Introduction to Bioinformatics Training 2020

: Training; 28 January 2020; Hits: 19992

Training

Course Overview: 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. A baseline level of the understanding of the central dogma of biology (DNA -> RNA -> Protein) is a requirement.

Keywords: Genetics, Genomics, Nucleic acids analysis

Skill level of training: Beginner

Language: English

Credential awarded: Letter of completion

Type of training: Blended/hybrid learning

Logistics

Venue of workshop: Local classrooms ( usually 30 physical sites across Africa) and online

Dates for the workshop: 04 May – 31 July 2020; Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT.

Workshop organisers: Paballo Chauke, Verena Ras, Shaun Aron, Sumir Panji and Nicola Mulder

Participation: The course is available to any classroom who meets the requirements and to any participant who is able to attend a physical classroom, if one has been set up at a local institution, provided they have been selected via the selection process.

Workshop Sponsors: H3ABioNet

Classroom applications:

Registration for classrooms opens: 03 February 2020

Registration for classrooms closes: 28 February 2020

Link to classroom application form: https://is.gd/IBT_2020_Classroom_Host

Notification date for successful classrooms: 05 March 2020

Participant applications:

Registration for participants opens: 08 March 2020

Registration for participants closes: 03 April 2020

Link to participant application form: https://redcap.link/IBT_participants_2020

Course Curriculum:

Syllabus and Tools:

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)

**All modules make use of predominantly web-based tools such as NCBI, Ensembl, etc.

Prerequisites: A basic background/understanding of of biochemistry and/or genetics.

Objectives: After this workshop 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

Workshop limitations: This workshop will only provide a foundation for continued learning in bioinformatics and will not teach any advanced coding.

Training Material Availability:

Training materials for this course are available here: https://zivahub.uct.ac.za/projects/Introduction_to_Bioinformatics_Training_Course_Materials/131552. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.

Materials have been made available as a single archive per module containing lecture slides, transcribed videos, practical assignments and any other resources important to complete each module:

Module 1: Databases and Resources