Introduction to Bioinformatics Training

    H3ABioNet‘s Introduction to Bioinformatics 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.

     

    In 2018 IBT was hosted in 29 classrooms across 13 African countries. The map below shows the distribution of classrooms.

    IBT map of classrooms in 2018

     

     Interested in hosting an IBT classroom at your institution? contact  

     

    Why?

    A number of H3Africa members expressed an interest in and need for basic Bioinformatics training for individuals entering the discipline, or for those who need a basic foundational understanding of Bioinformatics before moving on to more complex areas. A task force, from the H3ABioNet Education and Training Working Group, has therefore developed an Introduction to Bioinformatics course in order to meet this need.

     

    Who?

     

    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 basic Bioinformatics users. A base line level of the understanding of the central dogma of molecular biology (i.e. DNA to RNA to Protein) is a requirement.

     

    How?

    Course logistics

    A distance-based learning model is used for this course. Classrooms are set up at different sites (which meet certain infrastructure requirements) and link to the trainer via the Adobe conferencing system during biweekly contact sessions. 

    To ensure that internet instability is not a barrier to education, lectures are pre-recorded, downloaded, and watched locally in classrooms.

    There are appropriately trained local teaching assistants at each of the sites to assist with the practical components of the course, which run using online tools as far as possible.

    There is no application or participation fee. Local sites provide the physical resources for the course and the course core team provides logistic and course management support via the Vula platform.

     

    What?

     

    Course objectives

    By the end of the course participants should be able to:
    • Explain the use of Bioinformatics
    • Name 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

     

    Course modules

    Databases and Resources

    • Biological databases and resources (NCBI, EBI)
    • Advanced literature searching – PubMed
    • DNA analysis – e.g. sequence features, start site, restriction sites etc
    • Protein function classification

    Linux

    • Introduction to Linux, UNIX and the command line
    • Manipulating files – useful commands and tips
    • Permissions, groups, and process control

    Sequence Alignment

    • Introduction to searching and sequence alignment
    • Pairwise sequence alignment
    • BLAST algorithm

    Multiple Sequence Alignment

    • Applications of multiple sequence alignment
    • Choosing the right sequences with the right software

    Genomics

    • Genome sequences – sequencing technology and brief NGS overview
    • Genome browsers and annotation
    • Comparative Genomics
    • Human variation

    Molecular Evolution and Phylogenetics

    • Historical perspective, mechanisms of molecular evolution, and speciation.
    • Traits, phylogenies, evolutionary models and divergence times.
    • Tree building with distance matrix methods. Parsimony approaches.
    • Tree building with maximum likelihood approaches. Bayesian viewpoint. Branch support measures.

     

    Additional elements of the course:

    Staff Training

    Introduction Week

    Wrap up Session

    Bonus Module – Gene Expression


    Subcategories

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