An introduction to computing for bioinformatics

Overview
This high level course is suitable both for those with a biological sciences background and those with a computing background who need an integrated overview of the underlying biological and computing concepts and technologies that form the foundations for bioinformatics. A key aim of the course is to get biological scientists and software engineers up to a common skill level that can serve as the foundation for effective communication and collaboration in the development of new applications and new research strategies.
The course is mainly lecture with demonstrations. Depending on the interests and background of attendees, time may be made available for practical labs.

Course Benefits
The course provides and overview of the current state of bioinformatics and the molecular biological sciences. The bias is towards "computational approaches to biological questions".
Starting off with a wide ranging, but reasonably thorough, overview of the standard concepts and models in molecular biology (revision for some and getting up to speed for others) the course goes on to consider practical issues such as setting up a bioinformatics workstation and the tools available for bioinformatics. It then proceeds to cover the standard problems and approaches to tackling these that form the core of bioinformatics, namely:

• Sequence analysis, pairwise alignment, and database searching
• More complex pattern matching involving multiple sequence alignments, phylogenetic tree analysis, profiles and motifs
• Visualisation of proteint and receptor structures and the computation of structural properties
• Approaches to the prediction of protein structure and function from sequence
• Annotation and analysis of genome sequences
• Functional genomics and the modeling of biochemical pathways and physiological processes
• Pattern matching and biological database technologies (using Perl scripting, relational databases such as MySQL and PostgreSQL, and BLAST)
• Visualisation and data mining technologies and their potential uses

Course Contents
An intensive overview of molecular biology - concepts, models and terminology

• Cells and macromolecules
• Protein structure
• Structure and properties of nucleic acids
• Prokaryotic and eukaryotic chromosome structure
• DNA replication
• DNA damage, repair and recombination
• Gene manipulation
• Cloning vectors
• Gene libraries and screening
• Analysis and uses of cloned DNA
• Transcription and its regulation in prokaryotes
• Transcription and its regulation in eukaryotes
• RNA processing and RNPs
• The genetic code and tRNA
• Protein synthesis
• Viruses - bacteriophages, eukaryotic viruses, tumour viruses, oncogenes
• Functional genomics, cell and molecular imaging

Setting up and configuring a Unix / Linux bioinformatics workstation [ Where specifically requested a section on setting up a bioinformatics workstation running on either Microsoft Windows or Macintosh platforms can be substituted ]

• Understanding Unix and the Unix commands
• Working with the Unix file system
• Simple shell programming
• Understanding TCP/IP networking under Unix

Tools and techniques for bioinformatics

• Web resources
  • Search engines and finding scientific articles
  • Public biological databases and how to search them
  • Depositing data into the public databases
  • Locating and downloading bioinformatics open source and commercial software
• Sequence analysis
  • How DNA is sequenced
  • Feature detection in DNA sequences
  • Pairwise sequence comparison
  • Performing sequence queries against biological databases
  • Multiple sequence alignments
  • Phylogenetic analysis
  • Profiles and motifs
• Protein structure - computation and prediction from sequence data
  • Web based protein-structure tools
  • Protein structure visualisation and classification
  • Structural alignment and analysis
  • Protein-solvent interaction, phospholipids and membrane proteins
  • Tools and techniques for protein structure optimisation
  • Protein resource databases on the web
  • Feature detection in protein sequences
  • Protein secondary structure prediction
  • Protein 3D structure prediction
• Genomics and proteomics
  • Sequencing genomes and sequence assembly
  • Accessing genome information on the web
  • Annotation and analysis of entire genome sequences
  • Functional genomics - issues and challenges
  • Proteomics
  • Working with biochemical pathway databases
  • Approaches to biochemical pathway kinetics modeling
  • Approaches to modeling physiological systems
• Programming and Databases
  • Overview and introduction to Perl programming
  • Pattern matching and regular expressions
  • Parsing BLAST output using Perl
  • An overview of applying Perl to bioinformatics
  • Principles of databases ( hierarchical, relational, object-relational and object oriented )
  • Introduction and overview of SQL (Structured Query Language)
  • Overview of the features of commonly used databases (MySQL, PostgreSQL, Oracle, and Sybase and Microsoft SQL Server (only if specifically requested))
• A Survey of Visualisation Techniques
  • Data preparation
  • Graphics display tools and techniques
  • Visualisation of sequence data
  • Visualisation of networks and pathways
  • Numerical data analysis approaches
• Data mining techniques
  • Statistical pattern recognition
  • Neural networks
  • Genetic algorithms
  • Rule induction
  • Cluster analysis