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 |