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Course Overview: This one-day workshop offers participants the possibility of gaining lots of hands-on experience in the use of the Ensembl genome browser (https://ensembl.org/), but also provides them with the necessary background information. The workshop consists of a series of modules which include a presentation and a demonstration of the tools, followed by the opportunity to do exercises. Participants are encouraged to bring problems/questions about their research and we will try to tackle these during the workshop using Ensembl.
Intended audience: Wet-lab scientists and bioinformaticians new to Ensembl
Keywords: Ensembl, Genomes, Genome Browser, Sequencing, Genomics
Skill level of training: Beginner
Language: English
Credential awarded: Certificate of Attendance
Type of training: Online
Venue of workshop: Online via Zoom (link to be sent in due course)
Date for the workshop: 06 September 2023 from 9 am to 5 pm CAT
Workshop organisers: H3ABioNet and European Bioinformatics Institute
Workshop sponsors: H3ABioNet and European Bioinformatics Institute
Registration for participants opens: 14th August 2023
Registration for participants closes: 18th August 2023
Notification date for successful participants: between the 28th of August and the 1st of September 2023
Maximum number of participants that will be accepted will be capped at 40
Objectives:
At the end of the workshop participants should be able to:
Workshop Schedule:
Time (CAT, GMT+2) |
Module |
09:00 - 10:00 |
Introduction to Ensembl |
10:00 - 10:45 |
Exploring genomic regions |
10:45 - 11:00 |
Coffee break |
11:00 - 12:00 |
Genes and transcripts |
12:00 - 13:00 |
Lunch break |
13:00 - 14:30 |
Variation and the Variant Effect Predictor (VEP) |
14:30 - 15:30 |
Comparative genomics and/or Regulatory data* |
15:30 - 15:45 |
Coffee break |
15:45 - 16:45 |
BioMart |
16:45 - 17:00 |
Wrap-up |
* optional modules depending on the interests of the participants
Prerequisites:
Participants should have degree-level understanding of molecular biology/genetics and be proficient at using web browsers.
Workshop Requirements:
Tailored Courses: We can also run tailored courses that focus on particular aspects of the Ensembl browser or on particular topics. In the past we have held courses that focus on:
We are open to your ideas – just let us know and we can discuss your requirements. Because of the specialisation of these courses, it is sometimes necessary to have a second instructor to teach some parts of the course. We may also suggest further pre-requisites and software requirements depending on the topics of interest.
Training material availability: Training materials used for this course were not directly produced by H3ABioNet but may be accessed here: https://training.ensembl.org/events/2023/2023-09-06-UCT_browser. 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.
Course Overview: 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:
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/
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: 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:
Licensing for course materials: Creative commons
Prerequisites:
Learning objectives/outcomes: After this workshop participants should be able to:
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 |
Phelelani Mpangase |
|
15:00 – 15:30 |
Parameters, Channels and Processes
|
Phelelani Mpangase |
15:30 – 16:00 |
Phelelani Mpangase |
|
16:00 – 16: 30 |
Phelelani Mpangase |
|
16:30 – 17:00 |
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.
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Tools and Services
Communication