Introduction to Bioinformatics Training (IBT)

This course provides an introduction to the field of bioinformatics, with a focus on important bioinformatic tools 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. During contact sessions, classrooms meet virtually to discuss the session’s content with each other and the trainer.

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

Course modules:

Databases and Resources

• Biological databases and resources (NCBI, EBI)
• Advanced literature searching – PubMed
• DNA analysis – e.g. sequence features, start site, restriction sites etc
• Protein function classification

Linux

• Introduction to Linux, UNIX and the command line
• Manipulating files – useful commands and tips
• Permissions, groups, and process control

Sequence Alignment

• Introduction to searching and sequence alignment
• Pairwise sequence alignment
• BLAST algorithm

Multiple Sequence Alignment

• Applications of multiple sequence alignment
• Choosing the right sequences with the right software

Genomics

• Genome sequences – sequencing technology and brief NGS overview
• Genome browsers and annotation
• Comparative Genomics
• Human variation

Molecular Evolution and Phylogenetics

• Historical perspective, mechanisms of molecular evolution, and speciation.
• Traits, phylogenies, evolutionary models and divergence times.
• Tree building with distance matrix methods. Parsimony approaches.
• Tree building with maximum likelihood approaches. Bayesian viewpoint. Branch support measures.

Additional elements of the course:

Staff Training

Introduction Week

Wrap up Session

Bonus Module – Gene Expression