Basics Of Perl Scripting Language - Installation On Windows, Coding Environment, Simple Perl Scripts And Functions To Implement A Workflow

Intermediate Topics In Perl Scripting Such As References, Objects, Classes, Modules, Packages And Exception Handling Are Covered.

Introduction: Perl is a high-level programming language mainly used for writing scripts. It has strong capabilities for text processing and pattern matching and many programming tasks can be completed in very few lines of code. The code then does not even need to be compiled (as is the case in other programming languages like C, C++ and Java), making it ideal for applications where rapid prototyping and automation is desired.


Why learn Perl? Perl, because of its powerful features for processing text, is ideally suited for bioinformatics. Fewer lines of code are needed to be written, and the code is intuitive and easy to learn and implement. Reading a FASTA file takes 1 line of code. Finding patterns in a long DNA sequence is just 1 line of code. DNA can be converted to RNA or reverse complemented in one line of code. Modules like Bioperl makes it easier to bring powerful functionality at the fingertips of biologists who can then build powerful, automated workflows.


Logistics: This online Perl course is divided into 4 sessions and comes with slides, pre-recorded videos, reference cards, examples, data, scripts and quizzes. Enrollees can contact the instructor with questions and get help on the projects. The main topics are listed below. Homework assignments will involve running commands learned in the live lectures.


Pre-requisitesBasic knowledge of computers is essential such as installing programs, starting up the DOS prompt, writing in notepad, etc


Price: $1200 for Commercial/Government enrollees and $600 for Academic researchers and students.


Instructor: Shailender Nagpal


Syllabus:

  • Getting started with programming in Perl. Installing Perl
  • Variables: creating, printing, interpolating
  • Operations on variables. Mathematical and logical expressions
  • If-then-else statements
  • For and while loops
  • List and string operations
  • Pattern matching with regular expressions. DNA sequence operations
  • Writing custom functions
  • Bioinformatics project

Introduction: This course builds upon the fundamental concepts covered in the Level 1 Linux course. In this course, we cover Perl best practices, error checking, references, object-oriented programming, modules and building your own packages.


Why learn Perl? Perl, because of its powerful features for processing text, is ideally suited for bioinformatics. Fewer lines of code are needed to be written, and the code is intuitive and easy to learn and implement. Reading a FASTA file takes 1 line of code. Finding patterns in a long DNA sequence is just 1 line of code. DNA can be converted to RNA or reverse complemented in one line of code. Modules like Bioperl makes it easier to bring powerful functionality at the fingertips of biologists who can then build powerful, automated workflows.


Logistics: This online Perl course is divided into 4 sessions and comes with slides, pre-recorded videos, reference cards, examples, data, scripts and quizzes. Enrollees can contact the instructor with questions and get help on the projects. The main topics are listed below. Homework assignments will involve running commands learned in the live lectures.


Pre-requisitesPerl Level 1 or equivalent training required


Price: $1200 for Commercial/Government enrollees and $600 for Academic researchers and students.


Instructor:Shailender Nagpal


Syllabus:

  • - Good programming practices, special notes, shortcuts, basic commands you may have forgotten
  • - Creating and using modules, namespaces, packages
  • - References and object-oriented programming
  • - The Perl DBI and DBD for the MySQL DBMS
  • - Project: Microarray database with sequence information
  • - Case studies involving gene annotation and literature mining
  • - Exception handling and debugging
  • - Bioperl project