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Course Overview
African Genomics Data Hub collaboration with H3ABioNet aim to host the 10th iteration of Introduction to Bioinformatics (IBT). This introductory course, IBT, provides an introduction to the field of bioinformatics, with a focus on important bioinformatic tools and resources. Over a period of 3 months of intensive biweekly contact sessions, the course combines theoretical and practical sessions to allow participants to gain practical experience in using various tools and resources. During contact sessions, classrooms meet virtually to discuss the session’s content with each other and the trainer.
Intended Audience
The course is aimed at individuals from a molecular biology background who have a basic understanding of biochemistry and/or genetics and would like to become bioinformatics users. For an explanation on who 'bioinformatics users' might be, see Figure 2 in http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003496. A baseline level of the understanding of the central dogma of biology (DNA -> RNA -> Protein) is a requirement.
Keywords: Genetics, Genomics, Nucleic acids analysis
Skill level of training: Beginner
Language: English
Credential awarded: Letter of completion/attendance
Type of training: Blended/hybrid learning
Venue of the course:
Dates for the course:
Course organisers: Sindiswa Lukhele, Tshinakaho Malesa, Shaun Aron, Sumir Panji, Suresh Maslamoney, Nicola Mulder
Participation:
Course Sponsors: AfriGen-D + Local classrooms
Course objectives

After this workshop participants should be able to:

 

  • Explain the use of bioinformatics
  • Name the key bioinformatics techniques and tools
  • Locate important biological databases and retrieve data
  • Use selected tools effectively to run specific bioinformatics analyses
  • Understand the strengths and limitations of the various techniques
 

Classroom applications

Registration for classrooms opens: Fri, 13/12/2024
Registration for classrooms closes: Fri, 17/01/2025
Notification date for successful classrooms: Mon, 03/02/2025
Maximum number of participants that may be accepted per classroom will be capped at 40

Participant applications

Registration for participants opens: Mon, 17/02/2025
Registration for participants closes: Fri, 21/03/2025
Participant registration link:

Syllabus and Tools

The course curriculum will cover the following main themes (subject to slight changes):

 

  • Bioinformatics resources and databases
    • Introduction to bioinformatics, biological databases and resources (NCBI and EBI), data formats, ontologies
  • Linux
    • Introduction to Linux, general overview of Linux environment, overview of command line interface, navigating Linux directory structure, manipulating files and directories, basic Linux commands
  • Sequence alignment theory and applications
    • Introduction to searching and sequence alignment, BLAST, pairwise sequence alignment
  • Multiple sequence alignment (MSA)
    • MSA theory, generating and interpreting MSAs using various tools, visualising and assessing MSA quality
  • Molecular evolution and phylogenetics
    • Molecular evolution, phylogenetic approaches and methods (Introduction and overview of methods)
  • Genomics
    • Overview of sequencing and annotation, Ensembl genome browser, Genetic variation, HapMap, 1000 genomes

 

 **All modules make use of predominantly web-based tools such as NCBI, genome browsers, etc.

 

Licensing for course materials: The default licensing attached to any workshop and materials will be a creative commons license. Please do specify if a different license is required or whether materials will not be available publicly. If materials cannot be linked to our website, please specify a contact person in order to gain access to materials in future.

Workshop Programme:

 

Modules

Dates

Time

Topics

Staff orientation

15 April – 17 April

10h00 am -14h30 pm CAT

 

Participant orientation

22 April

Introduction to Bioinformatics

24 April

What is Bioinformatics and why it is important?

Module 1

29 April – 8 May

Databases and Resources

Module 2

13 May -22 May

Linux

Module 3

27 May – 03 June

Sequence alignment

Module 4

10 June – 12 June

Multiple sequence alignment

Module 5

17 June – 19 June

Molecular Evolution and Phylogenetics

Module 6

24 June – 8 July

Genomics

Course wrap up

15 July

Feedback and evaluation

 

Prerequisites

A basic background/understanding of biochemistry and/or genetics.


Course limitations

This course will only provide a foundation for continued learning in bioinformatics and will not teach any advanced coding.
For more information, please visit For more information on IBT, please visit https://www.h3abionet.org/training/ibt  

Training material availability