H3ABioNet

Pan African Bioinformatics Network for H3Africa

H3ABioNet Introduction to Bioinformatics online course (IBT_2016)

Course Title: H3ABioNet Introduction to Bioinformatics online course (IBT_2016)

Course website: http://training.h3abionet.org/IBT_2016/

Venue of course: 19 classrooms across 11 African countries. Classrooms connect to the trainer via Mconf (‘virtual classroom’).

Dates for the course: 6th July – 9th October 2016, every Wednesday and Thursday, 10:00-14:00 CAT each day

Course organisers: H3ABioNet Education and Training working group and the IBT core team (Kim Gurwitz, Shaun Aron, Sumir Panji and Nicola Mulder)

Participation via Classrooms: A call was sent out for institutions to apply to host a classroom. Classroom selection was based on the availability of certain infrastructure requirements, as well as the availability of dedicated, local teaching assistants. Classrooms hosted at both H3ABioNet and non-H3ABioNet institutions.

Participants: Participants applied to a particular classroom via a centralised application form and were informed of the outcome of their application.

Course Sponsors: H3ABioNet

Course Overview: The IBT_2016 course is an introduction to the field of Bioinformatics, with a focus on important Bioinformatic tools, algorithms and resources. Over a period of 3 months of intensive biweekly contact sessions, the course combines theoretical and practical sessions to allow 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 basic Bioinformatics users.

Syllabus and Tools: The participants will cover an introduction to various Bioinformatics topics, namely; Databases and Resources, Genomics, Linux, Sequence alignment theory and application, Multiple sequence alignment, Protein structural Bioinformatics, Phylogenetics and molecular evolution. For practical sessions, web-based tools are used as far as possible.

Prerequisites: A base line level of the understanding of the central dogma of molecular biology (i.e. DNA to RNA to Protein) is a requirement.

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 limitations: This course will provide an introduction to the field of Bioinformatics. Participants must be able to attend biweekly contact sessions at one of the classroom sites.

Course costs: There is no application or participation fee. Local sites provide the physical resources for the course and the course core team provides logistic and course management support

IBT_2016 course schedule(*subject to slight changes)

Date Topic Trainer
Welcome to the course!

Wednesday,

6 July

Introductory session (+- 1 hour)

- get to know where your classroom is and meet your teaching assistants and fellow participants

(NOTE: a repeat of this session will be held on Monday, 11 July for those unable to make the session on the 6 July. A written document detailing the logistics of the course will also be available)

IBT core team
Introduction to databases and resources
Wednesday, 13 July Guest lecturers: ‘What is bioinformatics and why is it important?’

Pedro Fernandes

Instituto Gulbenkian de Ciência, Oeiras, Portugal

and

David P Judge

Freelance independent Bioinformatics instructor

Thursday,

14 July

Biological databases and resources (NCBI, EBI)

Shaun Aron

University of Witwaterstrand, South Africa

Wednesday, 20 July

Advanced literature searching – PubMed

Shaun Aron

Thursday,

21 July

DNA analysis – e.g. sequence features, start site, restriction sites etc

Nicola Mulder University of Cape Town, South Africa

*Thursday,

21 July

Assessment available for the ‘introduction to databases and resources’ module via Vula ‘Tests and Quizzes’ tab individual

*Tuesday,

26 July

FINAL hand-in date for ‘introduction to databases and resources’ assessment

individual
  Genomics  

Wednesday,

27 July

Genome sequences – sequencing technology and NGS overview

 

Fatma Guerfali Institute Pasteur de Tunis, Tunisia

Thursday,

28 July

Genome annotation including genome browsers (feature finding etc)

 

Colleen Saunders

South African National Biodiversity Institute, South Africa

Wednesday,

3 August

Comparative genomics

 

Fatma Guerfali

Thursday,

4 August

Human variation

 

Colleen Saunders

*Thursday,

4 August

Assessment available for the ‘genomics’ module via Vula ‘Tests and Quizzes’ tab individual

*Tuesday,

9 August

FINAL hand-in date for ‘genomics’ assessment individual
Linux
Wednesday, 10 August

Introduction to Linux and UNIX and the command line

Amel Ghouila

Institute Pasteur de Tunis, South Africa

Thursday,

11 August

Manipulating files. Useful commands and tips

Amel Ghouila
Wednesday, 17 August

Permissions, groups and process control

Amel Ghouila
*Wednesday, 17 August Assessment available for the ‘Linux’ module via Vula ‘Tests and Quizzes’ tab individual

*Wednesday,

24 August

FINAL hand-in date for ‘Linux’ assessment individual
Sequence alignment theory and application

Thursday,

18 August

Introduction to searching and sequence alignment

Pandam Salifu

Kumasi Centre for Collaborative Research, Ghana

Wednesday, 24 August

Pairwise sequence alignment

Pandam Salifu

Thursday,

25 August

BLAST algorithm

Pandam Salifu

*Thursday,

25 August

Assessment available for the ‘sequence alignment theory and application’ module via Vula ‘Test and Quizzes’ tab individual

*Wednesday,

31 August

FINAL hand-in date for ‘sequence alignment theory and application’ assessment individual
Multiple sequence alignment
Wednesday, 31 August Overview of multiple sequence alignments applications

Ahmed Mansour Alzohairy

Zagazig University, Egypt

Thursday,

1 September

Choosing the right sequences with the right software

Ahmed Mansour Alzohairy

*Thursday,

1 September

Assessment available for the ‘multiple sequence alignment’ module via Vula ‘Tests and Quizzes’ tab individual

*Wednesday,

7 September

FINAL hand-in date for ‘multiple sequence alignment’ assessment individual
Protein structural bioinformatics

Wednesday,

7 September

(To be confirmed) TBC

Ruben Cloete

South African National Biodiversity Institute, South Africa

Thursday,

8 September

TBC Ruben Cloete
Wednesday, 14 September NO SESSION NO SESSION

Thursday,

15 September

TBC Ruben Cloete

*Thursday,

15 September

Assessment available for the ‘protein structural bioinformatics’ module via Vula ‘Tests and Quizzes’ tab individual

*Wednesday,

21 September

FINAL hand-in date for ‘protein structural bioinforamtics’ assessment individual
                                                 Consolidation week

Wednesday,

21 September

TBC TBC

Thursday,

22 September

TBC TBC
Molecular evolution and phylogenetics
Wednesday, 28 September TBC

Jean-Baka Domelevo Entfellner

University of the Western Cape, South Africa

Thursday,

29 September

TBC Jean-Baka Domelevo Entfellner

Wednesday,

5 October

TBC Jean-Baka Domelevo Entfellner

Thursday,

6 October

TBC Jean-Baka Domelevo Entfellner

Thursday,

6 October

Assessment available for the ‘molecular evolution and phylogenetics’ module via Vula ‘Tests and Quizzes’ tab individual

Wednesday,

12 October

FINAL hand-in date for ‘molecular evolution and phylogenetics’ assessment individual
     

Wednesday,

12 October

Course end