Dear IBT applicant

Welcome to H3ABioNet’s IBT_2024

We are pleased to inform you that your application for the H3ABioNet Introduction to Bioinformatics

Training course (IBT_2024) has been successful.

You have applied to join a specific classroom, the IBT_2024 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_2024. 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
[email protected]) to join the IBT 2024 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 H3ABioNet’s IBT_2024. 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 H3ABioNet’s IBT_2024.

Kind Regards

IBT core team

H3ABioNet Introduction to Bioinformatics Training Course: IBT_2024

16 April 2024 – 30 July 2024

Course Sponsors: H3ABioNet

This course is provided free of charge - there is no cost associated with hosting a classroom for
IBT_2024. 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 H3ABioNet 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
http://training.h3abionet.org/IBT_2016/. 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 23 April 2024 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
● Genomics
Overview of sequencing and annotation, Ensembl genome browser, Genetic variation, HapMap,
1000 genomes
● Molecular evolution and phylogenetics
Molecular evolution, phylogenetic approaches, and methods (Introduction and overview of
methods)
 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.
 Course schedule

IBT_2024 course schedule

*subject to slight changes. Up-to-date due dates reflected in Vula

Date Topic Trainer

Welcome to the course!
Tuesday, 16 April Staff training day session 1 Sindiswa Lukhele
University of Cape Town, South Africa
Thursday, 18 April Staff training day session 2 Sindiswa Lukhele
University of Cape Town, South Africa
Tuesday, 23 April Introductory session 1 Sindiswa Lukhele
(Welcome to the course!) University of Cape Town, South Africa

Tuesday, 30 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, 7 May Session 1: Biological databases and resources Shaun Aron
(NCBI, EBI) University of the Witwatersrand, South Africa
Thursday, 9 May Session 2: Advanced literature searching – Shaun Aron
PubMed University of the Witwatersrand, South Africa
Tuesday, 14 May Session 3: DNA analysis – e.g. sequence features, TBC
start site, restriction sites etc
Thursday, 16 May Session 4: Protein function classification Shaun Aron
University of the Witwatersrand, South Africa
Fri, 17 May Module 1 assessment (available on Vula)

TBC Final hand-in date for Module 1 assessment via Individual

Vula
Module 2: Linux
Tuesday, 21 May Session 1: Introduction to Linux and UNIX and the Sumir Panji
command line University of Cape Town, South Africa
Thursday, 23 May Session 2: Manipulating files. Useful commands Sumir Panji
and tips University of Cape Town, South Africa
Tuesday, 28 May Session 3: Permissions, groups, and process Sumir Panji
control University of Cape Town, South Africa
Thursday, 30 May Session 4: Consolidation session – applications Sumir Panji
of Linux University of Cape Town, South Africa

Friday, 31 May Module 2 assessment (available on Vula) Individual

TBC Final hand-in date for Module 2 assessment via Individual

Vula

Module 3: Sequence alignment theory and application

Tuesday, 4 June Session 1: Introduction to searching and Jonathan Kayondo
sequence alignment Uganda Virus Research Institute, Uganda
Thursday, 6 June Session 2: Pairwise sequence alignment Jonathan Kayondo
Uganda Virus Research Institute, Uganda
Tuesday, 11 June Session 3: BLAST algorithm Sonal Henson
International Centre of Insect Physiology and Ecology,
Kenya
Thursday, 13 June NO SESSION

Friday, 14 June Module 3 assessment (available on Vula) Individual

TBC Final hand-in date for Module 3 assessment via Individual

Vula
Module 4: Multiple sequence alignment
Tuesday, 18 June Session 1: Applications of multiple sequence Ahmed Mansour Alzohairy
alignment Zagazig University, Egypt
Thursday, 20 June Session 2: Choosing the right sequences and the Ahmed Mansour Alzohairy
right software Zagazig University, Egypt
Friday, 21 June Module 4 assessment (available on Vula) Individual

TBC Final hand-in date for Module 4 assessment via Individual

Vula
Module 5: Genomics
Tuesday, 25 June Session 1: Genome sequences – sequencing Fatma Guerfali
technology and NGS overview Institute Pasteur de Tunis, Tunisia
Thursday, 27 June Session 2: Genome annotation including genome Benjamin, Louisse, and Aleena
browsers (feature finding etc)* European Bioinformatics Institute, EMBL-EBI, UK
Tuesday, 2 July Session 3: Comparative genomics Fatma Guerfali
Institute Pasteur de Tunis, Tunisia
Thursday, 4 July Session 4: Human variation* Benjamin, Louisse, and Aleena
European Bioinformatics Institute, EMBL-EBI, UK
Tuesday, 9 July Session 5: Consolidation session Fatma Guerfali
Institute Pasteur de Tunis, Tunisia
Thursday, 11 July NO SESSION

Friday, 12 July Module 5 assessment (available on Vula) Individual

TBC Final hand-in date for Module 5 assessment via Individual

Vula
Module 6: Molecular evolution and phylogenetics
Tuesday, 16 July Session 1: TBC TBC

Thursday, 18 July Session 2: TBC TBC

Friday, 19 July Module 6 assessment (available on Vula) Individual

TBC Final hand-in date for Module 6 assessment via Individual

Vula
Wrap-up session
Tuesday, 30 July Course wrap-up session Sindiswa Lukhele
University of Cape Town, South Africa
Course Ends