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.

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.

 

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