Dear IBT Applicant
Welcome to AfriGen-D’s IBT_2025
We are pleased to inform you that your application for the AfriGen-D Introduction to
Bioinformatics Training course (IBT_2025) has been successful.
You have applied to join a specific classroom, the IBT_2025 course will be running in
hybrid/blended learning mode this year. Your classroom may go ahead as either an in person (i.e.
face-to-face style) classroom or may shift to a fully virtual/online format. Please reach out to your
local classroom staff (who would have sent you this letter) for further information around exactly
how your particular classroom will run. The classroom you applied to attend will have one or
more teaching assistants (TAs) available to facilitate the course locally or online. These teaching
assistants will still be available to assist you remotely even if your class should run in a
virtual/fully online format for the duration of IBT_2025. You will be managed by these local staff
and any queries you have should firstly be directed at your classroom’s TAs and if necessary, your
classroom TAs will escalate queries to the IBT core team. As some of you will not be able to
interact with your TA’s directly this year, the use of the forums on the course learning
management platform Vula (explained below) will become a vital tool for discussion and to gain
answers to questions. Your classroom (if virtual) may also elect to create an independent online
room (Zoom, WhatsApp, slack) in order to remain in touch. Again, your local classroom will be
best placed to advise you on these as well as other matters pertaining to the course.
VULA
In the next few days you will receive an invitation from Vula ([email protected] or cilt-
[email protected]) to join the IBT 2025 Participant Vula site (you may have received this email
already). Vula will be used as the course management tool for the IBT course. Follow the
instructions in the email from help@vula or cilt-helpdesk to set up your Vula guest account.
Please check your spam/junk folder for this email. If you are having trouble accessing your Vula
account, please DO NOT contact help@vula – rather contact the TAs for your classroom. In most
cases you will be added to Vula roughly 1 week before the course start but in rare cases you may
only be added the weekend ahead of the first session. Please bare this in mind.
ADDITIONAL INFORMATION
Below you will find some additional information about AfriGen-D’s IBT_2025. If you have any
questions, please address them to the TAs for your classroom. The IBT core team will not respond
to questions or comments coming directly from course participants due to the large number of
participants and will only respond to queries by the TAs and classroom staff (unless too
urgent/personal).
We hope that you enjoy AfriGen-D’s IBT_2025.
Kind Regards
IBT core team
Introduction to Bioinformatics Training Course: IBT_2025
15 April 2025 – 15 July 2025
Course Sponsors: African Genomics Data Hub
This course is provided free of charge - there is no cost associated with hosting a classroom for
IBT_2025. Further, attendance for participants and volunteer staff must be completely free of-
charge. If classrooms have running costs, they need to find alternate ways to cover these costs.
Introduction
A number of groups in Africa have expressed an interest in and need for basic bioinformatics
training for individuals entering the discipline, or for those who need a basic foundational
understanding of bioinformatics before moving on to more complex areas. The AfriGen-D
Education and Training Working Group have developed the Introduction to Bioinformatics course
in order to meet this need.
For its first iteration in 2016, the course ran successfully with a total of over 350 enrolled
participants and over 70 volunteer staff across 20 classroom sites spanning 10 African countries.
The 2017 iteration of this course saw a steady increase in both the number of participants (599)
as well as the numbers of classrooms (27) and staff (over 150) and the demand continued to grow
into the third and fourth iterations hosted in 2018 and 2019. Last year we had a record number of
1050 participants enrol to take the course. This demand has once again continued to grow with
over 1800 applications received for the course this year.
Aim
The course aims to provide an introduction to the field of bioinformatics, with a focus on
important bioinformatics tools and resources.
The course aims to use a combination of theoretical and practical sessions in order for
participants to gain practical experience in using various tools and resources.
Intended audience
The course is aimed at individuals from a molecular biology background who have a basic
understanding of biochemistry and/or genetics and would like to become bioinformatics users.
For an explanation on who 'bioinformatics users' might be, see Figure 2 in
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003496 .
Course logistics
•The course will start on 22 April 2025 and will run for approximately 3 months.
•A distance-based learning model will be used for this course.
