1. Overview of Bioinformatics Module Denis Manley.

2. Contact Details Lecturer Name: Denis Manley Room number: KE-1-013a Email : denis.manley@dit.iedenis.manley@dit.ie Website: www.comp.dit.ie/dmanleywww.comp.dit.ie/dmanley Phone: 01 402 4949

3. What is bioinformatics Bioinformatics is the use of computers and computational methods to analyse large sets of molecular biological data that is used for : – The investigation of “living organisms” and their evolution. – The discovery of genes, gene regulation; genetic networks and protein functionality, which can be used to understand: human disease; human development (conception to adulthood) etc. – the results of which can facilitate our understanding of diseases like cystic fibrosis; suggest therapies; and the development of cures such as drug development, viral therapy… Bioinformatics is one of the fastest growing areas in computing and is only set to increase as it is now starting to produce information that facilitates our understanding and the development of cures for many diseases.

4. The module syllabus. Part 1: – Introduction to fundamental genetics: Cell Biology: the Cell; cellular states and organism development Genes, inheritance and evolution Molecular cell biology: DNA and proteins. The central “dogma” of Genetics: DNA -> RNA->Proteins Gene “expression” regulation Part 2 – Basic introduction to PERL: a common scripting language used in the field of bioinformatics Basic bioinformatics related data structures Pattern matching techniques: the basics of sequence matching and bioinformatics files manipulation

5. What is bioinformatics Part 3 – Computational methods used in bioinformatics Techniques, including Artificial intelligent techniques, used to match gene and protein sequences and measure their similarity… ; this is then used in: – Analysing and determining the evolution of life ; – Determining the steps in human development as well as that in other organisms including bacteria, viruses… ; – Analysing and understanding the development of disease such as malignancy, bacterial/viral infection; e.g. A.I.D.s and many others as well as possibly suggesting ways of combating them. – Determining the protein structure and the subsequent protein synthesis; including the development of drugs related to the disease whose origins are understood; e.g. from the above research in to disease development.

6. Assignment and exam 1 Assignment: – Based on writing a simple program to analyse DNA/AA data and discuss the findings in order to determine; e.g. potential functionality/ potential structure…. Exam: question 1 + 2 out of 4 other question – Question 1 compulsory: using perl to analyse DNA sequences. – Other questions related to areas the module and will take the form of discussions