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 ~40 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 workshop: 06 July – 12 October 2021; 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/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.

Workshop Sponsors: H3ABioNet + Local Classrooms

Classroom applications:

Registration for classrooms opens:  26 April 2021

Registration for classrooms closes: 11 May 2021

Link to classroom application form: <Classroom registration is now closed> 

Notification date for successful classrooms: 19 May 2021

Participant applications:

Registration for participants opens:  20 May 2021

Registration for participants closes: 14 June 2021 at 11:59 pm CAT

Application instructions: Participants must select a classroom within their region and that they are able to attend physically should that particular classroom choose to go ahead as a face-to-face classroom. Please be sure to adhere to this as selecting a classroom outside of your region/location may result in your application being rejected. Please also be aware that applying for the course does not guarantee entry - you will undergo a formal selection process.

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