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 ~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.

     

    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

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


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