H3ABioNet Introduction to Bioinformatics online course (IBT_2016)

    June 2019
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    Course websitehttp://training.h3abionet.org/IBT_2016/

    Venue of course: 19 classrooms across 11 African countries. Classrooms connect to the trainer via Mconf (‘virtual classroom’).

    Dates for the course: 6th July – 9th October 2016, every Wednesday and Thursday, 10:00-14:00 CAT each day

    Course organisers: H3ABioNet Education and Training working group and the IBT core team (Kim Gurwitz, Shaun Aron, Sumir Panji and Nicola Mulder)

    Participation via Classrooms: A call was sent out for institutions to apply to host a classroom. Classroom selection was based on the availability of certain infrastructure requirements, as well as the availability of dedicated, local teaching assistants. Classrooms hosted at both H3ABioNet and non-H3ABioNet institutions.

    Participants: Participants applied to a particular classroom via a centralised application form and were informed of the outcome of their application.

    Course Sponsors: H3ABioNet

    Course Overview: The IBT_2016 course is an introduction to the field of Bioinformatics, with a focus on important Bioinformatic tools, algorithms 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.

    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.

    Syllabus and Tools: The participants will cover an introduction to various Bioinformatics topics, namely; Databases and Resources, Genomics, Linux, Sequence alignment theory and application, Multiple sequence alignment, Protein structural Bioinformatics, Phylogenetics and molecular evolution. For practical sessions, web-based tools are used as far as possible.

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

    Objectives: By the end of the course 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

    Course limitations: This course will provide an introduction to the field of Bioinformatics. Participants must be able to attend biweekly contact sessions at one of the classroom sites.

    Course costs: 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

     

    IBT_2016 course schedule(*subject to slight changes)

     

    Date Topic Trainer
    Welcome to the course!

    Wednesday,

    6 July

    Introductory session (+- 1 hour)

    - get to know where your classroom is and meet your teaching assistants and fellow participants

    (NOTE: a repeat of this session will be held on Monday, 11 July for those unable to make the session on the 6 July. A written document detailing the logistics of the course will also be available)

    IBT core team
    Introduction to databases and resources
    Wednesday, 13 July Guest lecturers: ‘What is bioinformatics and why is it important?’

    Pedro Fernandes

    Instituto Gulbenkian de Ciência, Oeiras, Portugal

    and

    David P Judge

    Freelance independent Bioinformatics instructor

    Thursday,

    14 July

    Biological databases and resources (NCBI, EBI)

    Shaun Aron

    University of Witwaterstrand, South Africa

    Wednesday, 20 July

    Advanced literature searching – PubMed

    Shaun Aron

    Thursday,

    21 July

    DNA analysis – e.g. sequence features, start site, restriction sites etc

    Nicola Mulder University of Cape Town, South Africa

    *Thursday,

    21 July

    Assessment available for the ‘introduction to databases and resources’ module via Vula ‘Tests and Quizzes’ tab individual

    *Tuesday,

    26 July

    FINAL hand-in date for ‘introduction to databases and resources’ assessment

    individual
      Genomics  

    Wednesday,

    27 July

    Genome sequences – sequencing technology and NGS overview

     

    Fatma Guerfali Institute Pasteur de Tunis, Tunisia

    Thursday,

    28 July

    Genome annotation including genome browsers (feature finding etc)

     

    Colleen Saunders

    South African National Biodiversity Institute, South Africa

    Wednesday,

    3 August

    Comparative genomics

     

    Fatma Guerfali

    Thursday,

    4 August

    Human variation

     

    Colleen Saunders

    *Thursday,

    4 August

    Assessment available for the ‘genomics’ module via Vula ‘Tests and Quizzes’ tab individual

    *Tuesday,

    9 August

    FINAL hand-in date for ‘genomics’ assessment individual
    Linux
    Wednesday, 10 August

    Introduction to Linux and UNIX and the command line

    Amel Ghouila

    Institute Pasteur de Tunis, South Africa

    Thursday,

    11 August

    Manipulating files. Useful commands and tips

    Amel Ghouila
    Wednesday, 17 August

    Permissions, groups and process control

    Amel Ghouila
    *Wednesday, 17 August Assessment available for the ‘Linux’ module via Vula ‘Tests and Quizzes’ tab individual

    *Wednesday,

    24 August

    FINAL hand-in date for ‘Linux’ assessment individual
    Sequence alignment theory and application

    Thursday,

    18 August

    Introduction to searching and sequence alignment

    Pandam Salifu

    Kumasi Centre for Collaborative Research, Ghana

    Wednesday, 24 August

    Pairwise sequence alignment

    Pandam Salifu

    Thursday,

    25 August

    BLAST algorithm

    Pandam Salifu

    *Thursday,

    25 August

    Assessment available for the ‘sequence alignment theory and application’ module via Vula ‘Test and Quizzes’ tab individual

    *Wednesday,

    31 August

    FINAL hand-in date for ‘sequence alignment theory and application’ assessment individual
    Multiple sequence alignment
    Wednesday, 31 August Overview of multiple sequence alignments applications

    Ahmed Mansour Alzohairy

    Zagazig University, Egypt

    Thursday,

    1 September

    Choosing the right sequences with the right software

    Ahmed Mansour Alzohairy

    *Thursday,

    1 September

    Assessment available for the ‘multiple sequence alignment’ module via Vula ‘Tests and Quizzes’ tab individual

    *Wednesday,

    7 September

    FINAL hand-in date for ‘multiple sequence alignment’ assessment individual
    Protein structural bioinformatics

    Wednesday,

    7 September

    (To be confirmed) TBC

    Ruben Cloete

    South African National Biodiversity Institute, South Africa

    Thursday,

    8 September

    TBC Ruben Cloete
    Wednesday, 14 September NO SESSION NO SESSION

    Thursday,

    15 September

    TBC Ruben Cloete

    *Thursday,

    15 September

    Assessment available for the ‘protein structural bioinformatics’ module via Vula ‘Tests and Quizzes’ tab individual

    *Wednesday,

    21 September

    FINAL hand-in date for ‘protein structural bioinforamtics’ assessment individual
                                                     Consolidation week

    Wednesday,

    21 September

    TBC TBC

    Thursday,

    22 September

    TBC TBC
    Molecular evolution and phylogenetics
    Wednesday, 28 September TBC

    Jean-Baka Domelevo Entfellner

    University of the Western Cape, South Africa

    Thursday,

    29 September

    TBC Jean-Baka Domelevo Entfellner

    Wednesday,

    5 October

    TBC Jean-Baka Domelevo Entfellner

    Thursday,

    6 October

    TBC Jean-Baka Domelevo Entfellner

    Thursday,

    6 October

    Assessment available for the ‘molecular evolution and phylogenetics’ module via Vula ‘Tests and Quizzes’ tab individual

    Wednesday,

    12 October

    FINAL hand-in date for ‘molecular evolution and phylogenetics’ assessment individual
         

    Wednesday,

    12 October

    Course end  

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