BASICS OF PERL:
Introduction to BioPerl and BioPerl Objects - Brief descriptions (Seq, PrimarySeq, LocatableSeq, RelSegment, LiveSeq, LargeSeq, RichSeq, SeqWithQuality, SeqI), Location objects, Interface objects and Implementation objects. Sequence Representation: Representing large sequences (LargeSeq), Representing changing sequences (LiveSeq). Accessing Sequence data - Using Bioperl: Accessing sequence data from local and remote databases, Accessing remote databases (Bio::DB::GenBank, etc), Indexing and accessing local databases (Bio::Index::*,bp_index.pl, bp_fetch.pl, Bio::DB::*). Sequence and Alignment format Interconversion - Transforming sequence files (SeqIO), Transforming alignment files (AlignIO). Performing Sequence analysis – Global alignment, Local alignment, Multiple sequence alignment, Parsing BLAST alignment report and Parsing multiple sequence alignment.
INTRODUCTION TO PYTHON:
Python basics – Variables, Operators, Data types and Assignments. Statements – Input/output statements, flow control - IF…THEN….ELSE, SWITCH, FOR, MAP, FILTER and WHILE, goto statements. Names, Functions and Modules. Object Oriented Programming in Python: Introduction to object oriented programming in python. Classes and objects. Inheritance, Polymorphism. Constructors and Destructors
EXCEPTION HANDLING BIOPYTHON BIOINFORMATICS:
Parsing DNA data files, Image manipulation, Sequence analysis – Sequence alignment (pair wise and multiple sequence alignment), Dynamic Programming, Detecting tandem repeats and generating Hidden Marko Models, Simulation of EST Clustering. Data mining – Text mining, Simulating Genetic algorithm. Analysis of Microarray data – Spot finding and Measurement.
INTRODUCTION TO THE NCBI C++ TOOLKIT: INTRODUCTION TO C++ MODULES :
CORELIB, ALGORITHM,CGI, CONNECT, CTOOL, DBAPI, GUI, HTML, OBJECT MANAGER, SERIAL and UTIL module. C++ Toolkit Library Reference: CORELIB Module - Writing simple applications, Namespaces, CNcbiRegistry Class, Portable Stream Wrappers. Working with diagnostic streams - Debug Macros, Handling exceptions, CObject and CRef Classes and Atomic counters. Executing commands and Spawining processes using CExec class, working with files and directories using CFile and CDir, Input /Output utility class.
OVERVIEW OF THE R LANGUAGE:
Defining the R project, Obtaining R, Generating R codes, Scripts, Text editors for R, Graphical User Interfaces (GUIs) for R, Packages. R Objects and data structures: Variable classes, Vectors and matrices, Data frames and lists, Data sets included in R packages, Summarizing and exploring data, Reading data from external files, Storing data to external files, Creating and storing R workspaces. Manipulating objects in R: Mathematical operations (recycling rules, propagation of names, dimensional attributes, NA handling), Basic matrix computation (elementwise multiplication, matrix multiplication, outer product, transpose, eigenvalues, eigenvectors), Textual operations, Basic graphics (high-level plotting, lowlevel plotting, interacting with graphics