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.
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.
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
Participant 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
- 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:
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Modules |
Dates |
Time |
Topics |
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Staff orientation |
15 April – 17 April |
10h00 am -14h30 pm CAT |
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Participant orientation |
22 April |
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Introduction to Bioinformatics |
24 April |
What is Bioinformatics and why it is important? |
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Module 1 |
29 April – 8 May |
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Module 2 |
13 May -22 May |
Linux |
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Module 3 |
27 May – 03 June |
Sequence alignment |
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Module 4 |
10 June – 12 June |
Multiple sequence alignment |
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Module 5 |
17 June – 19 June |
Molecular Evolution and Phylogenetics |
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Module 6 |
24 June – 8 July |
Genomics |
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Course wrap up |
15 July |
Feedback and evaluation |
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.
Training material availability
