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
Type of training: Blended/hybrid learning
Logistics
Venue of workshop: Local classrooms ( usually 30 physical sites across Africa) and online
Dates for the workshop: 04 May – 31 July 2020; Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT.
Workshop organisers: Paballo Chauke, Verena Ras, Shaun Aron, Sumir Panji and 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 classroom, if one has been set up at a local institution, provided they have been selected via the selection process.
Workshop Sponsors: H3ABioNet
Classroom applications:
Registration for classrooms opens: 03 February 2020
Registration for classrooms closes: 28 February 2020
Link to classroom application form: https://is.gd/IBT_2020_Classroom_Host
Notification date for successful classrooms: 05 March 2020
Participant applications:
Registration for participants opens: 08 March 2020
Registration for participants closes: 03 April 2020
Link to participant application form: https://redcap.link/IBT_participants_2020
Course Curriculum:
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 of biochemistry and/or genetics.
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
Workshop 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 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