Training - H3ABioNet - Pan African Bioinformatics Network

H3ABioNet Training Guide

: Training; 28 April 2021; Hits: 8758

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.

Introduction to Git and Github 30 Nov 2020

: Training; 25 November 2020; Hits: 5503

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: 30^th 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: 24^th November 2020

Registration closes: 27^th November 2020 at 10 pm CAT

Notification date: 29^th 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:

Familiarity with command line and unix
A basic user account on GitHub (https://github.com/)
A web browser and an internet connection
Installation of git (https://git-scm.com/book/en/v2/Getting-Started-Installing-Git ; https://www.digitalocean.com/community/tutorials/how-to-contribute-to-open-source-getting-started-with-git)
Windows OS users should ensure that git bash is part of their installation: https://gitforwindows.org/

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/

bioinformatics introduction

16SrRNA Microbiome Intermediate Bioinformatics Training_2020

: Training; 08 June 2020; Hits: 7100

Course Overview: The H3ABioNet 16S rRNA Microbiome Intermediate Bioinformatics course will provide training to enable participants to gain the knowledge and skills to perform 16S rRNA microbiome data analyses using a variety of bioinformatics methods and tools.

The H3ABioNet 16S rRNA Microbiome Intermediate Bioinformatics course will use a blended learning approach similar to the popular H3ABioNet Introduction to Bioinformatics Training (IBT) through the use of a combination of theoretical and practical sessions in order for participants to gain knowledge in the use of various tools and resources needed for 16S rRNA microbiome data analysis. There will be 2 contact sessions per week consisting of both theoretical and practical coursework. Participants will generally watch pre-recorded videos in their classrooms (theory) followed by a practical exercise for the remainder of the session. Contact sessions will generally be 4 hours each however the exact format and length of classes will be communicated in due course.

Keywords: 16S, Microbiome, NGS, Genomics, Nucleic acid analysis

Skill level of training: Intermediate

Language: English

Credential awarded: Letter of completion

Type of training: Blended/hybrid learning

Dates for the Course: September to November 2020 (exact dates and times to be confirmed)

Venue of the Course: Successful hosting classrooms

Course Organizers: Verena Ras, Gerrit Botha, Shaun Aron, Sumir Panji, Nicola Mulder

Course Objectives: By the end of the course participants should be able to:

Describe the importance of the microbiome and why it should be studied
Understand how to design 16S rRNA microbiome studies
Be able to apply basic syntax and operations in R
Understand the different NGS data types (e.g. MiSeq reads) produced for a 16S rRNA microbiome study
Evaluate the quality of NGS sequence reads and samples
Understand the various bioinformatics tools used for 16S microbiome studies
Understand the various 16S rRNA bioinformatics pipelines being used to study the microbiome.
Apply the H3ABioNet’s 16S rRNA pipeline and understand how to execute this
Understand the use of workflow languages (Nextflow) and containerized images (Singularity) to automate analyses
Analyze 16S rRNA microbiome data and interpret results

Intended Audience: Anyone who will be working with 16S rRNA microbiome data and would like to learn more about the bioinformatics analyses.

Syllabus and Tools:

Introduction to the Linux command line / intro to R
Introduction to the microbiome and study design – why 16S?
Sample collection, extraction and library prep for 16S NGS analyses
16S rRNA gene amplicon sequencing bioinformatics pipeline: the theory
16S analysis pipeline - QC, ASV picking, taxonomic classification and alignment
Downstream analysis in R - using the packages phyloseq, NMF, vegan, metagenomeSeq (among others)

Prerequisites (for participants): As this is an intermediate course, some familiarity with the Unix command line and R scripting will be assumed. However, should participants wish to gain some background knowledge before the start of the course, the following tutorials will provide a good foundation.

Linux: http://www.ee.surrey.ac.uk/Teaching/Unix/

R: https://www.statmethods.net/r-tutorial/index.html

R: https://www.datacamp.com/courses/free-introduction-to-r

Workshop limitations: This workshop provides an overview and guidance on 16S rRNA microbiome analyses and will provide you with the ability to perform a variety of analyses on microbiome data. The course however will not teach any advanced programming or go into depth with R or Unix. Participants are encouraged to explore these tools in greater depth independently.

Apply to be a Participant Here >	Applications are now closed
Apply to Host a Classroom Here >	Applications are now closed

Training Materials Availability:

Training materials for this course are available as a single downloadable archive here: https://doi.org/10.25375/uct.19106780. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.

Click here to go to main course site

current , bioinformatics intermediate

Introduction to Nextflow Workshop 2020

: Training; 25 November 2020; Hits: 6787

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): 1^st 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: 25^th November 2020

Registration closes: 27^th November 2020 at 10 pm CAT

Notification date: 29^th 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:

Familiarity with command line and unix
Installation of Nextflow (https://www.nextflow.io/docs/latest/getstarted.html)
A web browser and an internet connection

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

Training Materials Availability:

Training materials for this course are available as a single downloadable archive here: https://doi.org/10.25375/uct.19105979. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.

bioinformatics introduction

Introductory Python based Software Carpentry_2018

: Training; 31 March 2020; Hits: 3344

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.

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

Keywords: Python, programming, GIT, Software Carpentry

Language: English

Type of training: face-to-face

Credential awarded: none

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

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

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:

Training Materials Availability:

Training materials used for this course were not directly produced by H3ABioNet but may be accessed here: https://h3abionet.github.io/2018-10-30-SWC-course/. Please note, these materials may be governed by different sharing/re-use policies, and you are encouraged to follow the policies of the external providers regarding material re-use and/or sharing.

past , bioinformatics introduction