Course Overview
The course aims to provide an introduction to the field of bioinformatics, with a focus on important bioinformatics tools, and resources. The course aims to use a combination of theoretical and practical sessions in order for participants to gain practical experience in using various tools and resources.

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: Local classrooms ( usually ~50 physical/online sites across Africa).

Dates for the course: 16 April - 30 July 2024. Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT

Course organisers: Sindiswa Lukhele, Tshinakaho Malesa, Shaun Aron, Sumir Panji, Verena Ras, Nicola Mulder and local classrooms across Africa

Participation: The course is available to any classroom who meets the requirements and to any participant who is able to attend a physical/online classroom, provided they have been selected via the selection process. Should a classroom decide to host a face-to-face classroom, the participant must be able to attend this classroom in person for the duration of the course. Notification of success will be sent to successful applicants.

Course Sponsors: H3ABioNet 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

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
• Genomics
  • Overview of sequencing and annotation, Ensembl genome browser, Genetic variation, HapMap, 1000 genomes
• Molecular evolution and phylogenetics
  • Molecular evolution, phylogenetic approaches and methods (Introduction and overview of methods)

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

 

Prerequisites

A basic background/understanding of biochemistry and/or genetics

Course limitations
This workshop will only provide a foundation for continued learning in bioinformatics and will not teach any advanced coding.

Training material availability

Training materials for this workshop will be linked here as soon as they are available. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.