Introduction: Linux is an Operating System (OS) for computers. It is software that drives the memory, hard disk, CPU and other computer hardware and software components. In this sense, it is similar to the Windows OS from Microsoft, but there are major differences between the two. This course aims at teaching students how to use the powerful Linux operating system to work with biological data

Why learn Linux? The Linux OS offers many features that are well-suited for bioinformatics projects such as faster execution of programs, multi-threading, job management, scheduling, file and data processing with linux programs like grep, awk and sed, wide variety of available open source command line applications, automation through scripting and programming syntax available. Our Linux course teaches users how to obtain, store and work with biological data. Several applications such as BLAST, FASTA, Primer3 and mFold are used to illustrate the benefits of using Linux.

Introduction:Linux is an Operating System (OS) for computers. It is software that drives the memory, hard disk, CPU and other computer hardware and software components. In this sense, it is similar to the Windows OS from Microsoft, but there are major differences between the two. This course aims at teaching students how to use the powerful Linux operating system to work with biological data


Why learn Linux? The Linux OS offers many features that are well-suited for bioinformatics projects such as faster execution of programs, multi-threading, job management, scheduling, file and data processing with linux programs like grep, awk and sed, wide variety of available open source command line applications, automation through scripting and programming syntax available. Our Linux course teaches users how to obtain, store and work with biological data. Several applications such as BLAST, FASTA, Primer3 and mFold are used to illustrate the benefits of using Linux.


Logistics: This online Linux course is divided into 4 session and comes with slides, pre-recorded videos, reference cards, examples, data, scripts and quizzes. Enrollees can contact the instructor with questions and get help on the projects. The main topics are listed below. Homework assignments will involve running commands learned in the live lectures.


Basic knowledge of computers and a need to work with biological data. or curiosity to know what possibly can be done with data on a Linux machine.


Price: $1200 for Commercial/Government enrollees and $600 for Academic researchers and students.


Instructor: Shailender Nagpal


Topics included:

  • Fundamentals of the Linux OS and connecting to a Linux server
  • Linux file system, navigation and basic structure of a command
  • Features of the linux shell
  • Basic file operations such as reading, writing, merging, copying and moving files
  • Setting permissions of files and directories
  • File search and manipulations using grep, awk, cut, sort, uniq and sed
  • Output redirection and piping of commands
  • Command line execution of various bioinformatics programs
  • Exercise to demonstrate getting data and software from the internet

Introduction:This course builds upon the fundamental concepts covered in the Level 1 Linux course. In this course, we cover intermediate topics such as regular expressions, shell scripting, automation with cronjobs and process management. Syllabus is shown below


Why take Linux 2? The Linux OS offers many features that are well-suited for bioinformatics projects that were not covered in the Level 1 course. In this course, we take it up a notch and discuss many useful ways of leveraging Linux such as scripting and automation.


Logistics: This Linux course is divided into 4 sessions and comes with slides, pre-recorded videos, reference cards, examples, data, scripts and quizzes. Enrollees can contact the instructor with questions and get help on the projects. The main topics are listed below. Homework assignments will involve running commands learned in the live lectures.


Linux Level 1 or equivalent basic knowledge of Linux is required.


Price: $1200 for Commercial/Government enrollees and $600 for Academic researchers and students.


Instructor: Shailender Nagpal


Syllabus:

  • Monitoring Linux resources
  • Environment and shell variables
  • System services: FTP, database server, web server, file server
  • Arithmetic operations in the shell
  • Customizing bash shell
  • Shell scripting
  • Regular expressions
  • Process management
  • Code versioning
  • Automation and scheduling with crontab