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Linux and Shell Scripting Training

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This module introduces learners to the Linux operating system. Linux supports a lot of open source Bioinformatics tools and software. It is therefore important for learners to develop skills that will enable them use Linux effectively to solve Bioinformatics problems.

Aim of the Module

By the end of this module learners will be able to:

  • Demonstrate understanding of computer operating systems.
  • Acquire in depth knowledge of the Linux system
  • Use the basic features of the Linux operating system.
  • Effectively work in the Linux command line
  • Navigate the Linux directory system
  • Demonstrate knowledge of Linux files system concepts and organization.
  • Manipulate files and directories
  • Apply file operations including changing permissions, ownership creation, deletion, moving and renaming
  • Create user accounts,
  • Get information using commands on a Linux system.
  • Install tools and programs on Linux system
  • Use regular expressions to describe the search patterns
  • Write simple shell scripts in bash
  • Connect to remote computers and transfer files using Linux commands.
  • Create and edit text files in a Linux text editor to illustrate knowledge of the text editor functions and commands.

Venue

  • College of Medicine IT lab

Dates

  • Monday 14 November 2016 to 16 November, 2016

Instructors

  • Chikumbutso Gremu
  • Arthur Mtegha
  • Benjamin Kumwenda

IT Support

  • Joel Kumwenda

Course Admin

  • Mrs M. Chavula

Participants

 

  Name Institution Sex
1 Elias Mwakilama Chancellor College M
2 Joe Nkhula Chancellor College M
3 Chikondi Malamba College of Medicine F
4 Dan Banda College of Medicine M
5 Dr Janelisa Musaya College of Medicine F
6 Linda Malimusi College of Medicine F
7 Victor Ndhlovu College of Medicine M
8 Wanangwa Ndovi College of Medicine M
9 Thoko Saulosi Catholic University M
10 Kumbukani Kondowe Dignitas M
11 Chikondi Peno MLW F
12 Chifundo Chipendo Malawi University of Science and Technology F
13 Edwin Khundi Malawi University of Science and Technology M
14 Menard Phiri Malawi University of Science and Technology M
15 Chimango Nyasulu Mzuzu University M
16 Emmanuel Ngalande Mzuzu University M
17 Khwima Mukalira QECH F
18 Charles Nyasa Zero Investigates M
19 Ibrahim Chikowi College of Medicine M
20 Angeziwa Chirambo Malawi-Liverpool  

Wellcome Trust

F
21 Dr Elizabeth Kampira College of Medicine F

Programme

Times 14 November 2016   15 November 2016   16 November 2016
8.00 – 8.45 Registration, Opening Remarks        
8.45 – 10.30 Introduction to Operating Systems, Introduction to Linux system, A brief history of Linux, Architecture of Linux  

Instructor: Benjamin

  Introduction networking in Linux -Lecturer  

 

Instructor: Chikumbutso

  Introduction to biological sequences and the biology central dogma – Lecture  

Instructor: Benjamin

10.30 – 11.00 Coffee Break
11.00 – 12.30 The Linux file system, Linux directory structure, Directory and file handling  

Creating, copying, naming, deleting files and directories

Instructor: Benjamin

  Connecting to remote computers and running jobs remotely  

Transferring files on networked computers using ssh, scp,

Instructor: Chikumbutso

  Introduction to shell scripting  

Advanced text file processing

Introduction to regular expressions. Searching and printing text in text editors and command line

Instructor: Arthur

12.30 – 13.30 Lunch Break
13.30 – 15.00 File and directory permissions  

File and directory ownership, Inspecting contents of file contents. Finding files using Linux command line (locate, find)

Finding text in files, Sorting files. Making symbolic links

Instructor: Arthur

  Installing, running programs on a Linux system. Installing programs from the Internet. Setting up shell and environmental variables, Creating cron jobs, File compression, Using removable media  

Instructor: Arthur

  Installing, running programs on a Linux system. Installing programs from the Internet. Setting up shell and environmental variables, Creating cron jobs. File compression.Using removable media  

Instructor: Arthur

15.00 – 15.30 Coffee Break
15.30 – 16.30 Creation of users, groups, setting permissions and ownership on directories and files, Logging to Linux system, Changing passwords  

Instructor: Arthur

  Creating and monitoring processes  

Pipes, Redirecting input and output

Instructor: Arthur

  End of Training  

 

mlw_logoThe Malawi-liverpool Wellcome Trust is funding this training