Module 1. Foundations of Bioinformatics

Bioinformatics is driving the collection, analysis and interpretation of big data in the biosciences. This module provides an introduction to practical issues of computer-based handling and interpretation of biomolecular and genomic datasets. We specifically target bioinformatics software and data resources freely available on the Internet.

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1.1 Lecture Introduction to bioinformatics
  Lab Bioinformatics databases and major online resources
1.2 Lecture Sequence alignment and database searching
  Lab Sequence alignment algorithms and applications
1.3 Lecture Structural bioinformatics
  Lab Structure visualization, analysis and small molecule docking
1.4 Lecture Genome informatics
  Lab Web resources for analyzing genomic data




Lecture (1-1): Introduction to bioinformatics

ScreenCast1.1


Lab (1-1): Bioinformatics databases and major online resources

  • Instructor: Dr. Barry Grant
  • Time: 2:30 – 4:00 PM, Jan 14 (Thursday) or Jan 15, 10:30 - 12:00 PM, (Friday)
  • Topics:
    The purpose of this lab session is to introduce a range of core bioinformatics databases and associated online services whilst investigating the molecular basis of several common human disease.
  • Material:
    Lab worksheet
    Muddy point assessment




Lecture (1-2): Sequence alignment and database searching


Lab (1-2): Sequence alignment algorithms and applications

  • Instructor: Dr. Barry Grant
  • Time: 2:30 – 4:00 PM, Jan 21 (Thursday) or Jan 22, 10:30 - 12:00 PM, (Friday)
  • Topics:
    Aligning novel sequences with previously characterized genes or proteins provides important insights into their common attributes and evolutionary origins. In this lab session we will explore the principles underlying the computational tools that can be used to compute and evaluate sequence alignments.
  • Material:
    Lab worksheet
    Muddy point assessment



Lecture (1-3): Structural bioinformatics


Lab (1-3): Structure visualization, analysis and small molecule docking

  • Instructor: Dr. Barry Grant
  • Time: 2:30 – 4:00 PM, Jan 28 (Thursday) or Jan 29, 10:30 - 12:00 PM, (Friday)
  • Topics:
    The RCSB PDB resource. Interactive biomolecular structure visualization with VMD. Structural analysis of protein families and prediction of protein flexibility with Bio3D. In silico docking and virtual screening strategies for drug design.
  • Material:
    Lab worksheet
    Supporting Files: indinavir.pdbqt, config.txt, log.txt, all.pdbqt
    Muddy point assessment



Lecture (1-4): Genome informatics


Lab (1-4): Web resources for analyzing genomic data


Reference material

Class Handout on Major Databases