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  • The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility
  • Computing Resources
    • Active Data Storage
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      • FAQs
    • Other Resources
  • Bioinformatics Topics
    • Tools - A Basic Bioinformatics Toolkit
      • Getting more out of Microsoft Excel
      • Bioinformatics Applications of Unix
        • Unix commands applied to bioinformatics
        • Manipulate NGS files using UNIX commands
        • Manipulate alignment files using UNIX commands
      • Alignments and Mappers
      • Relational databases
        • Running Joins on Galaxy
      • Spotfire
    • Tasks - Bioinformatics Methods
      • UCSC Genome Bioinformatics
        • Interacting with the UCSC Genome Browser
        • Obtaining DNA sequence from the UCSC Database
        • Obtaining genomic data from the UCSC database using table browser queries
        • Filtering table browser queries
        • Performing a BLAT search
        • Creating Custom Tracks
        • UCSC Intersection Queries
        • Viewing cross-species alignments
        • Galaxy
          • Intro to Galaxy
          • Galaxy NGS Illumina QC
          • Galaxy NGS Illumina SE Mapping
          • Galaxy SNP Interval Data
        • Editing and annotation gene structures with Argo
      • GeneGO MetaCore
        • GeneGo Introduction
        • Loading Data Into GeneGO
        • Data Management in GeneGO
        • Setting Thresholds and Background Sets
        • Search And Browse Content Tab
        • Workflows and Reports Tab
        • One-click Analysis Tab
        • Building Network for Your Experimental Data
      • Functional Annotation of Gene Lists
      • Multiple Sequence Alignment
        • Clustalw2
      • Phylogenetic analysis
        • Neighbor Joining method in Phylip
      • Microarray data processing with R/Bioconductor
    • Running Jupyter notebooks on luria cluster nodes
  • Data Management
    • Globus
  • Mini Courses
    • Schedule
      • Previous Teaching
    • Introduction to Unix and KI Computational Resources
      • Basic Unix
        • Why Unix?
        • The Unix Tree
        • The Unix Terminal and Shell
        • Anatomy of a Unix Command
        • Basic Unix Commands
        • Output Redirection and Piping
        • Manual Pages
        • Access Rights
        • Unix Text Editors
          • nano
          • vi / vim
          • emacs
        • Shell Scripts
      • Software Installation
        • Module
        • Conda Environment
      • Slurm
    • Introduction to Unix
      • Why Unix?
      • The Unix Filesystem
        • The Unix Tree
        • Network Filesystems
      • The Unix Shell
        • About the Unix Shell
        • Unix Shell Manual Pages
        • Using the Unix Shell
          • Viewing the Unix Tree
          • Traversing the Unix Tree
          • Editing the Unix Tree
          • Searching the Unix Tree
      • Files
        • Viewing File Contents
        • Creating and Editing Files
        • Manipulating Files
        • Symbolic Links
        • File Ownership
          • How Unix File Ownership Works
          • Change File Ownership and Permissions
        • File Transfer (in-progress)
        • File Storage and Compression
      • Getting System Information
      • Writing Scripts
      • Schedule Scripts Using Crontab
    • Advanced Utilization of IGB Computational Resources
      • High Performance Computing Clusters
      • Slurm
        • Checking the Status of Computing Nodes
        • Submitting Jobs / Slurm Scripts
        • Interactive Sessions
      • Package Management
        • The System Package Manager
        • Environment Modules
        • Conda Environments
      • SSH Port Forwarding
        • SSH Port Forwarding Jupyter Notebooks
      • Containerization
        • Docker
          • Docker Installation
          • Running Docker Images
          • Building Docker Images
        • Singularity
          • Differences from Docker
          • Running Images in Singularity
      • Running Nextflow / nf-core Pipelines
    • Python
      • Introduction to Python for Biologists
        • Interactive Python
        • Types
          • Strings
          • Lists
          • Tuples
          • Dictionaries
        • Control Flow
        • Loops
          • For Loops
          • While Loops
        • Control Flows and Loops
        • Storing Programs for Re-use
        • Reading and Writing Files
        • Functions
      • Biopython
        • About Biopython
        • Quick Start
          • Basic Sequence Analyses
          • SeqRecord
          • Sequence IO
          • Exploration of Entrez Databases
        • Example Projects
          • Coronavirus Exploration
          • Translating a eukaryotic FASTA file of CDS entries
        • Further Resources
      • Machine Learning with Python
        • About Machine Learning
        • Hands-On
          • Project Introduction
          • Supervised Approaches
            • The Logistic Regression Model
            • K-Nearest Neighbors
          • Unsupervised Approaches
            • K-Means Clustering
          • Further Resources
      • Data Processing with Python
        • Pandas
          • About Pandas
          • Making DataFrames
          • Inspecting DataFrames
          • Slicing DataFrames
          • Selecting from DataFrames
          • Editing DataFrames
        • Matplotlib
          • About Matplotlib
          • Basic Plotting
          • Advanced Plotting
        • Seaborn
          • About Seaborn
          • Basic Plotting
          • Visualizing Statistics
          • Visualizing Proteomics Data
          • Visualizing RNAseq Data
    • R
      • Intro to R
        • Before We Start
        • Getting to Know R
        • Variables in R
        • Functions in R
        • Data Manipulation
        • Simple Statistics in R
        • Basic Plotting in R
        • Advanced Plotting in R
        • Writing Figures to a File
        • Further Resources
    • Version Control with Git
      • About Version Control
      • Setting up Git
      • Creating a Repository
      • Tracking Changes
        • Exercises
      • Exploring History
        • Exercises
      • Ignoring Things
      • Remotes in Github
      • Collaborating
      • Conflicts
      • Open Science
      • Licensing
      • Citation
      • Hosting
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  1. Mini Courses
  2. Introduction to Unix and KI Computational Resources
  3. Basic Unix

Why Unix?

UNIX is an operating system (suite of programs), originally developed in 1969 at Bell Labs and has been under development ever since. UNIX is a very popular operating system for many reasons, including:

  • multi user (multiple users can log in to a computer at the same time, and use concurrently the resources of that computer).

  • multi-tasking (each user can perform many tasks at the same time).

  • network-ready (built-in TCP /IP networking makes easy to communicate between computers).

  • very powerful programming environments (free of the many limits imposed by other operating systems).

  • robust and stable.

  • scalable, portable, flexible.

  • open source.

UNIX systems also have a graphical user interface (GUI) similar to Microsoft Windows which provides an easy to use environment. However, knowledge of UNIX is required for operations which aren't covered by a graphical program, or for when there is no windows interface available (for example, in a telnet session).

UNIX at a glance

UNIX consists of three main components: kernel, shell, and programs.

  • KERNEL: hub of the operating system.

  • SHELL: command line interpreter.

  • PROGRAMS: collections of operations.

Each component has specific roles:

  • KERNEL: it allocates time and memory to programs and handles the filestore and communications in response to system calls.

  • SHELL: it interprets the commands the user types in and arranges for them to be carried out.

  • PROGRAM: execute a set of predefined operations.

As an illustration of the way the shell and the kernel work together, suppose a user types the following command:

rm myfile 

Internally,

  1. The shell searches the PATH environment variable for the file containing the program rm.

  2. The shell requests to the kernel, through system calls, to execute the program rm on myfile.

  3. When the process has finished running, the shell returns the UNIX prompt to the user, indicating that it is waiting for further commands.

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