lower
case and with underscores
instead of spaces
21. Sol Genomics Network
Locate a file
locate unix_class_file_samples.zip
Locate the path for the file unix_class_file_samples.zip
locate unix_class
Locate the path for all the files containing unix_class
22. Sol Genomics Network
Create, copy and delete directories
mkdir dir_name
creates an empty directory called dir_name
rmdir dir_name
deletes dir_name directory if it is empty
cp -r dir_name dir_copy
copy dir_name and its files in a new folder
rm -r dir_name delete dir_name and its files
23. Sol Genomics Network
wc file counts lines, words and bytes
paste file1 file2
concatenates the lines of input
files
paste -d “,”
concatenates the lines of input
files by commas
sed transforms text
locate file_name searches a file
man command shows commands manual
top shows process activity
df -h shows disk space info
Networking CommandsNetworking Commands
wget URL download a file from an URL
ssh user@server connects to a server
scp copy files between computers
apt-get install installs applications in linux
Compression commandsCompression commands
gzip/zip compress a file
gunzip/unzip decompress a file
tar -cvf groups files
tar -xvf ungroups files
tar -zcvf groups and gzip files
tar -zxvf gunzip and ungroups files
Text handling commandsText handling commands
command > file saves STDOUT in a file
command >> file appends STDOUT in a file
cat file concatenate and print files
cat file1 file2 > file3 merges files 1 and 2 into file3
cat *fasta > all.fasta
concatenates all fasta files in
the current directory
head file prints first lines from a file
head -n 5 file prints first five lines from a file
tail file prints last lines from a file
tail -n 5 file prints last five lines from a file
less file view a file
less -N file includes line numbers
less -S file wraps long lines
grep ‘pattern’ file Prints lines matching a pattern
grep -c ‘pattern’ file counts lines matching a pattern
cut -f 1,3 file
retrieves data from selected
columns in a tab-delimited file
sort file sorts lines from a file
sort -u file sorts and return unique lines
uniq -c file filters adjacent repeated lines
wc file counts lines, words and bytes
paste file1 file2
concatenates the lines of input
files
paste -d “,”
concatenates the lines of input
files by commas
sed transforms text
File system CommandsFile system Commands
ls lists directories and files
ls -a lists all files including hidden files
ls -lh formatted list including more data
ls -t lists sorted by date
pwd returns path to working directory
cd dir changes directory
cd .. goes to parent directory
cd / goes to root directory
cd goes to home directory
touch file_name creates en empty file
cp file file_copy copy a file
cp -r copy files contained in directories
rm file deletes a file
rm -r dir deletes a directory and its files
mv file1 file2 moves or renames a file
mkdir dir_name creates a directory
rmdir dir_name deletes a directory
locate file_name searches a file
man command shows commands manual
top shows process activity
df -h shows disk space info
Networking CommandsNetworking Commands
wget URL download a file from an URL
ssh user@server connects to a server
scp copy files between computers
apt-get install installs applications in linux
Compression commandsCompression commands
gzip/zip compress a file
gunzip/unzip decompress a file
tar -cvf groups files
tar -xvf ungroups files
tar -zcvf groups and gzip files
tar -zxvf gunzip and ungroups files
UNIX Command-Line Cheat Sheet
BTI-SGN Bioinformatics Course 2014
Compression commands
tar -zcvf file.tar.gz f1 f2
groups and compress files
tar -zxvf file.tar.gz
decompress and ungroup a tar.gz file files, directories or wildcards
24. Sol Genomics Network
Compression commands
gzip f1.txt
gunzip file.gz
unzip file.zip decompress file.zip
zip file.zip f1 f2
compress files f1 and f2 in file.zip
compress file f1.txt in f1.txt.gz
decompress file.gz
25. Sol Genomics Network
Text handling commandsText handling commands
command > file saves STDOUT in a file
command >> file appends STDOUT in a file
cat file concatenate and print files
cat file1 file2 > file3 merges files 1 and 2 into file3
