Tools and Services
Resources
Communication
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 learning
Venue of workshop: Online via Zoom (link to be sent in due course)
Date for the workshop: 06 September 2023
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.
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 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.
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:
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: 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:
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:
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.
Page 1 of 5
Tools and Services
Resources
Communication