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). Please be aware that the course is likely to make use of a combination of both physical and online sites depending on ongoing Covid-19 restrictions.

Dates for the course: Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT

Course organisers: Verena Ras, Shaun Aron, Sumir Panji, Nicola Mulder

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.

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.

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

For more information, please visit https://www.h3abionet.org/training/ibt

Training material availability

Training materials for this course are available here: https://zivahub.uct.ac.za/projects/Introduction_to_Bioinformatics_Training_Course_Materials/131552. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.

Materials have been made available as a single archive per module containing lecture slides, transcribed videos, practical assignments and any other resources important to complete each module:

Module 1: Databases and Resources

Module 2: Linux

Module 3: Sequence Alignment

Module 4: Multiple Sequence Alignment

Module 5: Genomics

Module 6: Phylogenetics (2018 - 2021)

Module 6: Structural Biology (2016 only)

Introduction Week

Wrap Up week