Perl is a powerful programming tool widely used in the analysis of biological data. It not only combines the modern robustness of Java with the expedient pragmatism of scripting languages but also offers both the low-level system access of C and the high-level elegance of Lisp. Perl is widely used in bioinformatics due to its powerful text-processing capacity. It allows the easy implementation of NLP and bio-informatics algorithms and the extraction and generation of textual data.
Perl is also easy to learn, is portable and multiplatform, has a large library of extensions, is component-oriented, is good in prototyping, and is efficient in the slicing, dicing, twisting, wringing, smoothing, summarizing and otherwise mangling of text. The objective of this course is to equip biologists who have little or no programming experience with the requisite skills.
This training will teach you how to:
Perl is also easy to learn, is portable and multiplatform, has a large library of extensions, is component-oriented, is good in prototyping, and is efficient in the slicing, dicing, twisting, wringing, smoothing, summarizing and otherwise mangling of text. The objective of this course is to equip biologists who have little or no programming experience with the requisite skills.
This training will teach you how to:
TOOLS AND SOFTWARE
DAY 1. GETTING STARTED WITH PERL
Getting Started with Perl
What is Perl?
Where Can I Get Perl?
Installing the Perl interpreter and checking that it has correctly installed
Checking if the path to the Perl interpreter has been added to the path list in C:/Autoexec.bat
A Simple Perl Program
Simple I/O
Perl Variables
Control Flow – Decisions
Control Flow – Loops
Altering Loop Control Flow
Statement Modifiers
What Is True And What Is False?
The Special Variable $_
Perl Operators
Introduction
Table Of Perl Operators
Arithmetic Operators
String Operators
Relational Operators
Logical Operators
Bitwise Operators
Assignment Operators
The Conditional Operator
Range Operator
String Functions
The eval Function
Input/Output
Introduction
String Literals
The print Function
Here Documents
The printf Function
The sprintf Function
Filehandles
Opening Disk Files
File Open Errors
The die and warn Functions
File Operators
DAY 2. ARRAYS AND SUB-ROUTINES
Arrays
Basic Concepts
Assigning Values To An Array
Accessing Array Elements
Array Functions
push and pop
shift
sort, reverse, and chop
split and join
grep
splice
Command Line Arguments
Associative Arrays
Subroutines
CALLING SUBROUTINES
Passing Arguments to Subroutines
Returning Values from Subroutines
The require Function
Packages and Modules
The @INC Array
Predefined Subroutines
Comparison Subroutines for Sorting
DAY 3. PATTERN MATCHING, REGULAR EXPRESSIONS AND ACCESSING SYSTEM RESOURCES
Pattern Matching
Introduction
Regular Expression Syntax
The Match Operator
Regular Expression Meta-Characters
Anchors
Single Character Matches
Some Special Issues
Character Classes
Multiple Character Matches
Alternation
The Substitution Operator
The Translation Operator
Remembered Matches
Greedy Regular Expressions
Nested Remembered Patterns
Matching for Multiple Occurrences in a Loop
Accessing System Resources
Introduction
File and Directory System Calls
The stat Function
The utime Function
The fork Function
The exec and wait Functions
Handling Signals
The system Function
Command Substitution
Opening Pipe Files
DAY 4. GENERATING REPORTS WITH PERL, PERL AND CGI, AND COMMAND LINE OPTIONS AND DEBUGGING
Generating Reports with Perl
Formats
Formatting Examples
Multi-Line Values
Multi-Line Text Blocks
Sending a Report to a File
The select Function
The Special Variable $~
Top-of-Page Formats
Bottom-of-Page Formats
A Sample Report
Perl and CGI
What is CGI?
Web Servers and Browsers
HTML
HTML Forms
Form Elements
A Typical CGI Application
CGI Input
CGI Output
Using the CGI.pm Module
CGI Environment Variables
Command Line Options and Debugging
Running Perl on the Command Line
Summary of Command Line Options
The Perl Debugger
Perl Debugger Commands
Other Debugging Aids
The strict Module
DAY 5. SOLVING BIOLOGICAL PROBLEMS USING PERL
DAY 5. EXERCISES
DAY 5. AWARD OF CERTIFICATES
Getting Started with Perl
What is Perl?
Where Can I Get Perl?
Installing the Perl interpreter and checking that it has correctly installed
Checking if the path to the Perl interpreter has been added to the path list in C:/Autoexec.bat
A Simple Perl Program
Simple I/O
Perl Variables
Control Flow – Decisions
Control Flow – Loops
Altering Loop Control Flow
Statement Modifiers
What Is True And What Is False?
The Special Variable $_
Perl Operators
Introduction
Table Of Perl Operators
Arithmetic Operators
String Operators
Relational Operators
Logical Operators
Bitwise Operators
Assignment Operators
The Conditional Operator
Range Operator
String Functions
The eval Function
Input/Output
Introduction
String Literals
The print Function
Here Documents
The printf Function
The sprintf Function
Filehandles
Opening Disk Files
File Open Errors
The die and warn Functions
File Operators
DAY 2. ARRAYS AND SUB-ROUTINES
Arrays
Basic Concepts
Assigning Values To An Array
Accessing Array Elements
Array Functions
push and pop
shift
sort, reverse, and chop
split and join
grep
splice
Command Line Arguments
Associative Arrays
Subroutines
CALLING SUBROUTINES
Passing Arguments to Subroutines
Returning Values from Subroutines
The require Function
Packages and Modules
The @INC Array
Predefined Subroutines
Comparison Subroutines for Sorting
DAY 3. PATTERN MATCHING, REGULAR EXPRESSIONS AND ACCESSING SYSTEM RESOURCES
Pattern Matching
Introduction
Regular Expression Syntax
The Match Operator
Regular Expression Meta-Characters
Anchors
Single Character Matches
Some Special Issues
Character Classes
Multiple Character Matches
Alternation
The Substitution Operator
The Translation Operator
Remembered Matches
Greedy Regular Expressions
Nested Remembered Patterns
Matching for Multiple Occurrences in a Loop
Accessing System Resources
Introduction
File and Directory System Calls
The stat Function
The utime Function
The fork Function
The exec and wait Functions
Handling Signals
The system Function
Command Substitution
Opening Pipe Files
DAY 4. GENERATING REPORTS WITH PERL, PERL AND CGI, AND COMMAND LINE OPTIONS AND DEBUGGING
Generating Reports with Perl
Formats
Formatting Examples
Multi-Line Values
Multi-Line Text Blocks
Sending a Report to a File
The select Function
The Special Variable $~
Top-of-Page Formats
Bottom-of-Page Formats
A Sample Report
Perl and CGI
What is CGI?
Web Servers and Browsers
HTML
HTML Forms
Form Elements
A Typical CGI Application
CGI Input
CGI Output
Using the CGI.pm Module
CGI Environment Variables
Command Line Options and Debugging
Running Perl on the Command Line
Summary of Command Line Options
The Perl Debugger
Perl Debugger Commands
Other Debugging Aids
The strict Module
DAY 5. SOLVING BIOLOGICAL PROBLEMS USING PERL
DAY 5. EXERCISES
DAY 5. AWARD OF CERTIFICATES
Perl Programming for Bio Scientists is aimed at researchers who have little or no programming skills and who are applying or planning to use bioinformatics techniques in their work.
Kindly fill the form details below to register for your course of interest.