training material url: https://training.ensembl.org/events/2023/2023-09-06-UCT_browser
    training material license: https://creativecommons.org/licenses/by/4.0/
    Training EDAM ontology term: data_3210

    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:

    • Navigate Ensembl using the web browser platform
    • Access main data types in Ensembl: genomes, genes, genetic variation, regulatory features and comparative genomics
    • View genomic regions and manipulate the view to add features.
    • Explore information about genes and their sequences.
    • Analyse genomic variants and associated phenotypes and your own variation data using the Variant Effect Predictor (VEP).
    • View homologous genes and genomic regions.
    • View functional elements involved in gene regulation and their activity in different cell types.
    • Export gene data in bulk using BioMart.

     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:

    • Computer/Laptop
    • Computer/Laptop should have a (reasonably fast) internet connection
    • Computer/Laptop should have an up-to-date internet browser installed (preferably Chrome or FireFox)

    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:

    • Comprehensive Ensembl Browser
    • Ensembl and the 1000 Genomes Project
    • Ensembl and gene regulation, including data from ENCODE, Blueprint, RoadMap epigenomics and more
    • Particular Ensembl Genomes taxa (eg Plants, Fungi, Protists, Metazoa or Bacteria)
    • Particular Ensembl species

    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.



    The H3ABioNet recently co-organised a Scientific Communication Workshop from the 26th to the 27th of April 2021.
     
    The links below are the video recordings and resources that were used for the two days.
     

    Day 1 of Workshop: https://youtu.be/U2el7Zcyb-Y

    Day 2 of Workshop: https://youtu.be/XT8Lx8lR6-0

     

    Resources:

     
    1. Writing an effective abstract: Abstract document
    2. Communicating science exercise: Exercise document
    3. How to write good research manuscript: Manuscript document
    4. From trainee to tenure-track: Ten tips document
    5. How to give a “good” oral presentation: Oral presentation guidelines
    6. How to read, summarize, and critique a research article: Article critique document
    7. Opportunities for After Your Studies: Identifying Transferable Skills
    8. Personal Development Transferable Skills Profile and Action Plan: Transferable Skills Profile
    9. Transferable skills for a competitive edge: Transferable skills document
     

    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/


     

    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:

    • 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

    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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