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Project Work in Immunological Bioinformatics


Unix
Setting up your PC to work with unix (SSH/Xwin32)
Vaccine group setup
Basic unix commands/Introduction to using Unix for Immunological Bioinformatics
Post script hacking
pdbfile manipulation using unix commnds

Pymol
Pymol tutorial

Perl
Program templates
Parsing lines
Sub
Librares
Help on the web
exercises
exercise directory

Need for speed: programming in C
Templates
Compilation and execution
Command line options
Data structures
Memory management
Setting up and working with standard and custom libraries

Databases on CBS and on the web
Swissprot/GenBank/PDB
Immunological databases

Searching databases
Blast - local and on the web
Exercise directory

Conversion of file formats
Saco_convert
Other converters

Neural networks
Training/testing/using networks on a the unix system
EasyPred

Sequence information, Logos and HMMs
Sequence information
Sequence weighting and pseudo counts
Sequnece logos (Plain and Kullbach)
Weight matrices
Gibbs sampling
Hidden Markov Models

Immunological prediction tools at CBS
MHC/TAP/Proteasome
Making atlases


Trees based on specificity comparisons

Homology modelling and fold recognition
CPHmodels
Exercises in fold recognition and homology modelling

Working with array data
The Stanford micro array database
GenePublisher

Working with Sql Databases (Mysql)

Searching information
Making figures
Report/Paper writing