This document aims to serve as a general guideline to assist in developing and running (Bioinformatics) training events. It summarizes the major steps taken by H3ABioNet to plan/organize a short-term workshop or course. H3ABioNet often tailors these approaches depending on the needs of a particular training but examples have been included where available.

    A separate archive is available containing (only) the original template documents that have been provided as part of the main guide (for easy reference) here: https://doi.org/10.25375/uct.14229752.

     



    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

     


    Venue of workshop: University of Cape Town – venue (TBA)


    Dates for the workshop: 30th October – 31st October 2018: Face to face practical workshop (bring your own laptop)

    Workshop organisers: Ziyaad Parker, Suresh Maslamoney, Sumir Panji, Nicola Mulder

    Application opens: 26th September 2018

    Application for the workshop closes: 11th October 2018

    Notification or acceptance date for the workshop: 12th October 2018

    Link to application form: https://tinyurl.com/cbio-sfc

    Course Overview Participation: The workshop is open to anybody who is interested in learning the Introduction to Python programming using the
    principles of Software Carpentry.

    Workshop Sponsor: UCT Computational Biology Division (CBIO) and H3ABioNet

    Intended Audience: Students and Staff who would like to learn more about the basics of Python programming.

    Tools: Python, Jypter Notebook, GitHub, Git, Numpy, Pandas, Linux/Mac/Windows

    Objectives: After this workshop participants should:

    • Be familiar Git and GitHub as well as using it
    • Be familiar with Jupyter Notebook
    • Be familiar with Python and executing scripts
    • Understand the different Python packages
    • Be familiar with steps and procedures involved in working with Python

    Workshop limitations: The workshop is set for two days. This course will teach the foundations of Python programming Linux and Git.

    Prerequisites: The participants must have their own laptop and install software below before the workshop:

    • Python 3
    • Numpy and Pandas Python package,
    • Git
      and
    • Jupyter Notebook

    Without the above installed participants will not be able to complete the course. Follow these instructions on this link to install: https://swcarpentry.github.io/python-novice-gapminder/setup/

    Contact Person:

     

    Link to course website: https://h3abionet.github.io/2018-10-30-SWC-course/ 


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