•There will be no face to face classrooms for this iteration, but the course will still strictly follow the
provided schedule. We will have two “contact sessions” per week, Tuesdays and Thursdays, during
which time the trainer for a particular module will be available online to answer any questions you
might have. TAs will actively monitor forums between 10:30 and 14:30 on both days as well.
•Trainers will pre-record their lectures, which will then be uploaded onto Vula and watched by you
remotely ahead of the live session. Each session generally contains a practical assignment which
you will need to complete and submit approximately 2 weeks after the session ends. We suggest you
start this practical assignment ahead of the live contact session to ensure you are able to address
any difficulties with the trainer during this time. You will not be penalised if you are not online during
these sessions.
•The course traditionally followed a day plan which gave specific instructions and time periods
during which videos had to be watched, or activities completed. Although it will not be strictly
required, we suggest you still follow these day plans (which will be made available ahead of every
session) as it will typically allow you to maintain momentum throughout the course. Of course, you
are welcome to complete the course material at any time, provided you meet relevant deadlines.
We will indicate the time a particular trainer will be online via the day plan so please carefully monitor
the day plans to ensure you know when a trainer will be online even if you are not following it
explicitly.
Example of a day plan from the Introductory week of the course:
• A zoom room will be made available for the contact sessions and this link will be
communicated shortly. The trainers will also be available to assist TAs in answering content
related questions via Vula - the course management platform https://vula.uct.ac.za/portal .
• There will be an appropriately trained system administrator registered to each classroom site
to provide technical support. The course does require the installation of one or two tools and
the sys admin should be available either via email or on Vula to assist with any potential
issues.
• The practical components of the course will be run using open source, online tools as far as
possible.
• ALL of the course videos, lecture slides, additional material as well as all assignments
and assessments will be made available directly within Vula. Please ensure you check
this platform for any updates to assignments, deadlines or any other general course
announcements daily.
Course curriculum
Informed by responses from a previous survey sent out to H3Africa members, the course curriculum
will cover the following main themes (subject to slight changes):
• Bioinformatics resources and databases
Introduction to bioinformatics, biological databases, and resources (NCBI and EBI), data formats,
ontologies
• Linux
Introduction to Linux, general overview of Linux environment, overview of command line interface,
navigating Linux directory structure, manipulating files and directories, basic Linux commands
• Sequence alignment theory and applications
Introduction to searching and sequence alignment, BLAST, pairwise sequence alignment
• Multiple sequence alignment (MSA)
MSA theory, generating and interpreting MSAs using various tools, visualising and assessing MSA
quality
• Molecular evolution and phylogenetics
Molecular evolution, phylogenetic approaches, and methods (Introduction and overview of
methods)
• Genomics
Overview of sequencing and annotation, genome browser, Genetic variation, HapMap, 1000
genomes
Course objectives
By the end of the course participants should be able to:
• Explain the use of bioinformatics
• Name the key bioinformatics techniques and tools
• Locate important biological databases and retrieve data
• Use selected tools effectively to run specific bioinformatics analyses
• Understand the strengths and limitations of the various techniques
Course requirements
In order to pass the course and obtain the course ‘letter of completion’ (i.e. course
certificate), participants are required to:
• Submit 90% of practical assignments overall by the relevant hand-in date.
• Submit assessments by the relevant hand-in date and obtain a minimum grade of 60%
overall for the assessments.
*PLEASE NOTE*
• Successful candidates will receive the course 'letter of completion' as an attachment in an
email to the email address provided in this application form.
• Each participant's IBT grades will be shared with their supervisor (as indicated on this form)
if the supervisor asks for them.
• Should a hand in date for an assessment be missed, you will forfeit that score.
• Lecture recordings will be available on Vula, and past videos are available on YouTube
(https://www.youtube.com/channel/UCMYQE_GYsOKY6-j8z9N6Adw ). A number of
modules will feature some updated or possibly different content to the videos on YouTube
so we encourage you to primarily follow the videos loaded onto Vula. Should Vula for any
reason be inaccessible, the videos on YouTube will still deliver the fundamental concepts for
a module and/or session but may deviate in assignment instructions, etc.
IBT_2025 Course schedule
*subject to slight changes. Up-to-date due dates reflected in Vula
Date Topic Trainer
Welcome to the course!
