Course Overview/description: The use of repositories and version control tools such as GitHub and Git for hosting, pulling, installing and collaborative development of code and software in bioinformatics is now commonplace. The “Introduction to Git and Github” course will provide an overview of version control, creating a GitHub account and how to use Git for version control and collaboratively work in code repositories hosted on GitHub.

    Keywords: Version control, Git, GitHub, software, code

    Skill level of training: Beginner

    Language: English

    Credential awarded: None

    Type of training: Online training

    Venue of workshop: Virtual

    Dates for the workshop: 30th November 2020 – 10am CAT

    Workshop organisers: Jon Ambler, Shaun Aron, Christopher Fields, Gerrit Botha, Suresh Maslamoney, Yasmina Jaufeerally Fakim, Shakuntala Baichoo, Itunuoluwa Isewon, Scott Hazelhurst, Sumir Panji, Nicky Mulder

    Registration opens: 24th November 2020

    Registration closes: 27th November 2020 at 10 pm CAT

    Notification date: 29th November 2020

    Link to application form: https://redcap.h3abionet.org/redcap/surveys/?s=MWT9CEDMNE

    Workshop Sponsors: CIDRI-Africa and H3ABioNet

    Intended Audience: Persons wishing to get familiar with and use Git and GitHub. Reference Graph and Containerization Hackathon participants needing to gain familiarity with Git and GitHub.

    Licensing for course materials: Creative Commons

    Prerequisites:

    Learning objectives/outcomes: After this workshop participants should be able to:

    • Define version control and its importance
    • Gain familiarity with git commands and functions
    • Commit code to a GitHub repository
    • Pull code from a GitHub repository
    • Tracking changes and versions using git
    • Use Git for collaborative projects

    Workshop limitations: This workshop will only provide a foundation for continued learning in using version control and tools such as Git and GitHub.

    Materials adapted from: https://swcarpentry.github.io/git-novice/



    Course Overview/Description: The use of workflow technologies such as Nextflow is becoming increasingly pervasive in bioinformatics. Workflows automate the execution of various bioinformatics tools and pipelines and reduces the time one spends on running the different steps in a particular pipeline while testing various parameters as well as enabling reproducible analysis. The “Introduction to Nextflow” workshop will provide an introduction to workflows, some basic usage and syntax for using Nextflow.

    Keywords: Workflows, bioinformatics, reproducible

    Skill level of training: Beginner

    Language: English

    Credential awarded: None

    Type of training: Online training

    Venue of workshop: Virtual

    Dates for the workshop (duration if run as a MOOC): 1st December 2020 – 2:30pm CAT

    Workshop organisers: Phelelani Mpangase, Shaun Aron, Christopher Fields, Gerrit Botha, Suresh Maslamoney, Yasmina Jaufeerally Fakim, Shakuntala Baichoo, Itunuoluwa Isewon, Scott Hazelhurst, Sumir Panji, Nicky Mulder

    Registration opens: 25th November 2020

    Registration closes: 27th November 2020 at 10 pm CAT

    Notification date: 29th November 2020

    Link to application form: https://redcap.h3abionet.org/redcap/surveys/?s=RDMT38HXMH

    Workshop Sponsors: Sydney Brenner Institute for Molecular Biology and H3ABioNet

    Intended Audience: Persons wishing to get familiar with and use Nextflow. Reference Graph and Containerization Hackathon participants needing to gain familiarity with Nextflow.

    Syllabus and Tools:

    • Introduction to Nextflow
    • Use of workflow systems for automation / reproducibility
    • Basic syntax of Nextflow
    • Transform and execute a workflow in Nextflow

    Licensing for course materials: Creative commons

    Prerequisites:

    Learning objectives/outcomes: After this workshop participants should be able to:

    • Find and use Nextflow tool definitions online.
    • Understand how to write Nextflow scripts and definitions for command line tools.
    • Understand the concepts of Nextflow Channels, Processes and Channel operators.
    • Understand how to handle multiple inputs and outputs in Nextflow.
    • Understand Nextflow's configuration file (nextflow.config), profiles and input parameters.
    • Use Docker/Singularity with Nextflow to provide software dependencies and ensure reproducibility.
    • Join Nextflow tools into a workflow.
    • Run Nextflow workflows on local, HPC and cloud systems.

     Workshop limitations: This workshop will only provide a foundation for continued learning for using Nextflow to create bioinformatics workflows.

     Workshop Programme: 

    Time

    Topic

    Trainer

    1 December 2020

    14:00 – 15:00

    Introduction to Nextflow

    Phelelani Mpangase

    15:00 – 15:30

    Parameters, Channels and Processes

     

    Phelelani Mpangase

    15:30 – 16:00

    Docker/Singularity

    Phelelani Mpangase

    16:00 – 16: 30

    Executors

    Phelelani Mpangase

    16:30 – 17:00

    Channel Operations

    Phelelani Mpangase

     


    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:10 July – 15 October; Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT.

    Workshop organisers: Kim GurwitzShaun 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

     

    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 ONLY 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.

     

    See course website here: https://training.h3abionet.org/IBT_2017/


    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: 11 September – 13 December; 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:  07 June 2018

    Registration for classrooms closes: 07 July 2018

    Link to classroom application form: applications are now closed

    Notification date for successful classrooms: 10 July 2018

    Participant applications:

    Registration for participants opens:  15 July 2018

    Registration for participants closes: 10 August 2018

    Link to participant application form: https://is.gd/IBT_participant_registration

    Notification date for successful participants: 20 August 2018

    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 ONLY 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

    IBT Youtube channel: https://www.youtube.com/playlist?list=PLcQ0XMykNhCQXNXiv6jtEo8WnOMlT7XeS 


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