cat *fasta > all.fasta
concatenates all fasta files in
the current directory
head file prints first lines from a file
head -n 5 file prints first five lines from a file
tail file prints last lines from a file
tail -n 5 file prints last five lines from a file
less file view a file
less -N file includes line numbers
less -S file wraps long lines
grep ‘pattern’ file Prints lines matching a pattern
grep -c ‘pattern’ file counts lines matching a pattern
cut -f 1,3 file
retrieves data from selected
columns in a tab-delimited file
sort file sorts lines from a file
sort -u file sorts and return unique lines
uniq -c file filters adjacent repeated lines
wc file counts lines, words and bytes
paste file1 file2
concatenates the lines of input
files
paste -d “,”
concatenates the lines of input
files by commas
sed transforms text
File system CommandsFile system Commands
ls lists directories and files
ls -a lists all files including hidden files
ls -lh formatted list including more data
ls -t lists sorted by date
pwd returns path to working directory
cd dir changes directory
cd .. goes to parent directory
cd / goes to root directory
cd goes to home directory
touch file_name creates en empty file
cp file file_copy copy a file
cp -r copy files contained in directories
rm file deletes a file
rm -r dir deletes a directory and its files
mv file1 file2 moves or renames a file
mkdir dir_name creates a directory
rmdir dir_name deletes a directory
locate file_name searches a file
man command shows commands manual
top shows process activity
df -h shows disk space info
Networking CommandsNetworking Commands
wget URL download a file from an URL
ssh user@server connects to a server
scp copy files between computers
apt-get install installs applications in linux
Compression commandsCompression commands
gzip/zip compress a file
gunzip/unzip decompress a file
tar -cvf groups files
tar -xvf ungroups files
tar -zcvf groups and gzip files
tar -zxvf gunzip and ungroups files
UNIX Command-Line Cheat Sheet
BTI-SGN Bioinformatics Course 2014
•Networking commands
Networking Commands
26. Sol Genomics Network
scp noe@boyce.sgn.cornell.edu:/home/noe/file.txt .
copy file.txt from your home in the server to the current directory in your computer
Networking Commands
wget http://btiplantbioinfocourse.files.wordpress.com/2014/01/unix_command_sheet_2014.pdf
downloads the UNIX command line cheat sheet PDF file
ssh user_name@server_adress
connects your terminal to your account in a server
Tip: use the command pwd to get the path for cp and scp
27. Sol Genomics Network
scp file.txt noe@boyce.sgn.cornell.edu:
copy file.txt from the current directory in my computer to my home in the server
Networking Commands
ssh noe@boyce.sgn.cornell.edu
connects my terminal to my account Boyce, the BTI server
scp -r dir/ noe@boyce.sgn.cornell.edu:
copy the folder dir and all its files and subdirectories to my home in the server
28. Sol Genomics Network
Useful commands in the server
top
display and update sorted information about processes
df -h shows disk space information
29. Sol Genomics Network
q quit
u user (top -u user)
M sort by memory usage
Top displays and update sorted information about processes
30. Sol Genomics Network
Commands to install software
sudo apt-get install pbzip2
installs pbzip2 in your computer
call the command with super user permissions
aptitude search blast
sudo aptitude install blast2
31. Sol Genomics Network
1. Go to your Desktop directory using the command cd
2. Use the command touch to create a file called:
Do not Use “special characters” in file names!.txt
3. Use the command rm to delete that file
4. Use the command mkdir to create a folder called unix_data in your desktop
5. Copy the file unix_class_file_samples.zip from your folder Data, in your home, to the
folder unix_data, in your desktop
6. Uncompress the file unix_class_file_samples.zip in /home/bioinfo/Desktop/unix_data
7. Use the command rm with the option -r to remove the _MACOSX folder
8. Use the command wget to download the “UNIX command line cheat sheet” PDF from:
https://btiplantbioinfocourse.files.wordpress.com/2014/02/unix_command_sheet_2014.pdf
Exercises