Tuesday, 22 April Introductory session 1 Sindiswa Lukhele
(Welcome to the course!) University of Cape Town, South Africa
Thursday, 24 April Introductory session 2 David Judge
- what is bioinformatics and why is it important? Freelance independent Bioinformatics instructor
Pedro L. Fernandes
Instituto Gulbenkian de Ciência, Oeiras, Portugal
Module 1: Introduction to databases and resources
Tuesday, 29 April Session 1: Biological databases and resources Shaun Aron
(NCBI, EBI) University of the Witwatersrand, South Africa
Thursday, 1 May Session 2: Advanced literature searching – PubMed Shaun Aron
University of the Witwatersrand, South Africa
Tuesday, 6 May Session 3: DNA analysis – e.g. sequence features, Jane Njeri
start site, restriction sites etc PAMCA
Thursday, 8 May Session 4: Protein function classification Shaun Aron
University of the Witwatersrand, South Africa
Fri, 9 May Module 1 assessment (available on Vula)
TBC Final hand-in date for Module 1 assessment via Vula Individual
Module 2: Linux
Tuesday, 13 May Session 1: Introduction to Linux and UNIX and the Sumir Panji
command line University of Cape Town, South Africa
Thursday, 15 May Session 2: Manipulating files. Useful commands and Sumir Panji
tips University of Cape Town, South Africa
Tuesday, 20 May Session 3: Permissions, groups, and process control Sumir Panji
University of Cape Town, South Africa
Thursday, 22 May Session 4: Consolidation session – applications of Sumir Panji
Linux University of Cape Town, South Africa
Friday, 23 May Module 2 assessment (available on Vula) Individual
TBC Final hand-in date for Module 2 assessment via Vula Individual
Module 3: Sequence alignment theory and application
Tuesday, 27 May Session 1: Introduction to searching and sequence Jonathan Kayondo
alignment Uganda Virus Research Institute, Uganda
Thursday, 29 May Session 2: Pairwise sequence alignment Jonathan Kayondo
Uganda Virus Research Institute, Uganda
Tuesday, 3 June Session 3: BLAST algorithm Sonal Henson
University of Nottingham, UK
Thursday, 5 June NO SESSION
Friday, 6 June Module 3 assessment (available on Vula) Individual
TBC Final hand-in date for Module 3 assessment via Vula Individual
Module 4: Multiple sequence alignment
Tuesday, 10 June Session 1: Applications of multiple sequence Ahmed Mansour Alzohairy
alignment Zagazig University, Egypt
Thursday, 12 June Session 2: Choosing the right sequences and the Ahmed Mansour Alzohairy
right software Zagazig University, Egypt
Friday, 13 June Module 4 assessment (available on Vula) Individual
TBC Final hand-in date for Module 4 assessment via Vula Individual
Module 5: Molecular evolution and phylogenetics
Tuesday, 17 June Session 1: Introduction to phylogenetics Progress Dube
Great Zimbabwe University
Thursday, 19 June Session 2: TBC Progress Dube
Great Zimbabwe University
Friday, 20 June Module 5 assessment (available on Vula) Individual
TBC Final hand-in date for Module 5 assessment via Vula Individual
Module 6: Genomics
Tuesday, 24 June Session 1: Genome sequences – sequencing Felix Maingi
technology and NGS overview ICIPE, Kenya
Thursday, 26 June Session 2: Genome annotation including genome Jorge, Louisse, and Aleena
browsers (feature finding etc)* European Bioinformatics Institute, EMBL-EBI, UK
Tuesday, 1 July Session 3: Comparative genomics Felix Maingi
ICIPE, Kenya
Thursday, 3 July Session 4: Human variation* Jorge, Louisse, and Aleena
European Bioinformatics Institute, EMBL-EBI, UK
Tuesday, 8 July Session 5: Consolidation session Felix Maingi
ICIPE, Kenya
Thursday, 10 July NO SESSION
Friday, 11 July Module 6 assessment (available on Vula) Individual
TBC Final hand-in date for Module 6 assessment via Vula Individual
Wrap-up session
Tuesday, 15 July Course wrap-up session Sindiswa Lukhele
University of Cape Town, South Africa
END OF COURSE
